Prof Jeremy Farrar

Research Area: Global Health
Scientific Themes: Tropical Medicine & Global Health
Keywords: Central Nervous System Infections, Dengue, Emerging Infections, Influenza and Tuberculous
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Jeremy Farrar's research interests are in Infectious Diseases and Global Health and include work on Emerging Infections, Infections of the Central Nervous System, TB, Dengue, Typhoid Malaria, and Influenza.  The work integrates clinical research with epidemiology, basic science and policy.

There are no collaborations listed for this principal investigator.

Baker S, Duy PT, Nga TVT, Dung TTN, Phat VV, Chau TT, Keith Turner A, Farrar J, Boni MF. 2013. Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure eLife, 2013 (2), Read abstract | Read more

Fluoroquinolones (FQ) are the recommended antimicrobial treatment for typhoid, a severe systemic infection caused by the bacterium Salmonella enterica serovar Typhi. FQ-resistance mutations in S. Typhi have become common, hindering treatment and control efforts. Using in vitro competition experiments, we assayed the fitness of eleven isogenic S. Typhi strains with resistance mutations in the FQ target genes, gyrA and parC. In the absence of antimicrobial pressure, 6 out of 11 mutants carried a selective advantage over the antimicrobial-sensitive parent strain, indicating that FQ resistance in S. Typhi is not typically associated with fitness costs. Double-mutants exhibited higher than expected fitness as a result of synergistic epistasis, signifying that epistasis may be a critical factor in the evolution and molecular epidemiology of S. Typhi. Our findings have important implications for the management of drug-resistant S. Typhi, suggesting that FQ-resistant strains would be naturally maintained even if fluoroquinolone use were reduced. © Dellas et al. Hide abstract

Nguyen KV, Thi Do NT, Chandna A, Nguyen TV, Pham CV, Doan PM, Nguyen AQ, Thi Nguyen CK et al. 2013. Antibiotic use and resistance in emerging economies: a situation analysis for Viet Nam. BMC Public Health, 13 (1), pp. 1158. Read abstract | Read more

Antimicrobial resistance is a major contemporary public health threat. Strategies to contain antimicrobial resistance have been comprehensively set forth, however in developing countries where the need for effective antimicrobials is greatest implementation has proved problematic. A better understanding of patterns and determinants of antibiotic use and resistance in emerging economies may permit more appropriately targeted interventions.Viet Nam, with a large population, high burden of infectious disease and relatively unrestricted access to medication, is an excellent case study of the difficulties faced by emerging economies in controlling antimicrobial resistance. Hide abstract

Shieh M, Thompson C, Phan Vu Tra M, Thi Thuy Linh V, Tediosi F, Merson L, Farrar JJ, Manh Tuan H, Lu Viet H, Thi Ngoc Tuyet P, Baker S. 2013. The policy of free healthcare for children under the age of 6 years in Vietnam: Assessment of the uptake for children hospitalised with acute diarrhoea in Ho Chi Minh City Tropical Medicine and International Health, 18 (12), pp. 1444-1451. Read abstract | Read more

Objective: To assess the proportion of, and reasons for, households not utilising the policy of free healthcare for children under 6 years of age (FCCU6) for hospitalisation with diarrhoea, and assess the risk of catastrophic expenditure for households that forgo FCCU6 and pay out of pocket. Methods: Invoices detailing insurance information and charges incurred from 472 hospitalised diarrhoeal cases in one paediatric hospital in Ho Chi Minh City were retrieved. Hospital charges and the utilisation of elective services were analysed for patients utilising and not utilising FCCU6. Associations between socio-economic factors with non-utilisation of FCCU6 were evaluated. Results: Overall, 29% of patients were FCCU6 non-users. The FCCU6 non-users paid a median hospital charge of $29.13 (interquartile range, IQR: $18.57-46.24), consuming no more than 1.4% of a medium-income household's annual income. Seventy per cent of low-income FCCU6 non-users utilised less-expensive elective services, whereas only 43% of medium income patients and 21% of high-income patients did (P = 0.036). Patients from larger households and those with a parent working in government were more likely to use FCCU6. Conclusions: The rate of FCCU6 non-usage in this study population was 29%. A significant proportion of those that did not use FCCU6 was from lower income households and may perceive a justifiable cost-benefit ratio when forgoing FCCU6. Although a single diarrhoeal hospitalisation is unlikely to induce a catastrophic expenditure, FCCU6 non-usage may disproportionately increase the risk of catastrophic expenditure for lower income households over multiple illnesses. © 2013 John Wiley & Sons Ltd. Hide abstract

Crusat M, Liu J, Palma AS, Childs RA, Liu Y, Wharton SA, Lin YP, Coombs PJ et al. 2013. Changes in the hemagglutinin of H5N1 viruses during human infection - Influence on receptor binding Virology, 447 (1-2), pp. 326-337. Read abstract | Read more

As avian influenza A(H5N1) viruses continue to circulate in Asia and Africa, global concerns of an imminent pandemic persist. Recent experimental studies suggest that efficient transmission between humans of current H5N1 viruses only requires a few genetic changes. An essential step is alteration of the virus hemagglutinin from preferential binding to avian receptors for the recognition of human receptors present in the upper airway. We have identified receptor-binding changes which emerged during H5N1 infection of humans, due to single amino acid substitutions, Ala134Val and Ile151Phe, in the hemagglutinin. Detailed biological, receptor-binding, and structural analyses revealed reduced binding of the mutated viruses to avian-like receptors, but without commensurate increased binding to the human-like receptors investigated, possibly reflecting a receptor-binding phenotype intermediate in adaptation to more human-like characteristics. These observations emphasize that evolution in nature of avian H5N1 viruses to efficient binding of human receptors is a complex multistep process. © 2013 The Authros. Hide abstract

Van TT, Farrar J. 2014. Tuberculous meningitis. J Epidemiol Community Health, 68 (3), pp. 195-196. | Read more

Nhu NT, Heemskerk D, Thu DODA, Chau TT, Mai NT, Nghia HD, Loc PP, Ha DT et al. 2014. Evaluation of GeneXpert MTB/RIF for diagnosis of tuberculous meningitis. J Clin Microbiol, 52 (1), pp. 226-233. Read abstract | Read more

Tuberculous meningitis (TBM) is the most severe form of tuberculosis. Microbiological confirmation is rare, and treatment is often delayed, increasing mortality and morbidity. The GeneXpert MTB/RIF test was evaluated in a large cohort of patients with suspected tuberculous meningitis. Three hundred seventy-nine patients presenting with suspected tuberculous meningitis to the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam, between 17 April 2011 and 31 December 2012 were included in the study. Cerebrospinal fluid samples were tested by Ziehl-Neelsen smear, mycobacterial growth indicator tube (MGIT) culture, and Xpert MTB/RIF. Rifampin (RIF) resistance results by Xpert were confirmed by an MTBDR-Plus line probe assay and all positive cultures were tested by phenotypic MGIT drug susceptibility testing. Overall, 182/379 included patients (48.0%) were diagnosed with tuberculous meningitis. Sensitivities of Xpert, smear, and MGIT culture among patients diagnosed with TBM were 59.3% (108/182 [95% confidence interval {CI}, 51.8 to 66.5%]), 78.6% (143/182 [95% CI, 71.9 to 84.3%]) and 66.5% (121/182 [95% CI, 59.1 to 73.3%]), respectively. There was one false-positive Xpert MTB/RIF test (99.5% specificity). Four cases of RIF resistance (4/109; 3.7%) were identified by Xpert, of which 3 were confirmed to be multidrug-resistant (MDR) TBM and one was culture negative. Xpert MTB/RIF is a rapid and specific test for the diagnosis of tuberculous meningitis. The addition of a vortexing step to sample processing increased sensitivity for confirmed TBM by 20% (P = 0.04). Meticulous examination of a smear from a large volume of cerebrospinal fluid (CSF) remains the most sensitive technique but is not practical in most laboratories. The Xpert MTB/RIF represents a significant advance in the early diagnosis of this devastating condition. Hide abstract

Lang T, Marsh K, Peeling R, Farrar J. 2013. Sharing methods for global health research: an assessment of methodology LANCET, 382 pp. 5-5.

Legand A, Briand S, Shindo N, Brooks WA, de Jong MD, Farrar J, Aguilera X, Hayden FG. 2013. Addressing the public health burden of respiratory viruses: the Battle against Respiratory Viruses (BRaVe) Initiative Future Virology, 8 (10), pp. 953-968. Read abstract | Read more

Given the enormous estimated burden of respiratory virus infections worldwide, a substantial number of research priorities exist in order to better understand their epidemiology, pathogenesis, prevention and clinical management across different populations and resource settings. New therapeutics and specific vaccines for noninfluenza respiratory virus infections could provide enormous benefits in reducing the morbidity and mortality associated with these frequent infections and provide the foundation for responding to newly emerging threats. The BRaVe Initiative is a new WHO-led effort to catalyze multidisciplinary research on strategies to prevent and treat medically important respiratory virus infections with the goal of timely integration of scientific advances and technical innovations into public health practice. © 2013 Future Medicine Ltd. Hide abstract

Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, Campbell JI, Hoang NV et al. 2013. Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proc Natl Acad Sci U S A, 110 (43), pp. 17522-17527. Read abstract | Read more

Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population. Hide abstract

Carrique-Mas JJ, Bryant JE, Cuong NV, Hoang NV, Campbell J, Hoang NV, Dung TT, Duy DT et al. 2014. An epidemiological investigation of Campylobacter in pig and poultry farms in the Mekong delta of Vietnam. Epidemiol Infect, 142 (7), pp. 1425-1436. Read abstract | Read more

Campylobacter are zoonotic pathogens commonly associated with gastroenteritis. To assess the relevance of Campylobacter in Vietnam, an economically transitioning country in SE Asia, we conducted a survey of 343 pig and poultry farms in the Mekong delta, a region characterized by mixed species farming with limited biosecurity. The animal-level prevalence of Campylobacter was 31·9%, 23·9% and 53·7% for chickens, ducks and pigs, respectively. C. jejuni was predominant in all three host species, with the highest prevalence in pigs in high-density production areas. Campylobacter isolates demonstrated high levels of antimicrobial resistance (21% and 100% resistance against ciprofloxacin and erythromycin, respectively). Multilocus sequence type genotyping showed a high level of genetic diversity within C. jejuni, and predicted C. coli inter-species transmission. We suggest that on-going intensification of animal production systems, limited biosecurity, and increased urbanization in Vietnam is likely to result in Campylobacter becoming an increasingly significant cause of human diarrhoeal infections in coming years. Hide abstract

Lam PK, Tam DT, Diet TV, Tam CT, Tien NT, Kieu NT, Simmons C, Farrar J et al. 2013. Clinical characteristics of Dengue shock syndrome in Vietnamese children: a 10-year prospective study in a single hospital. Clin Infect Dis, 57 (11), pp. 1577-1586. Read abstract | Read more

Dengue shock syndrome (DSS) is a severe manifestation of dengue virus infection that particularly affects children and young adults. Despite its increasing global importance, there are no prospective studies describing the clinical characteristics, management, or outcomes of DSS. Hide abstract

Crusat M, Liu J, Palma AS, Childs RA, Liu Y, Wharton SA, Lin YP, Coombs PJ et al. 2013. Changes in the hemagglutinin of H5N1 viruses during human infection--influence on receptor binding. Virology, 447 (1-2), pp. 326-337. Read abstract | Read more

As avian influenza A(H5N1) viruses continue to circulate in Asia and Africa, global concerns of an imminent pandemic persist. Recent experimental studies suggest that efficient transmission between humans of current H5N1 viruses only requires a few genetic changes. An essential step is alteration of the virus hemagglutinin from preferential binding to avian receptors for the recognition of human receptors present in the upper airway. We have identified receptor-binding changes which emerged during H5N1 infection of humans, due to single amino acid substitutions, Ala134Val and Ile151Phe, in the hemagglutinin. Detailed biological, receptor-binding, and structural analyses revealed reduced binding of the mutated viruses to avian-like receptors, but without commensurate increased binding to the human-like receptors investigated, possibly reflecting a receptor-binding phenotype intermediate in adaptation to more human-like characteristics. These observations emphasize that evolution in nature of avian H5N1 viruses to efficient binding of human receptors is a complex multistep process. Hide abstract

Lam PK, Tam DTH, Diet TV, Tam CT, Tien NTH, Kieu NTT, Simmons C, Farrar J et al. 2013. Dengue shock syndrome in children: clinical features and a prognostic model for profound shock TROPICAL MEDICINE & INTERNATIONAL HEALTH, 18 pp. 53-54.

Carod-Artal FJ, Wichmann O, Farrar J, Gascón J. 2013. Neurological complications of dengue virus infection. Lancet Neurol, 12 (9), pp. 906-919. Read abstract | Read more

Dengue is the second most common mosquito-borne disease affecting human beings. In 2009, WHO endorsed new guidelines that, for the first time, consider neurological manifestations in the clinical case classification for severe dengue. Dengue can manifest with a wide range of neurological features, which have been noted--depending on the clinical setting--in 0·5-21% of patients with dengue admitted to hospital. Furthermore, dengue was identified in 4-47% of admissions with encephalitis-like illness in endemic areas. Neurological complications can be categorised into dengue encephalopathy (eg, caused by hepatic failure or metabolic disorders), encephalitis (caused by direct virus invasion), neuromuscular complications (eg, Guillain-Barré syndrome or transient muscle dysfunctions), and neuro-ophthalmic involvement. However, overlap of these categories is possible. In endemic countries and after travel to these regions, dengue should be considered in patients presenting with fever and acute neurological manifestations. Hide abstract

Giri A, Arjyal A, Koirala S, Karkey A, Dongol S, Thapa SD, Shilpakar O, Shrestha R et al. 2013. Aetiologies of central nervous system infections in adults in Kathmandu, Nepal: a prospective hospital-based study. Sci Rep, 3 pp. 2382. Read abstract | Read more

We conducted a prospective hospital based study from February 2009-April 2011 to identify the possible pathogens of central nervous system (CNS) infections in adults admitted to a tertiary referral hospital (Patan Hospital) in Kathmandu, Nepal. The pathogens of CNS infections were confirmed in cerebrospinal fluid (CSF) using molecular diagnostics, culture (bacteria) and serology. 87 patients were recruited for the study and the etiological diagnosis was established in 38% (n = 33). The bacterial pathogens identified were Neisseria meningitidis (n = 6); Streptococcus pneumoniae (n = 5) and Staphylococcus aureus (n = 2) in 13/87(14%). Enteroviruses were found in 12/87 (13%); Herpes Simplex virus (HSV) in 2/87(2%). IgM against Japanese encephalitis virus (JEV) was detected in the CSF of 11/73 (15%) tested samples. This is the first prospective molecular and serology based CSF analysis in adults with CNS infections in Kathmandu, Nepal. JEV and enteroviruses were the most commonly detected pathogens in this setting. Hide abstract

Charles RC, Sultana T, Alam MM, Yu Y, Wu-Freeman Y, Bufano MK, Rollins SM, Tsai L et al. 2013. Identification of Immunogenic Salmonella enterica Serotype Typhi Antigens Expressed in Chronic Biliary Carriers of S. Typhi in Kathmandu, Nepal PLoS Neglected Tropical Diseases, 7 (8), pp. e2335-e2335. Read abstract | Read more

Background:Salmonella enterica serotype Typhi can colonize and persist in the biliary tract of infected individuals, resulting in a state of asymptomatic chronic carriage. Chronic carriers may act as persistent reservoirs of infection within a community and may introduce infection to susceptible individuals and new communities. Little is known about the interaction between the host and pathogen in the biliary tract of chronic carriers, and there is currently no reliable diagnostic assay to identify asymptomatic S. Typhi carriage.Methodology/Principal Findings:To study host-pathogen interactions in the biliary tract during S. Typhi carriage, we applied an immunoscreening technique called in vivo-induced antigen technology (IVIAT), to identify potential biomarkers unique to carriers. IVIAT identifies humorally immunogenic bacterial antigens expressed uniquely in the in vivo environment, and we hypothesized that S. Typhi surviving in the biliary tract of humans may express a distinct antigenic profile. Thirteen S. Typhi antigens that were immunoreactive in carriers, but not in healthy individuals from a typhoid endemic area, were identified. The identified antigens included a number of putative membrane proteins, lipoproteins, and hemolysin-related proteins. YncE (STY1479), an uncharacterized protein with an ATP-binding motif, gave prominent responses in our screen. The response to YncE in patients whose biliary tract contained S. Typhi was compared to responses in patients whose biliary tract did not contain S. Typhi, patients with acute typhoid fever, and healthy controls residing in a typhoid endemic area. Seven of 10 (70%) chronic carriers, 0 of 8 bile culture-negative controls (0%), 0 of 8 healthy Bangladeshis (0%), and 1 of 8 (12.5%) Bangladeshis with acute typhoid fever had detectable anti-YncE IgG in blood. IgA responses were also present.Conclusions/Significance:Further evaluation of YncE and other antigens identified by IVIAT could lead to the development of improved diagnostic assays to identify asymptomatic S. Typhi carriers. © 2013 Charles et al. Hide abstract

Farrar JJ, Hien TT, Horstick O, Hung NT, Jaenisch T, Junghanns T, Kroeger A, Laksono IS et al. 2013. Dogma in classifying dengue disease. Am J Trop Med Hyg, 89 (2), pp. 198-201. | Read more

Pham Thanh D, Tran Vu Thieu N, Tran Thuy C, Lodén M, Tuin K, Campbell JI, Van Minh Hoang N, Voong Vinh P et al. 2013. Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification. J Clin Microbiol, 51 (9), pp. 2950-2958. Read abstract | Read more

Salmonella enterica serovar Typhi, the causative agent of typhoid fever, is highly clonal and genetically conserved, making isolate subtyping difficult. We describe a standardized multiplex ligation-dependent probe amplification (MLPA) genotyping scheme targeting 11 key phylogenetic markers of the S. Typhi genome. The MLPA method demonstrated 90% concordance with single nucleotide polymorphism (SNP) typing, the gold standard for S. Typhi genotyping, and had the ability to identify isolates of the H58 haplotype, which is associated with resistance to multiple antimicrobials. Additionally, the assay permitted the detection of fluoroquinolone resistance-associated mutations in the DNA gyrase-encoding gene gyrA and the topoisomerase gene parC with a sensitivity of 100%. The MLPA methodology is simple and reliable, providing phylogenetically and phenotypically relevant genotyping information. This MLPA scheme offers a more-sensitive and interpretable alternative to the nonphylogenetic subgrouping methodologies that are currently used in reference and research laboratories in areas where typhoid is endemic. Hide abstract

South East Asia Infectious Disease Clinical Research Network. 2013. Effect of double dose oseltamivir on clinical and virological outcomes in children and adults admitted to hospital with severe influenza: double blind randomised controlled trial. BMJ, 346 (may30 2), pp. f3039. Read abstract | Read more

To investigate the validity of recommendations in treatment guidelines to use higher than approved doses of oseltamivir in patients with severe influenza. Hide abstract

My PV, Thompson C, Phuc HL, Tuyet PT, Vinh H, Hoang NV, Minh PV, Vinh NT et al. 2013. Endemic norovirus infections in children, Ho Chi Minh City, Vietnam, 2009-2010. Emerg Infect Dis, 19 (6), pp. 977-980. Read abstract | Read more

We performed a case-control investigation to identify risk factors for norovirus infections among children in Vietnam. Of samples from 1,419 children who had diarrhea and 609 who were asymptomatic, 20.6% and 2.8%, respectively, were norovirus positive. Risk factors included residential crowding and symptomatic contacts, indicating person-to-person transmission of norovirus. Hide abstract

Andrews JR, Prajapati KG, Eypper E, Shrestha P, Shakya M, Pathak KR, Joshi N, Tiwari P et al. 2013. Evaluation of an electricity-free, culture-based approach for detecting typhoidal Salmonella bacteremia during enteric fever in a high burden, resource-limited setting. PLoS Negl Trop Dis, 7 (6), pp. e2292. Read abstract | Read more

In many rural areas at risk for enteric fever, there are few data on Salmonella enterica serotypes Typhi (S. Typhi) and Paratyphi (S. Paratyphi) incidence, due to limited laboratory capacity for microbiologic culture. Here, we describe an approach that permits recovery of the causative agents of enteric fever in such settings. This approach involves the use of an electricity-free incubator based upon use of phase-change materials. We compared this against conventional blood culture for detection of typhoidal Salmonella. Hide abstract

Live Dengue Vaccines Technical Consultation Reporting Group, Bentsi-Enchill AD, Schmitz J, Edelman R, Durbin A, Roehrig JT, Smith PG, Hombach J, Farrar J. 2013. Long-term safety assessment of live attenuated tetravalent dengue vaccines: deliberations from a WHO technical consultation. Vaccine, 31 (23), pp. 2603-2609. Read abstract | Read more

Dengue is a rapidly growing public health threat with approximately 2.5 billion people estimated to be at risk. Several vaccine candidates are at various stages of pre-clinical and clinical development. Thus far, live dengue vaccine candidates have been administered to several thousands of volunteers and were well-tolerated, with minimal short-term safety effects reported in Phase I and Phase II clinical trials. Based on the natural history of dengue, a theoretical possibility of an increased risk of severe dengue as a consequence of vaccination has been hypothesized but not yet observed. In October 2011, the World Health Organization (WHO) convened a consultation of experts in dengue, vaccine regulation and vaccine safety to review the current scientific evidence regarding safety concerns associated with live attenuated dengue vaccines and, in particular, to consider methodological approaches for their long-term evaluation. In this paper we summarize the scientific background and methodological considerations relevant to the safety assessment of these vaccines. Careful planning and a coordinated approach to safety assessment are recommended to ensure adequate long-term evaluation of dengue vaccines that will support their introduction and continued use. Hide abstract

Nguyet MN, Duong TH, Trung VT, Nguyen TH, Tran CN, Long VT, Dui LET, Nguyen HL et al. 2013. Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proc Natl Acad Sci U S A, 110 (22), pp. 9072-9077. Read abstract | Read more

Dengue is the most prevalent arboviral disease of humans. The host and virus variables associated with dengue virus (DENV) transmission from symptomatic dengue cases (n = 208) to Aedes aegypti mosquitoes during 407 independent exposure events was defined. The 50% mosquito infectious dose for each of DENV-1-4 ranged from 6.29 to 7.52 log10 RNA copies/mL of plasma. Increasing day of illness, declining viremia, and rising antibody titers were independently associated with reduced risk of DENV transmission. High early DENV plasma viremia levels in patients were a marker of the duration of human infectiousness, and blood meals containing high concentrations of DENV were positively associated with the prevalence of infectious mosquitoes 14 d after blood feeding. Ambulatory dengue cases had lower viremia levels compared with hospitalized dengue cases but nonetheless at levels predicted to be infectious to mosquitoes. These data define serotype-specific viremia levels that vaccines or drugs must inhibit to prevent DENV transmission. Hide abstract

Boni MF, Chau NV, Dong N, Todd S, Nhat NT, de Bruin E, van Beek J, Hien NT, Simmons CP, Farrar J, Koopmans M. 2013. Population-level antibody estimates to novel influenza A/H7N9. J Infect Dis, 208 (4), pp. 554-558. Read abstract | Read more

There are no contemporary data available describing human immunity to novel influenza A/H7N9. Using 1723 prospectively collected serum samples in southern Vietnam, we tested for antibodies to 5 avian influenza virus antigens, using a protein microarray. General-population antibody titers against subtype H7 virus are higher than antibody titers against subtype H5 and lower than titers against H9. The highest titers were observed for human influenza virus subtypes. Titers to avian influenza virus antigens increased with age and with geometric mean antibody titer to human influenza virus antigens. There were no titer differences between the urban and the rural location in our study. Hide abstract

Ross AG, Olds GR, Cripps AW, Farrar JJ, McManus DP. 2013. Enteropathogens and chronic illness in returning travelers. N Engl J Med, 368 (19), pp. 1817-1825. | Read more

Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, Brownstein JS et al. 2013. The global distribution and burden of dengue Nature, 496 (7446), pp. 504-507. Read abstract | Read more

Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation. © 2013 Macmillan Publishers Limited. All rights reserved. Hide abstract

Tra My PV, Lam HM, Thompson CN, Phuc HL, Tuyet PT, Vinh H, Hoang NV, Minh P et al. 2013. The dynamics of GII.4 Norovirus in Ho Chi Minh City, Vietnam. Infect Genet Evol, 18 pp. 335-343. Read abstract | Read more

Norovirus (NoV) is a major cause of epidemic gastroenteritis in industrialized countries, yet the epidemiological significance of NoV in industrializing countries remains poorly understood. The spatiotemporal distribution of NoV genotypes identified in 2054 enrolled children was investigated between May 2009 and December 2010, in Ho Chi Minh City (HCMC), Vietnam. A total of 315 NoV extracted from stool samples were genotyped and GPS mapped to their source. Genogroup II NoV, particularly GII.4, were predominant, and the GII.4 strains could be subgrouped into GII.4-2006b (Minerva) and GII.4-2010 (New Orleans) variants. There was no spatiotemporal structure among the endemic GII strains; yet a significant spatiotemporal signal corresponding with the novel introduction of GII.4-2010 variant was detected. These data show that NoV GII.4 variants are highly endemic in HCMC and describe a scenario of rapid NoV strain replacement occurring in HCMC in early 2010. Hide abstract

Jacob ST, Lim M, Banura P, Bhagwanjee S, Bion J, Cheng AC, Cohen H, Farrar J et al. 2013. Integrating sepsis management recommendations into clinical care guidelines for district hospitals in resource-limited settings: the necessity to augment new guidelines with future research. BMC Med, 11 (1), pp. 107. Read abstract | Read more

Several factors contribute to the high mortality attributed to severe infections in resource-limited settings. While improvements in survival and processes of care have been made in high-income settings among patients with severe conditions, such as sepsis, guidelines necessary for achieving these improvements may lack applicability or have not been tested in resource-limited settings. The World Health Organization's recent publication of the Integrated Management of Adolescent and Adult Illness District Clinician Manual provides details on how to optimize management of severely ill, hospitalized patients in such settings, including specific guidance on the management of patients with septic shock and respiratory failure without shock. This manuscript provides the context, process and underpinnings of these sepsis guidelines. In light of the current deficits in care and the limitations associated with these guidelines, the authors propose implementing these standardized best practice guidelines while using them as a foundation for sepsis research undertaken in, and directly relevant to, resource-limited settings. Hide abstract

Pulickal AS, Callaghan MJ, Kelly DF, Maskey M, Mahat S, Hamaluba M, Dongol S, Adhikari N et al. 2013. Prevalence and genetic analysis of phenotypically Vi- negative Salmonella typhi isolates in children from Kathmandu, Nepal. J Trop Pediatr, 59 (4), pp. 317-320. Read abstract | Read more

The Vi capsular polysaccharide (ViPS) protects Salmonella enterica subspecies enterica serotype Typhi (S.Typhi) in vivo by multiple mechanisms. Recent microbiological reports from typhoid endemic countries suggest that acapsulate S.Typhi may occur in nature and contribute to clinical typhoid fever that is indistinguishable from disease caused by capsulate strains. The prevalence and genetic basis of ViPS-negative S.Typhi isolates in children from Kathmandu, Nepal, were tested in 68 isolates. Although 5.9% of isolates tested negative for capsular expression by slide agglutination tests, a novel multiplex PCR assay and individual PCR analyses demonstrated the presence of all 14 genes responsible for the synthesis, transportation and regulation of the ViPS. These data suggest that phenotypically acapsulate S.Typhi may not have a genetic basis for the same. Hide abstract

Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, Brownstein JS et al. 2013. The global distribution and burden of dengue. Nature, 496 (7446), pp. 504-507. Read abstract | Read more

Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation. Hide abstract

Day JN, Chau TT, Wolbers M, Mai PP, Dung NT, Mai NH, Phu NH, Nghia HD et al. 2013. Combination antifungal therapy for cryptococcal meningitis. N Engl J Med, 368 (14), pp. 1291-1302. Read abstract | Read more

Combination antifungal therapy (amphotericin B deoxycholate and flucytosine) is the recommended treatment for cryptococcal meningitis but has not been shown to reduce mortality, as compared with amphotericin B alone. We performed a randomized, controlled trial to determine whether combining flucytosine or high-dose fluconazole with high-dose amphotericin B improved survival at 14 and 70 days. Hide abstract

Duong V, Henn MR, Simmons C, Ngan C, Y B, Gavotte L, Viari A, Ong S et al. 2013. Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. Infect Genet Evol, 15 pp. 77-86. Read abstract | Read more

The Dengue National Control Program was established in Cambodia in 2000 and has reported between 10,000 and 40,000 dengue cases per year with a case fatality rate ranging from 0.7 to 1.7. In this study 39 DENV-2 and 57 DENV-3 viruses isolated from patients between 2000 and 2008 were fully sequenced. Five DENV2 and four DENV3 distinct lineages with different dynamics were identified. Each lineage was characterized by the presence of specific mutations with no evidence of recombination. In both DENV-2 and DENV-3 the lineages present prior to 2003 were replaced after that date by unrelated lineages. After 2003, DENV-2 lineages D2-3 and D2-4 cocirculated until 2007 when they were almost completely replaced by a lineage D2-5 which emerged from D2-3 Conversely, all DENV-3 lineages remained, diversified and cocirculated with novel lineages emerging. Years 2006 and 2007 were marked by a high prevalence of DENV-3 and 2007 with a large dengue outbreak and a high proportion of patients with severe disease. Selective sweeps in DENV-1 and DENV-2 were linked to immunological escape to a predominately DENV-3-driven immunological response. The complex dynamic of dengue in Cambodia in the last ten years has been associated with a combination of stochastic climatic events, cocirculation, coevolution, adaptation to different vector populations, and with the human population immunological landscape. Hide abstract

Duong V, Simmons C, Gavotte L, Viari A, Ong S, Chantha N, Lennon NJ, Birren BW et al. 2013. Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia Infection, Genetics and Evolution, 15 pp. 59-68. Read abstract | Read more

In Cambodia, dengue virus (DENV) was first isolated in 1963 and has become endemic with peak epidemic during raining season. Since 2000, the Dengue National Control Program has reported from 10,000 to 40,000 cases per year with fatality rates ranging from 0.7 to 1.7. All four dengue serotypes are found circulating in Cambodia with alternative predominance of serotypes DENV-2 and DENV-3. The DENV-1 represents from 5% to 20% of all circulating viruses, depending upon the year. In this work, 79 clinical strains of DENV-1 were isolated between 2000 and 2009 and their genome fully sequenced. Four distinct lineages with different dynamics were identified. The main evolutionary drive was negative selective pressure but each lineage was characterized by the presence of specific mutations acquired through evolution. Coexistence, extinction and replacement of lineages occurred over the 10-year period. Lineages 1, 2 and 3 were all detected since 2000-2002 and disappeared in 2003, 2004-2005 and 2007, respectively. Lineages 1 and 2 displayed different dynamics. Lineage 1 was very diverse whereas lineage 2 was very homogeneous. Lineage 4 which derived from lineage 3 in 2003 remained the only one at the end of the sampling period in 2008-2009 owing to a selective sweep. The lineages dynamic of DENV-1 viruses and consequences for molecular epidemiology are discussed. © 2011 Elsevier B.V. Hide abstract

Schultsz C, Bootsma MCJ, Loan HT, Nga TTT, Thao LTP, Thuy TTD, Campbell J, Vien LM et al. 2013. Effects of infection control measures on acquisition of five antimicrobial drug-resistant microorganisms in a tetanus intensive care unit in Vietnam Intensive Care Medicine, 39 (4), pp. 661-671. Read abstract | Read more

Purpose: To quantify the effects of barrier precautions and antibiotic mixing on prevalence and acquisition of five drug-resistant microorganisms within a single tetanus intensive care unit at a tertiary referral hospital in Ho Chi Minh City, Vietnam. Methods: All patients admitted within the study period were included. After a 1-year baseline period, barrier precautions were implemented and the single empirical treatment ceftazidime was changed to mixing (per consecutive patient) of three different regimens (ceftazidime, ciprofloxacin, piperacillin-tazobactam). Markov chain modeling and genotyping were used to determine the effects of interventions on prevalence levels and the relative importance of cross-transmission and antibiotic-associated selection. Results: A total of 190 patients were included in year 1 (2,708 patient days, 17,260 cultures) and 167 patients in year 2 (3,384 patient days, 20,580 cultures). In year 1, average daily prevalence rates for methicillin-resistant Staphylococcus aureus (MRSA), extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (excluding Klebsiella pneumoniae), Pseudomonas aeruginosa, gentamicin-resistant K. pneumoniae, and amikacin-resistant Acinetobacter species were 34.0, 61.3, 53.4, 65.7 and 57.1 %. After intervention, ceftazidime usage decreased by 53 %; the use of piperacillin-tazobactam and ciprofloxacin increased 7.2-fold and 4.5-fold, respectively. Adherence to hand hygiene after patient contact was 54 %. These measures were associated with a reduction of MRSA prevalence by 69.8 % (to 10.3 %), mainly because of less cross-transmission (88 % reduction), and of ESBL-producing Enterobacteriaceae prevalence by 10.3 % (non-significantly). In contrast, prevalence levels of the other three pathogens remained unaffected. Conclusion: The combination of simple infection control measures and antibiotic mixing was highly effective in reducing the prevalence of MRSA, but not of Gram-negative microorganisms. © 2013 The Author(s). Hide abstract

Hoa NT, Chieu TT, Do Dung S, Long NT, Hieu TQ, Luc NT, Nhuong PT, Huong VT et al. 2013. Streptococcus suis and porcine reproductive and respiratory syndrome, Vietnam. Emerg Infect Dis, 19 (2), pp. 331-333. | Read more

Kolader ME, Vinh H, Ngoc Tuyet PT, Thompson C, Wolbers M, Merson L, Campbell JI, Ngoc Dung TT et al. 2013. An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial. Trials, 14 (1), pp. 27. Read abstract | Read more

Diarrhoeal disease is a major global health problem, particularly affecting children under the age of 5 years. Besides oral rehydration solution, probiotics are also commonly prescribed to children with acute watery diarrhoea in some settings. Results from randomised clinical trials (RCTs) in which investigators studied the effect of probiotics on diarrhoeal symptoms have largely shown a positive effect; yet, the overall quality of the data is limited. In Vietnam, probiotics are the most frequently prescribed treatment for children hospitalised with acute watery diarrhoea, but there is little justification for this treatment in this location. We have designed a RCT to test the hypothesis that an oral preparation of Lactobacillus acidophilus is superior to placebo in the treatment of acute watery diarrhoea in Vietnamese children. Hide abstract

Nhu NT, Ha DT, Anh ND, Thu DD, Duong TN, Quang ND, Lan NT, Quyet TV et al. 2013. Evaluation of Xpert MTB/RIF and MODS assay for the diagnosis of pediatric tuberculosis. BMC Infect Dis, 13 (1), pp. 31. Read abstract | Read more

Tuberculosis (TB) in children is rarely confirmed due to the lack of effective diagnostic tools; only 10 to 15% of pediatric TB is smear positive due to paucibacillary samples and the difficulty of obtaining high-quality specimens from children. We evaluate here the accuracy of Xpert MTB/RIF in comparison with the Micoroscopic observation drug susceptibility (MODS) assay for diagnosis of TB in children using samples stored during a previously reported evaluation of the MODS assay. Hide abstract

Schultsz C, Bootsma MC, Loan HT, Nga TT, Thao LETP, Thuy TT, Campbell J, Vien LEM et al. 2013. Effects of infection control measures on acquisition of five antimicrobial drug-resistant microorganisms in a tetanus intensive care unit in Vietnam. Intensive Care Med, 39 (4), pp. 661-671. Read abstract | Read more

To quantify the effects of barrier precautions and antibiotic mixing on prevalence and acquisition of five drug-resistant microorganisms within a single tetanus intensive care unit at a tertiary referral hospital in Ho Chi Minh City, Vietnam. Hide abstract

Wertheim HF, Chandna A, Vu PD, Pham CV, Nguyen PD, Lam YM, Nguyen CV, Larsson M et al. 2013. Providing impetus, tools, and guidance to strengthen national capacity for antimicrobial stewardship in Viet Nam. PLoS Med, 10 (5), pp. e1001429. | Read more

Bentsi-Enchill AD, Schmitz J, Edelman R, Durbin A, Roehrig JT, Smith PG, Hombach J, Farrar J, Tech LDV. 2013. Long-term safety assessment of live attenuated tetravalent dengue vaccines: Deliberations from a WHO technical consultation VACCINE, 31 (23), pp. 2603-2609. | Read more

Schultsz C, Nga TTT, Thao LTP, Campbell J, Vien LM, Hoa NT, Hoang NVM, Farrar J et al. 2013. Effects of infection control measures on acquisition of five antimicrobial drug-resistant microorganisms in a tetanus intensive care unit in Vietnam Intensive Care Medicine, 39 (4), pp. 661-671. Read abstract | Read more

Purpose: To quantify the effects of barrier precautions and antibiotic mixing on prevalence and acquisition of five drug-resistant microorganisms within a single tetanus intensive care unit at a tertiary referral hospital in Ho Chi Minh City, Vietnam. Methods: All patients admitted within the study period were included. After a 1-year baseline period, barrier precautions were implemented and the single empirical treatment ceftazidime was changed to mixing (per consecutive patient) of three different regimens (ceftazidime, ciprofloxacin, piperacillin-tazobactam). Markov chain modeling and genotyping were used to determine the effects of interventions on prevalence levels and the relative importance of cross-transmission and antibiotic-associated selection. Results: A total of 190 patients were included in year 1 (2,708 patient days, 17,260 cultures) and 167 patients in year 2 (3,384 patient days, 20,580 cultures). In year 1, average daily prevalence rates for methicillin-resistant Staphylococcus aureus (MRSA), extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (excluding Klebsiella pneumoniae), Pseudomonas aeruginosa, gentamicin-resistant K. pneumoniae, and amikacin-resistant Acinetobacter species were 34.0, 61.3, 53.4, 65.7 and 57.1 %. After intervention, ceftazidime usage decreased by 53 %; the use of piperacillin-tazobactam and ciprofloxacin increased 7.2-fold and 4.5-fold, respectively. Adherence to hand hygiene after patient contact was 54 %. These measures were associated with a reduction of MRSA prevalence by 69.8 % (to 10.3 %), mainly because of less cross-transmission (88 % reduction), and of ESBL-producing Enterobacteriaceae prevalence by 10.3 % (non-significantly). In contrast, prevalence levels of the other three pathogens remained unaffected. Conclusion: The combination of simple infection control measures and antibiotic mixing was highly effective in reducing the prevalence of MRSA, but not of Gram-negative microorganisms. © 2013 The Author(s). Hide abstract

Whitehorn J, Chau TN, Nguyet NM, Kien DT, Quyen NT, Trung DT, Pang J, Wills B et al. 2013. Genetic variants of MICB and PLCE1 and associations with non-severe dengue. PLoS One, 8 (3), pp. e59067. Read abstract | Read more

A recent genome-wide association study (GWAS) identified susceptibility loci for dengue shock syndrome (DSS) at MICB rs3132468 and PLCE1 rs3740360. The aim of this study was to define the extent to which MICB (rs3132468) and PLCE1 (rs3740360) were associated with less severe clinical phenotypes of pediatric and adult dengue. Hide abstract

Sutanto I, Tjahjono B, Basri H, Taylor WR, Putri FA, Meilia RA, Setiabudy R, Nurleila S et al. 2013. Randomized, open-label trial of primaquine against vivax malaria relapse in Indonesia. Antimicrob Agents Chemother, 57 (3), pp. 1128-1135. Read abstract | Read more

Radical cure of Plasmodium vivax infection applies blood schizontocidal therapy against the acute attack and hypnozoitocidal therapy against later relapse. Chloroquine and primaquine have been used for 60 years in this manner. Resistance to chloroquine by the parasite now requires partnering other blood schizontocides with primaquine. However, the safety and efficacy of primaquine against relapse when combined with other drugs have not been demonstrated. This randomized, open-label, and relapse-controlled trial estimated the efficacy of primaquine against relapse when administered with quinine or dihydroartemisinin-piperaquine for treatment of the acute infection. Among 650 soldiers who had returned to their malaria-free base in Java, Indonesia, after 12 months in malarious Papua, Indonesia, 143 with acute P. vivax malaria were eligible for study. One hundred sixteen enrolled subjects were randomized to these treatments: artesunate (200-mg dose followed by 100 mg/day for 6 days), quinine (1.8 g/day for 7 days) plus concurrent primaquine (30 mg/day for 14 days), or dihydroartemisinin (120 mg) plus piperaquine (960 mg) daily for 3 days followed 25 days later by primaquine (30 mg/day for 14 days). Follow-up was for 12 months. One hundred thirteen subjects were analyzable. Relapse occurred in 32 of 41 (78%) subjects administered artesunate alone (2.71 attacks/person-year), 7 of 36 (19%) administered quinine plus primaquine (0.23 attack/person-year), and 2 of 36 (6%) administered dihydroartemisinin-piperaquine plus primaquine (0.06 attack/person-year). The efficacy of primaquine against relapse was 92% (95% confidence interval [CI] = 81% to 96%) for quinine plus primaquine and 98% (95% CI = 91% to 99%) for dihydroartemisinin-piperaquine plus primaquine. Antirelapse therapy with primaquine begun a month after treatment of the acute attack with dihydroartemisinin-piperaquine proved safe and highly efficacious against relapse by P. vivax acquired in Papua, Indonesia. Hide abstract

Dung TTN, Phat VV, Nga TVT, My PVT, Duy PT, Campbell JI, Thuy CT, Hoang NVM et al. 2013. The validation and utility of a quantitative one-step multiplex RT real-time PCR targeting Rotavirus A and Norovirus Journal of Virological Methods, 187 (1), pp. 138-143. Read abstract | Read more

Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect and quantify RoV and NoV simultaneously. The aim of the study was to develop, validate, and internally control a multiplex one-step RT real-time PCR to detect and quantify RoV and NoV in stool samples. PCR sensitivity was assessed by comparing amplification against the current gold standard, enzyme immunoassay (EIA), on stool samples from 94 individuals with diarrhea and 94 individuals without diarrhea. PCR detected 10% more RoV positive samples than EIA in stools samples from patients with diarrhea. PCR detected 23% more NoV genogroup II positive samples from individuals with diarrhea and 9% more from individuals without diarrhea than EIA, respectively. Genotyping of the PCR positive/EIA negative samples suggested the higher rate of PCR positivity, in comparison to EIA, was due to increased sensitivity, rather than nonspecific hybridization. Quantitation demonstrated that the viral loads of RoV and NoV in the stools of diarrheal patients were an order of magnitude greater than in individuals without diarrhea. This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits. © 2012 Elsevier B.V. Hide abstract

Campbell JI, Lan NP, Qui PT, Dung LET, Farrar JJ, Baker S. 2013. A successful antimicrobial regime for Chromobacterium violaceum induced bacteremia. BMC Infect Dis, 13 (1), pp. 4. Read abstract | Read more

Chromobacterium violaceum is a proteobacterium found in soil and water in tropical regions. The organism rarely causes infection in humans, yet can cause a severe systemic infection by entering the bloodstream via an open wound. Hide abstract

Zhang D, Pan H, Cui B, Law F, Farrar J, Ba-Thein W. 2013. Sexual behaviors and awareness of sexually transmitted infections among Chinese university students The Journal of Infection in Developing Countries, 7 (12), pp. 966-974. Read abstract | Read more

Introduction: This study investigated the current state of attitudes, behaviors, and knowledge concerning sex and sexually transmitted infections (STIs) among Chinese university students. Methodology: A cross-sectional anonymous university intranet-based survey was given to students attending the Shantou University, Guangdong, China using a 28-item questionnaire. Results: Of 3425 website visitors, 1030 university students completed the survey, of which 80% were between 20 and 25 years of age, 76% considered pre-marital sex acceptable, 21% had had sexual intercourse, and 45% of sexually active students had engaged in oral sex, anal intercourse, or sex with strangers. Students had limited knowledge and awareness about common STIs, symptoms, and complications. Three percent of the sexually active students reported having had STIs and another 8% were not sure whether they had or not. Most students had misconceptions about transmission and prevention of STIs. The internet was the main information resource for 76% of students. Conclusions: Despite having more open attitudes and behaviors towards sex, students' STI knowledge and awareness of STI risks was considerably limited, raising concerns about a likely rise in STI incidence. Prior knowledge of STIs had no significant influence. Targeted educational measures such as online education and counseling via Chinese websites and social media, and the provision of safer sex and STI-related information by health experts to university students are suggested. © 2013 Zhang et al. Hide abstract

Trang NHT, Nga TVT, Campbell JI, Hiep NT, Farrar J, Baker S, Duy PT. 2013. The characterization of ESBL genes in Escherichia coli and Klebsiella pneumoniae causing nosocomial infections in Vietnam The Journal of Infection in Developing Countries, 7 (12), pp. 922-928. Read abstract | Read more

Background: Extended-spectrum β-lactamases (ESBLs) are enzymes capable of hydrolyzing oxyimino-β-lactams and inducing resistance to third generation cephalosporins. The genes encoding ESBLs are widespread and generally located on highly transmissible resistance plasmids. We aimed to investigate the complement of ESBL genes in E. coli and Klebsiella pneumoniae causing nosocomial infections in hospitals in Ho Chi Minh City, Vietnam. Methodology: Thirty-two non-duplicate isolates of E. coli and Klebsiella pneumoniae causing nosocomial infections, isolated between March and June 2010, were subjected to antimicrobial susceptibility testing. All isolates were PCR-amplified to detect the blaSHV, blaTEM and blaCTX-M ESBL genes and subjected to plasmid analysis. Results: We found that co-resistance to multiple antimicrobials was highly prevalent, and we report the predominance of the blaCTX-M-15 and blaCTX-M-27 genes, located on highly transmissible plasmids ranging from 50 to 170 kb in size. Conclusions: Our study represents a snap shot of ESBL-producing enteric bacteria causing nosocomial infections in this setting. We suggest that antimicrobial resistance in nosocomial E. coli and Klebsiella pneumoniae is rampant in Vietnam and ESBL organisms are widespread. In view of these data and the dramatic levels of antimicrobial resistance reported in Vietnam we advocate an urgent review of antimicrobial use in the Vietnamese healthcare system. © 2013 Trang et al. Hide abstract

Nguyen TH, Nguyen TH, Vu TT, Farrar J, Hoang TL, Dong TH, Ngoc Tran V, Phung KL et al. 2013. Corticosteroids for dengue - why don't they work? PLoS Negl Trop Dis, 7 (12), pp. e2592. Read abstract | Read more

Dysregulated immune responses may contribute to the clinical complications that occur in some patients with dengue. Hide abstract

Baker S, Duy PT, Nga TV, Dung TT, Phat VV, Chau TT, Turner AK, Farrar J, Boni MF. 2013. Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure. Elife (Cambridge), 2 pp. e01229. Read abstract | Read more

Fluoroquinolones (FQ) are the recommended antimicrobial treatment for typhoid, a severe systemic infection caused by the bacterium Salmonella enterica serovar Typhi. FQ-resistance mutations in S. Typhi have become common, hindering treatment and control efforts. Using in vitro competition experiments, we assayed the fitness of eleven isogenic S. Typhi strains with resistance mutations in the FQ target genes, gyrA and parC. In the absence of antimicrobial pressure, 6 out of 11 mutants carried a selective advantage over the antimicrobial-sensitive parent strain, indicating that FQ resistance in S. Typhi is not typically associated with fitness costs. Double-mutants exhibited higher than expected fitness as a result of synergistic epistasis, signifying that epistasis may be a critical factor in the evolution and molecular epidemiology of S. Typhi. Our findings have important implications for the management of drug-resistant S. Typhi, suggesting that FQ-resistant strains would be naturally maintained even if fluoroquinolone use were reduced. DOI: http://dx.doi.org/10.7554/eLife.01229.001. Hide abstract

Koirala S, Basnyat B, Arjyal A, Shilpakar O, Shrestha K, Shrestha R, Shrestha UM, Agrawal K et al. 2013. Gatifloxacin versus ofloxacin for the treatment of uncomplicated enteric fever in Nepal: an open-label, randomized, controlled trial. PLoS Negl Trop Dis, 7 (10), pp. e2523. Read abstract | Read more

Fluoroquinolones are the most commonly used group of antimicrobials for the treatment of enteric fever, but no direct comparison between two fluoroquinolones has been performed in a large randomised trial. An open-label randomized trial was conducted to investigate whether gatifloxacin is more effective than ofloxacin in the treatment of uncomplicated enteric fever caused by nalidixic acid-resistant Salmonella enterica serovars Typhi and Paratyphi A. Hide abstract

Shieh M, Thompson C, Phan VT, Van TT, Tediosi F, Merson L, Farrar JJ, Ha MT, Ho LV, Pham TN, Baker S. 2013. The policy of free healthcare for children under the age of 6 years in Vietnam: assessment of the uptake for children hospitalised with acute diarrhoea in Ho Chi Minh City. Trop Med Int Health, 18 (12), pp. 1444-1451. Read abstract | Read more

To assess the proportion of, and reasons for, households not utilising the policy of free healthcare for children under 6 years of age (FCCU6) for hospitalisation with diarrhoea, and assess the risk of catastrophic expenditure for households that forgo FCCU6 and pay out of pocket. Hide abstract

Karkey A, Thompson CN, Tran Vu Thieu N, Dongol S, Le Thi Phuong T, Voong Vinh P, Arjyal A, Martin LB et al. 2013. Differential epidemiology of Salmonella Typhi and Paratyphi A in Kathmandu, Nepal: a matched case control investigation in a highly endemic enteric fever setting. PLoS Negl Trop Dis, 7 (8), pp. e2391. Read abstract | Read more

Enteric fever, a systemic infection caused by the bacteria Salmonella Typhi and Salmonella Paratyphi A, is endemic in Kathmandu, Nepal. Previous work identified proximity to poor quality water sources as a community-level risk for infection. Here, we sought to examine individual-level risk factors related to hygiene and sanitation to improve our understanding of the epidemiology of enteric fever in this setting. Hide abstract

Fox A, Hung TM, Wertheim H, Hoa LENM, Vincent A, Lang B, Waters P, Ha NH et al. 2013. Acute measles encephalitis in partially vaccinated adults. PLoS One, 8 (8), pp. e71671. Read abstract | Read more

The pathogenesis of acute measles encephalitis (AME) is poorly understood. Treatment with immune-modulators is based on theories that post-infectious autoimmune responses cause demyelination. The clinical course and immunological parameters of AME were examined during an outbreak in Vietnam. Hide abstract

Badurdeen S, Valladares DB, Farrar J, Gozzer E, Kroeger A, Kuswara N, Ranzinger SR, Tinh HT et al. 2013. Sharing experiences: towards an evidence based model of dengue surveillance and outbreak response in Latin America and Asia. BMC Public Health, 13 (1), pp. 607. Read abstract | Read more

The increasing frequency and intensity of dengue outbreaks in endemic and non-endemic countries requires a rational, evidence based response. To this end, we aimed to collate the experiences of a number of affected countries, identify strengths and limitations in dengue surveillance, outbreak preparedness, detection and response and contribute towards the development of a model contingency plan adaptable to country needs. Hide abstract

Tan LEV, van Doorn HR, Nghia HD, Chau TT, Tu LETP, de Vries M, Canuti M, Deijs M et al. 2013. Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. MBio, 4 (3), pp. e00231-e00213. Read abstract | Read more

Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus. Hide abstract

Khanh TH, Sabanathan S, Thanh TT, Thoa LEPK, Thuong TC, Hang VT, Farrar J, Hien TT, Chau NV, van Doorn HR. 2012. Enterovirus 71-associated hand, foot, and mouth disease, Southern Vietnam, 2011. Emerg Infect Dis, 18 (12), pp. 2002-2005. Read abstract | Read more

We prospectively studied 3,791 children hospitalized during 2011 during a large outbreak of enterovirus 71-associated hand, foot, and mouth disease in Vietnam. Formal assessment of public health interventions, use of intravenous immunoglobulin and other therapies, and factors predisposing for progression of disease is needed to improve clinical management. Hide abstract

Hien TT, Thuy-Nhien NT, Phu NH, Boni MF, Thanh NV, Nha-Ca NT, Thai LEH, Thai CQ et al. 2012. In vivo susceptibility of Plasmodium falciparum to artesunate in Binh Phuoc Province, Vietnam. Malar J, 11 (1), pp. 355. Read abstract | Read more

By 2009, there were worrying signs from western Cambodia that parasitological responses to artesunate-containing treatment regimens for uncomplicated Plasmodium falciparum malaria were slower than elsewhere which suggested the emergence of artemisinin resistance. Vietnam shares a long land border with Cambodia with a large number of migrants crossing it on a daily basis. Therefore, there is an urgent need to investigate whether there is any evidence of a change in the parasitological response to the artemisinin derivatives in Vietnam. Hide abstract

Dung TT, Phat VV, Nga TV, My PV, Duy PT, Campbell JI, Thuy CT, Hoang NV et al. 2013. The validation and utility of a quantitative one-step multiplex RT real-time PCR targeting rotavirus A and norovirus. J Virol Methods, 187 (1), pp. 138-143. Read abstract | Read more

Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect and quantify RoV and NoV simultaneously. The aim of the study was to develop, validate, and internally control a multiplex one-step RT real-time PCR to detect and quantify RoV and NoV in stool samples. PCR sensitivity was assessed by comparing amplification against the current gold standard, enzyme immunoassay (EIA), on stool samples from 94 individuals with diarrhea and 94 individuals without diarrhea. PCR detected 10% more RoV positive samples than EIA in stools samples from patients with diarrhea. PCR detected 23% more NoV genogroup II positive samples from individuals with diarrhea and 9% more from individuals without diarrhea than EIA, respectively. Genotyping of the PCR positive/EIA negative samples suggested the higher rate of PCR positivity, in comparison to EIA, was due to increased sensitivity, rather than nonspecific hybridization. Quantitation demonstrated that the viral loads of RoV and NoV in the stools of diarrheal patients were an order of magnitude greater than in individuals without diarrhea. This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits. Hide abstract

Wertheim HF, Ngoc DM, Wolbers M, Binh TT, Hải NT, Loan NQ, Tú PT, Sjodin A et al. 2012. Studying the effectiveness of activated carbon R95 respirators in reducing the inhalation of combustion by-products in Hanoi, Vietnam: a demonstration study. Environ Health, 11 (1), pp. 72. Read abstract | Read more

Urban air pollution is an increasing health problem, particularly in Asia, where the combustion of fossil fuels has increased rapidly as a result of industrialization and socio-economic development. The adverse health impacts of urban air pollution are well established, but less is known about effective intervention strategies. In this demonstration study we set out to establish methods to assess whether wearing an R95 activated carbon respirator could reduce intake of polycyclic aromatic hydrocarbons (PAH) in street workers in Hanoi, Vietnam. Hide abstract

Thompson CN, Phan VT, Le TP, Pham TN, Hoang LP, Ha V, Nguyen VM, Pham VM et al. 2013. Epidemiological features and risk factors of Salmonella gastroenteritis in children resident in Ho Chi Minh City, Vietnam. Epidemiol Infect, 141 (8), pp. 1604-1613. Read abstract | Read more

Non-typhoidal Salmonella are an important but poorly characterized cause of paediatric diarrhoea in developing countries. We conducted a hospital-based case-control study in children aged <5 years in Ho Chi Minh City to define the epidemiology and examine risk factors associated with Salmonella diarrhoeal infections. From 1419 diarrhoea cases and 571 controls enrolled between 2009 and 2010, 77 (5∙4%) diarrhoea cases were stool culture-positive for non-typhoidal Salmonella. Salmonella patients were more likely to be younger than controls (median age 10 and 12 months, respectively) [odds ratio (OR) 0∙97; 95% confidence interval (CI) 0∙94-0∙99], to report a recent diarrhoeal contact (8∙1% cases, 1∙8% controls; OR 5∙98, 95% CI 1∙8-20∙4) and to live in a household with >2 children (cases 20∙8%, controls 10∙2%; OR 2∙32, 95% CI 1∙2-4∙7). Our findings indicate that Salmonella are an important cause of paediatric gastroenteritis in this setting and we suggest that transmission may occur through direct human contact in the home. Hide abstract

Simmons CP, Wolbers M, Nguyen MN, Whitehorn J, Shi PY, Young P, Petric R, Nguyen VV, Farrar J, Wills B. 2012. Therapeutics for dengue: recommendations for design and conduct of early-phase clinical trials. PLoS Negl Trop Dis, 6 (9), pp. e1752. | Read more

Tam DT, Ngoc TV, Tien NT, Kieu NT, Thuy TT, Thanh LT, Tam CT, Truong NT et al. 2012. Effects of short-course oral corticosteroid therapy in early dengue infection in Vietnamese patients: a randomized, placebo-controlled trial. Clin Infect Dis, 55 (9), pp. 1216-1224. Read abstract | Read more

Patients with dengue can experience a variety of serious complications including hypovolemic shock, thrombocytopenia, and bleeding. These problems occur as plasma viremia is resolving and are thought to be immunologically mediated. Early corticosteroid therapy may prevent the development of such complications but could also prolong viral clearance. Hide abstract

Nguyen NM, Tran CN, Phung LK, Duong KT, Huynh HLEA, Farrar J, Nguyen QT, Tran HT et al. 2013. A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients. J Infect Dis, 207 (9), pp. 1442-1450. Read abstract | Read more

Dengue is the most common arboviral infection of humans. There are currently no specific treatments for dengue. Balapiravir is a prodrug of a nucleoside analogue (called R1479) and an inhibitor of hepatitis C virus replication in vivo. Hide abstract

Tham NT, Hang VT, Khanh TH, Viet DOC, Hien TT, Farrar J, Chau NV, van Doorn HR. 2012. Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam. Diagn Microbiol Infect Dis, 74 (2), pp. 131-136. Read abstract | Read more

Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable. Hide abstract

Dunstan SJ, Rockett KA, Quyen NT, Teo YY, Thai CQ, Hang NT, Jeffreys A, Clark TG et al. 2012. Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese. Genes Immun, 13 (6), pp. 503-508. Read abstract | Read more

The genetic basis for susceptibility to malaria has been studied widely in African populations but less is known of the contribution of specific genetic variants in Asian populations. We genotyped 67 single-nucleotide polymorphisms (SNPs) in 1030 severe malaria cases and 2840 controls from Vietnam. After data quality control, genotyping data of 956 cases and 2350 controls were analysed for 65 SNPs (3 gender confirmation, 62 positioned in/near 42 malarial candidate genes). A total of 14 SNPs were monomorphic and 2 (rs8078340 and rs33950507) were not in Hardy-Weinberg equilibrium in controls (P<0.01). In all, 7/46 SNPs in 6 genes (ICAM1, IL1A, IL17RC, IL13, LTA and TNF) were associated with severe malaria, with 3/7 SNPs in the TNF/LTA region. Genotype-phenotype correlations between SNPs and clinical parameters revealed that genotypes of rs708567 (IL17RC) correlate with parasitemia (P=0.028, r(2)=0.0086), with GG homozygotes having the lowest parasite burden. Additionally, rs708567 GG homozygotes had a decreased risk of severe malaria (P=0.007, OR=0.78 (95% CI; 0.65-0.93)) and death (P=0.028, OR=0.58 (95% CI; 0.37-0.93)) than those with AA and AG genotypes. In summary, variants in six genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese. Further replicative studies in independent populations will be necessary to confirm these findings. Hide abstract

Dunstan SJ, Rockett KA, Quyen NTN, Teo YY, Thai CQ, Hang NT, Jeffreys A, Clark TG et al. 2012. Variation in human genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese Genes and Immunity, 13 (6), pp. 503-508. Read abstract | Read more

The genetic basis for susceptibility to malaria has been studied widely in African populations but less is known of the contribution of specific genetic variants in Asian populations. We genotyped 67 single-nucleotide polymorphisms (SNPs) in 1030 severe malaria cases and 2840 controls from Vietnam. After data quality control, genotyping data of 956 cases and 2350 controls were analysed for 65 SNPs (3 gender confirmation, 62 positioned in/near 42 malarial candidate genes). A total of 14 SNPs were monomorphic and 2 (rs8078340 and rs33950507) were not in Hardy-Weinberg equilibrium in controls (P<0.01). In all, 7/46 SNPs in 6 genes (ICAM1, IL1A, IL17RC, IL13, LTA and TNF) were associated with severe malaria, with 3/7 SNPs in the TNF/LTA region. Genotype-phenotype correlations between SNPs and clinical parameters revealed that genotypes of rs708567 (IL17RC) correlate with parasitemia (P=0.028, r2=0.0086), with GG homozygotes having the lowest parasite burden. Additionally, rs708567 GG homozygotes had a decreased risk of severe malaria (P=0.007, OR=0.78 (95% CI; 0.65-0.93)) and death (P=0.028, OR=0.58 (95% CI; 0.37-0.93)) than those with AA and AG genotypes. In summary, variants in six genes encoding adhesion and proinflammatory molecules are associated with severe malaria in the Vietnamese. Further replicative studies in independent populations will be necessary to confirm these findings. © 2012 Macmillan Publishers Limited. All rights reserved. Hide abstract

Khanh TH, Sabanathan S, Thoa LPK, Thuong TC, Farrar J, Hien TT, van Doorn HR. 2012. A large epidemic of enterovirus 71 associated hand, foot and mouth disease in southern Vietnam, 2011 INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E274-E274. | Read more

Yacoub S, Grifiths A, Chau TTH, Simmons C, Wills B, Hien TT, Henein M, Farrar J. 2012. Cardiac function and haemodynamics in Vietnemese patients with different dengue severity grades INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E119-E119. | Read more

Trung DT, Thao LETT, Dung NM, Ngoc TV, Hien TT, Chau NV, Wolbers M, Tam DT, Farrar J, Simmons C, Wills B. 2012. Clinical features of dengue in a large Vietnamese cohort: intrinsically lower platelet counts and greater risk for bleeding in adults than children. PLoS Negl Trop Dis, 6 (6), pp. e1679. Read abstract | Read more

As dengue spreads to new geographical regions and the force of infection changes in existing endemic areas, a greater breadth of clinical presentations is being recognised. Clinical experience suggests that adults manifest a pattern of complications different from those observed in children, but few reports have described the age-related spectrum of disease in contemporaneous groups of patients recruited at the same geographical location. Hide abstract

Darton T, Jones C, Waddington C, Dougan G, Sztein M, Levine M, Angus B, Farrar J et al. 2012. Demonstration of primary and asymptomatic DNAaemia in participants challenged with Salmonella Typhi (Quailes strain) during the development of a human model of typhoid infection INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E215-E215. | Read more

Whitehorn J, Rodriguez Roche R, Guzman MG, Martinez E, Gomez WV, Nainggolan L, Laksono IS, Mishra A et al. 2012. Prophylactic platelets in dengue: survey responses highlight lack of an evidence base. PLoS Negl Trop Dis, 6 (6), pp. e1716. Read abstract | Read more

Dengue is the most important arboviral infection of humans. Thrombocytopenia is frequently observed in the course of infection and haemorrhage may occur in severe disease. The degree of thrombocytopenia correlates with the severity of infection, and may contribute to the risk of haemorrhage. As a result of this prophylactic platelet transfusions are sometimes advocated for the prevention of haemorrhage. There is currently no evidence to support this practice, and platelet transfusions are costly and sometimes harmful. We conducted a global survey to assess the different approaches to the use of platelets in dengue. Respondents were all physicians involved with the treatment of patients with dengue. Respondents were asked that their answers reflected what they would do if they were the treating physician. We received responses from 306 physicians from 20 different countries. The heterogeneity of the responses highlights the variation in clinical practice and lack of an evidence base in this area and underscores the importance of prospective clinical trials to address this key question in the clinical management of patients with dengue. Hide abstract

Jones C, Waddington C, Darton T, Bowman J, Farrar J, Dougan G, Levine M, Lockhart S et al. 2012. Quantification of antibody secreting cell responses in a human challenge model of Salmonella Typhi infection INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E224-E224. | Read more

Phan VTM, Ha ML, Thompson C, Nguyen VMH, Pham VM, Nguyen TV, Cao TT, Nguyen TTN et al. 2012. Risk factors of norovirus infection and the spatiotemporal dynamics of GII.4 strain replacement in Ho Chi Minh City, Vietnam INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E101-E101. | Read more

Zhang D, Pan H, Cui B, Law F, Farrar J, Ba-Thein W. 2012. Risk of sexually transmitted infections due to changing sexual attitude and behaviors and limited knowledge among college students in southern China INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E336-E336. | Read more

Waddington C, Darton T, Jones C, Haworth K, Peters A, Kerridge S, Crook D, Lockhart S et al. 2012. Variations in attack rate in a single-blind, dose escalation challenge study of Salmonella Typhi in healthy adult volunteers INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E244-E244. | Read more

Tho DQ, Török ME, Yen NT, Bang ND, Lan NT, Kiet VS, van Vinh Chau N, Dung NH et al. 2012. Influence of antituberculosis drug resistance and Mycobacterium tuberculosis lineage on outcome in HIV-associated tuberculous meningitis. Antimicrob Agents Chemother, 56 (6), pp. 3074-3079. Read abstract | Read more

HIV-associated tuberculous meningitis (TBM) has high mortality. Aside from the devastating impact of multidrug resistance (MDR) on survival, little is understood about the influence of other bacterial factors on outcome. This study examined the influence of Mycobacterium tuberculosis drug resistance, bacterial lineage, and host vaccination status on outcome in patients with HIV-associated TBM. Mycobacterium tuberculosis isolates from the cerebrospinal fluid of 186 patients enrolled in two studies of HIV-associated TBM in Ho Chi Minh City, Vietnam, were tested for resistance to first-line antituberculosis drugs. Lineage genotyping was available for 122 patients. The influence of antituberculosis drug resistance and M. tuberculosis lineage on 9-month mortality was analyzed using Kaplan-Meier survival analysis and Cox multiple regression models. Isoniazid (INH) resistance without rifampin resistance was associated with increased mortality (adjusted hazard ratio [HR], 1.78, 95% confidence interval [CI], 1.18 to 2.66; P = 0.005), and multidrug resistance was uniformly fatal (n = 8/8; adjusted HR, 5.21, 95% CI, 2.38 to 11.42; P < 0.0001). The hazard ratio for INH-resistant cases was greatest during the continuation phase of treatment (after 3 months; HR, 5.05 [95% CI, 2.23 to 11.44]; P = 0.0001). Among drug-susceptible cases, patients infected with the "modern" Beijing lineage strains had lower mortality than patients infected with the "ancient" Indo-Oceanic lineage (HR, 0.29 [95% CI, 0.14 to 0.61]; P = 0.001). Isoniazid resistance, multidrug resistance, and M. tuberculosis lineage are important determinants of mortality in patients with HIV-associated TBM. Interventions which target these factors may help reduce the unacceptably high mortality in patients with TBM. Hide abstract

Akbar NA, Allende I, Balmaseda A, Coelho IC, da Cunha RV, Datta B, Devi SS, Farrar J et al. 2012. Regarding "Dengue--how best to classify it". Clin Infect Dis, 54 (12), pp. 1820-1821. | Read more

Farrar J. 2012. H5N1 surveillance: Shift expertise to where it matters. Nature, 483 (7391), pp. 534-535. | Read more

Farrar J. 2012. Shift expertise to where it matters NATURE, 483 (7391), pp. 534-535.

Thao VP, Le T, Török EM, Yen NT, Chau TT, Jurriaans S, van Doorn HR, de Jong MD, Farrar JJ, Dunstan SJ. 2012. HIV-1 drug resistance in antiretroviral-naive individuals with HIV-1-associated tuberculous meningitis initiating antiretroviral therapy in Vietnam. Antivir Ther, 17 (5), pp. 905-913. Read abstract | Read more

Access to antiretroviral therapy (ART) for HIV-infected individuals in Vietnam is rapidly expanding, but there are limited data on HIV drug resistance (HIVDR) to guide ART strategies. Hide abstract

Horby P, Mai LEQ, Fox A, Thai PQ, Thi Thu Yen N, Thanh LET, Le Khanh Hang N, Duong TN et al. 2012. The epidemiology of interpandemic and pandemic influenza in Vietnam, 2007-2010: the Ha Nam household cohort study I. Am J Epidemiol, 175 (10), pp. 1062-1074. Read abstract | Read more

Prospective community-based studies have provided fundamental insights into the epidemiology of influenza in temperate regions, but few comparable studies have been undertaken in the tropics. The authors conducted prospective influenza surveillance and intermittent seroprevalence surveys in a household-based cohort in Vietnam between December 2007 and April 2010, resulting in 1,793 person-seasons of influenza surveillance. Age- and sex-standardized estimates of the risk of acquiring any influenza infection per season in persons 5 years of age or older were 21.1% (95% confidence interval: 17.4, 24.7) in season 1, 26.4% (95% confidence interval: 22.6, 30.2) in season 2, and 17.0% (95% confidence interval: 13.6, 20.4) in season 3. Some individuals experienced multiple episodes of infection with different influenza types/subtypes in the same season (n = 27) or reinfection with the same subtype in different seasons (n = 22). The highest risk of influenza infection was in persons 5-9 years old, in whom the risk of influenza infection per season was 41.8%. Although the highest infection risk was in school-aged children, there were important heterogeneities in the age of infection by subtype and season. These heterogeneities could influence the impact of school closure and childhood vaccination on influenza transmission in tropical areas, such as Vietnam. Hide abstract

Beatty M, Boni MF, Brown S, Buathong R, Burke D, Coudeville L, Cummings DAT, Edelman R et al. 2012. Assessing the Potential of a Candidate Dengue Vaccine with Mathematical Modeling PLOS NEGLECTED TROPICAL DISEASES, 6 (3), pp. e1450-e1450. | Read more

Dang TM, Nguyen TN, Wolbers M, Vo SK, Hoang TT, Nguyen HD, To MH, Vuong MB et al. 2012. Evaluation of microscopic observation drug susceptibility assay for diagnosis of multidrug-resistant tuberculosis in Viet Nam. BMC Infect Dis, 12 (1), pp. 49. Read abstract | Read more

Early diagnosis of tuberculosis (TB) and multidrug resistant tuberculosis (MDR TB) is important for the elimination of TB. We evaluated the microscopic observation drug susceptibility (MODS) assay as a direct rapid drug susceptibility testing (DST) method for MDR-TB screening in sputum samples Hide abstract

Tisoncik JR, Korth MJ, Simmons CP, Farrar J, Martin TR, Katze MG. 2012. Into the eye of the cytokine storm. Microbiol Mol Biol Rev, 76 (1), pp. 16-32. Read abstract | Read more

The cytokine storm has captured the attention of the public and the scientific community alike, and while the general notion of an excessive or uncontrolled release of proinflammatory cytokines is well known, the concept of a cytokine storm and the biological consequences of cytokine overproduction are not clearly defined. Cytokine storms are associated with a wide variety of infectious and noninfectious diseases. The term was popularized largely in the context of avian H5N1 influenza virus infection, bringing the term into popular media. In this review, we focus on the cytokine storm in the context of virus infection, and we highlight how high-throughput genomic methods are revealing the importance of the kinetics of cytokine gene expression and the remarkable degree of redundancy and overlap in cytokine signaling. We also address evidence for and against the role of the cytokine storm in the pathology of clinical and infectious disease and discuss why it has been so difficult to use knowledge of the cytokine storm and immunomodulatory therapies to improve the clinical outcomes for patients with severe acute infections. Hide abstract

Koirala KD, Thanh DP, Thapa SD, Arjyal A, Karkey A, Dongol S, Shrestha UM, Farrar JJ, Basnyat B, Baker S. 2012. Highly resistant Salmonella enterica serovar Typhi with a novel gyrA mutation raises questions about the long-term efficacy of older fluoroquinolones for treating typhoid fever. Antimicrob Agents Chemother, 56 (5), pp. 2761-2762. Read abstract | Read more

As a consequence of multidrug resistance, clinicians are highly dependent on fluoroquinolones for treating the serious systemic infection typhoid fever. While reduced susceptibility to fluoroquinolones, which lessens clinical efficacy, is becoming ubiquitous, comprehensive resistance is exceptional. Here we report ofloxacin treatment failure in typhoidal patient infected with a novel, highly fluoroquinolone-resistant isolate of Salmonella enterica serovar Typhi. The isolation of this organism has serious implications for the long-term efficacy of ciprofloxacin and ofloxacin for typhoid treatment. Hide abstract

van Doorn HR, Kinh NV, Tuan HM, Tuan TA, Minh NN, Bryant JE, Hang VT, Uyen LETT et al. 2012. Clinical validation of a point-of-care multiplexed in vitro immunoassay using monoclonal antibodies (the MSD influenza test) in four hospitals in Vietnam. J Clin Microbiol, 50 (5), pp. 1621-1625. Read abstract | Read more

Point-of-care (POC) diagnostic tests for influenza can considerably shorten the time to clinical decision making. An investigational POC test based on a multiplexed immunoassay was developed by Meso Scale Diagnostics, LLC (MSD), with the objective to make a more sensitive rapid test that can also subtype influenza A viruses (1977 H1, H3, and H5). Between February and November 2010, we conducted a prospective multicenter study at four hospitals in Vietnam and compared the performance of this test to that of the WHO/CDC real-time reverse transcriptase PCR (RT-PCR) on nasal and throat swab specimens from patients presenting with influenza-like illness. Five hundred sixty-three adults and children with a median age of 25 months were enrolled. Sensitivity and specificity of the test with combined results from nasal and throat swab samples were 74.0% (131/177) and 99.7% (351/352), respectively, compared to RT-PCR. The POC test was as sensitive for influenza virus B as for influenza virus A (74.4% [64/86] versus 73.6% [67/91]). The positivity rate was associated with lower cycle threshold values (a marker for higher viral loads), sample type (73.6% for nasal swab versus 52.4% for throat swab), and younger age. A total of 210 (18.7%) out of 1,126 MSD tests failed, and for 34 (6%) of patients, both test samples failed (these were excluded from the performance analysis). Subtyping could be assessed only for influenza virus A/H3N2, as 1977 H1N1 was not circulating at the time and no H5N1-infected patients were enrolled, and was successful only in 9/54 patients infected with H3 influenza virus who had a positive POC test result for influenza virus A. This novel POC test provided highly sensitive detection of influenza viruses A and B compared to the reported sensitivities of other rapid tests. However, 18.7% of tests failed for technical reasons and subtyping for H3 was poor. Drawbacks to the technology include the requirement for a dedicated reader instrument and the need for continual updating of subtyping antibodies within the test array. Hide abstract

Gertsch JH, Corbett B, Mulcahy A, Watts M, Stillwagon NT, Casto AM, Abramson CH, Vaughan CPA et al. 2012. Altitude sickness in climbers and efficacy of NSAIDs trial (ASCENT): Randomized, controlled trial of ibuprofen versus placebo for prevention of altitude illness Wilderness and Environmental Medicine, 23 (4), pp. 307-315. Read abstract | Read more

Objective: To study the effectiveness of ibuprofen versus placebo in preventing acute mountain sickness (AMS) and high altitude headache (HAH). Methods: Double-blind, randomized, placebo-controlled trial. Results: Two hundred ninety-four healthy Western trekkers were recruited on the Everest approach at 4280 m or 4358 m and randomly assigned to receive either 600 mg of ibuprofen or placebo 3 times daily before and during ascent to 4928 m. One hundred eighty-three of 294 participants completed the trial. Of the participants who did not complete the trial, 62 were lost to follow-up and another 49 broke trial protocol. In an intent-to-treat analysis (232 participants), ibuprofen was found to be more effective than placebo in reducing the incidence of AMS (24.4% vs 40.4%; P =.01) and the incidence of HAH (42.3% vs 60.5%; P <.01). Ibuprofen was also superior to placebo in reducing the severity of HAH (4.9% vs 14.7%; P =.01). The end point of oxygen saturation was also higher in the ibuprofen group (80.8 % vs 82.4%; P =.035). For the 183 participants who completed the trial and conformed to the protocol, the incidence of AMS between placebo and treatment groups was not significant (32.9% vs 22.7%; P =.129 for AMS incidence, 9.6% vs 8.2%; P =.74 for AMS severity, 54.8% vs 42.7%; P =.11 for HAH incidence, and 8.2% vs 3.6%; P =.18 for HAH severity). Conclusions: Ibuprofen was found to be effective in preventing AMS in the intent-to-treat analysis group but not in those who completed the trial. This loss of significance in the subjects who completed the trial may be explained by persons in the placebo group having a higher burden of illness and associated decreased compliance with the protocol. An important limitation of this study may be the possibility that ibuprofen can mask headache, which is a compulsory criterion for the diagnosis of AMS. © 2012 Wilderness Medical Society. Hide abstract

Whitehorn J, Van Vinh Chau N, Truong NT, Tai LT, Van Hao N, Hien TT, Wolbers M, Merson L et al. 2012. Lovastatin for adult patients with dengue: protocol for a randomised controlled trial. Trials, 13 (1), pp. 203. Read abstract | Read more

Dengue is the most important vector-borne viral infection of man, with approximately 2 billion people living in areas at risk. Infection results in a range of manifestations from asymptomatic infection through to life-threatening shock and haemorrhage. One of the hallmarks of severe dengue is vascular endothelial disruption. There is currently no specific therapy and clinical management is limited to supportive care. Statins are a class of drug initially developed for lipid lowering. There has been considerable recent interest in their effects beyond lipid lowering. These include anti-inflammatory effects at the endothelium. In addition, it is possible that lovastatin may have an anti-viral effect against dengue. Observational data suggest that the use of statins may improve outcomes for such conditions as sepsis and pneumonia. This paper describes the protocol for a randomised controlled trial investigating a short course of lovastatin therapy in adult patients with dengue. Hide abstract

Gertsch JH, Corbett B, Holck PS, Mulcahy A, Watts M, Stillwagon NT, Casto AM, Abramson CH et al. 2012. Altitude Sickness in Climbers and Efficacy of NSAIDs Trial (ASCENT): randomized, controlled trial of ibuprofen versus placebo for prevention of altitude illness. Wilderness Environ Med, 23 (4), pp. 307-315. Read abstract | Read more

To study the effectiveness of ibuprofen versus placebo in preventing acute mountain sickness (AMS) and high altitude headache (HAH). Hide abstract

Dongol S, Thompson CN, Clare S, Nga TV, Duy PT, Karkey A, Arjyal A, Koirala S et al. 2012. The microbiological and clinical characteristics of invasive salmonella in gallbladders from cholecystectomy patients in kathmandu, Nepal. PLoS One, 7 (10), pp. e47342. Read abstract | Read more

Gallbladder carriage of invasive Salmonella is considered fundamental in sustaining typhoid fever transmission. Bile and tissue was obtained from 1,377 individuals undergoing cholecystectomy in Kathmandu to investigate the prevalence, characteristics and relevance of invasive Salmonella in the gallbladder in an endemic area. Twenty percent of bile samples contained a Gram-negative organism, with Salmonella Typhi and Salmonella Paratyphi A isolated from 24 and 22 individuals, respectively. Gallbladders that contained Salmonella were more likely to show evidence of acute inflammation with extensive neutrophil infiltrate than those without Salmonella, corresponding with higher neutrophil and lower lymphocyte counts in the blood of Salmonella positive individuals. Antimicrobial resistance in the invasive Salmonella isolates was limited, indicating that gallbladder colonization is unlikely to be driven by antimicrobial resistance. The overall role of invasive Salmonella carriage in the gallbladder is not understood; here we show that 3.5% of individuals undergoing cholecystectomy in this setting have a high concentration of antimicrobial sensitive, invasive Salmonella in their bile. We predict that such individuals will become increasingly important if current transmission mechanisms are disturbed; prospectively identifying these individuals is, therefore, paramount for rapid local and regional elimination. Hide abstract

Do LAH, van Doorn HR, Bryant JE, Farrar J, De Jong MD, Nghiem MN, Nguyen Van VC, Vo CK, Nguyen MD, Tran TH. 2012. A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus Journal of Virological Methods, 179 (1), pp. 250-255. Read abstract | Read more

Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0×10 and 6.0×10 copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV. © 2011 Elsevier B.V. Hide abstract

Ho Dang Trung N, Le Thi Phuong T, Wolbers M, Nguyen Van Minh H, Nguyen Thanh V, Van MP, Thieu NT, Van TL et al. 2012. Aetiologies of central nervous system infection in Viet Nam: a prospective provincial hospital-based descriptive surveillance study. PLoS One, 7 (5), pp. e37825. Read abstract | Read more

Infectious diseases of the central nervous system (CNS) remain common and life-threatening, especially in developing countries. Knowledge of the aetiological agents responsible for these infections is essential to guide empiric therapy and develop a rational public health policy. To date most data has come from patients admitted to tertiary referral hospitals in Asia and there is limited aetiological data at the provincial hospital level where most patients are seen. Hide abstract

Nhu NT, Lan NT, Phuong NT, Chau NV, Farrar J, Caws M. 2012. Association of streptomycin resistance mutations with level of drug resistance and Mycobacterium tuberculosis genotypes. Int J Tuberc Lung Dis, 16 (4), pp. 527-531. Read abstract | Read more

To determine 1) the relationship between specific streptomycin (SM) resistance mutations and the minimum inhibitory concentration (MIC), and 2) whether these mutations are preferentially associated with the Beijing genotype in Viet Nam. Hide abstract

Yacoub S, Griffiths A, Hong Chau TT, Simmons CP, Wills B, Hien TT, Henein M, Farrar J. 2012. Cardiac function in Vietnamese patients with different dengue severity grades Critical Care Medicine, 40 (2), pp. 477-483. Read abstract | Read more

Objective: Dengue continues to cause significant global morbidity and mortality. Severe disease is characterized by cardiovascular compromise from capillary leakage. Cardiac involvement in dengue has also been reported but has not been adequately studied. Setting: Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. Subjects and Design: Seventy-nine patients aged 8-6 yrs with different dengue severity grades were studied using echocardiography including tissue Doppler imaging. The patients were split into severity grades: dengue, dengue with warning signs, and severe dengue. Changes in cardiac functional parameters and hemodynamic indices were monitored over the hospital stay. Intervention: None. Measurements and Main Results; Patients with severe dengue had worse cardiac function compared with dengue in the form of left ventricular systolic dysfunction with increased left myocardial performance index (0.58 [0.26-0.80] vs. 0.38 [0.22-0.70], p = .006). Septal myocardial systolic velocities were reduced (6.4 [4.8-10] vs. 8.1 [6-13] cm/s, p = .01) as well as right ventricular systolic (11.4 [7.5-17] vs. 13.5 [10-17] cm/s, p = .016) and diastolic velocities (13 [8-23] vs. 17 [12-25] cm/s, p = .0026). In the severe group, these parameters improved from hospital admission to discharge; septal myocardial systolic velocities to 8.8 (7-11) cm/s (p = .002), right ventricular myocardial systolic velocities to 15.0 (11.8-23) cm/s, (p = .003), and diastolic velocity to 21 (11-25) cm/s (p = .002). Patients with cardiac impairment were more likely to have significant pleural effusions. Conclusions: Patients with severe dengue have evidence of systolic and diastolic cardiac impairment with septal and right ventricular wall being predominantly affected. Copyright © 2012 by the Society of Critical Care Medicine and Lippincott Williams & Wilkins. Hide abstract

Horne DJ, Randhawa AK, Chau TT, Bang ND, Yen NT, Farrar JJ, Dunstan SJ, Hawn TR. 2012. Common polymorphisms in the PKP3-SIGIRR-TMEM16J gene region are associated with susceptibility to tuberculosis. J Infect Dis, 205 (4), pp. 586-594. Read abstract | Read more

Tuberculosis has been associated with genetic variation in host immunity. We hypothesized that single-nucleotide polymorphisms (SNPs) in SIGIRR, a negative regulator of Toll-like receptor/IL-1R signaling, are associated with susceptibility to tuberculosis. Hide abstract

Tham NT, Hang VTT, Khanh TH, Viet DC, Hien TT, Farrar J, Chau NV, van Doorn HR. 2012. Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam Diagnostic Microbiology and Infectious Disease, 74 (2), pp. 131-136. Read abstract | Read more

Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable. © 2012 Elsevier Inc. Hide abstract

Simmons CP, Farrar JJ, Chau NVV, Wills B. 2012. CURRENT CONCEPTS Dengue NEW ENGLAND JOURNAL OF MEDICINE, 366 (15), pp. 1423-1432. | Read more

Thuong NTT, Hawn TR, Chau TTH, Bang ND, Yen NTB, Thwaites GE, Teo YY, Seielstad M et al. 2012. Epiregulin (EREG) variation is associated with susceptibility to tuberculosis Genes and Immunity, 13 (3), pp. 275-281. Read abstract | Read more

Although host genetics influences susceptibility to Mycobacterium tuberculosis, the human genes regulating pathogenesis remain largely unknown. We used M. tuberculosis-stimulated macrophage gene expression profiling in conjunction with a case-control genetic association study to discover epiregulin (EREG), as a novel candidate tuberculosis (TB) susceptibility gene. Using a genome-wide association study dataset, we found that among the 21 genes with greater than 50-fold induction, EREG had the most polymorphisms associated with TB. We genotyped haplotype-tagging polymorphisms in discovery (N=337 cases, N=380 controls) and validation (N=332 cases) datasets and an EREG polymorphism (rs7675690) was associated with susceptibility to TB (genotypic comparison; corrected P=0.00007). rs7675690 was also associated more strongly with infections caused by the Beijing lineage of M. tuberculosis when compared with non-Beijing strains (controls vs Beijing, OR 7.81, P=8.7 × 10 -5; non-Beijing, OR 3.13, P=0.074). Furthermore, EREG expression was induced in monocytes and peripheral blood mononuclear cells stimulated with M. tuberculosis as well as TLR4 and TLR2/1/6 ligands. In murine macrophages, EREG expression induced by M. tuberculosis was MYD88- and TLR2-dependent. Together, these data provide the first evidence for an important role for EREG as a susceptibility gene for human TB. © 2012 Macmillan Publishers Limited All rights reserved. Hide abstract

Minh Ha DT, Ngoc Lan NT, Wolbers M, Kiet VS, Thanh Hang HT, Duc NH, Huong TM, Bach VM et al. 2012. Evaluation of microscopic observation drug susceptibility assay for diagnosis of multidrug-resistant Tuberculosis in Viet Nam BMC Infectious Diseases, 12 Read abstract | Read more

Background: Early diagnosis of tuberculosis (TB) and multidrug resistant tuberculosis (MDR TB) is important for the elimination of TB. We evaluated the microscopic observation drug susceptibility (MODS) assay as a direct rapid drug susceptibility testing (DST) method for MDR-TB screening in sputum samples. Methods: All adult TB suspects, who were newly presenting to Pham Ngoc Thach Hospital from August to November 2008 were enrolled into the study. Processed sputum samples were used for DST by MODS (DST-MODS) (Rifampicin (RIF) 1 μg/ml and Isoniazid (INH) 0.4 μg/ml), MGIT culture (Mycobacterial Growth Indicator Tube) and Lowenstein Jensen (LJ) culture. Cultures positive by either MGIT or LJ were used for proportional DST (DST-LJ) (RIF 40 μg/ml and INH 0.2 μg/ml). DST profiles on MODS and LJ were compared. Discrepant results were resolved by multiplex allele specific PCR (MAS-PCR).Results: Seven hundred and nine TB suspects/samples were enrolled into the study, of which 300 samples with DST profiles available from both MODS and DST-LJ were analyzed. Cording in MODS was unable to correctly identify 3 Mycobacteria Other Than Tuberculosis (MOTT) isolates, resulting in 3 false positive TB diagnoses. None of these isolates were identified as MDR-TB by MODS. The sensitivity and specificity of MODS were 72.6% (95%CI: 59.8, 83.1) and 97.9% (95%CI: 95.2, 99.3), respectively for detection of INH resistant isolates, 72.7% (95%CI: 30.9, 93.7) and 99.7% (95%CI: 98.1, 99.9), respectively for detecting RIF resistant isolates and 77.8% (95%CI: 39.9, 97.1) and 99.7% (95%CI: 98.1, 99.9), respectively for detecting MDR isolates. The positive and negative predictive values (PPV and NPV) of DST-MODS were 87.5% (95%CI: 47.3, 99.6) and 99.3% (95%CI: 97.5, 99.9) for detection of MDR isolates; and the agreement between MODS and DST-LJ was 99.0% (kappa: 0.8, P < 0.001) for MDR diagnosis. The low sensitivity of MODS for drug resistance detection was probably due to low bacterial load samples and the high INH concentration (0.4 μg/ml). The low PPV of DST-MODS may be due to the low MDR-TB rate in the study population (3.8%). The turnaround time of DST-MODS was 9 days and 53 days for DST-LJ.Conclusion: The DST-MODS technique is rapid with low contamination rates. However, the sensitivity of DST-MODS for detection of INH and RIF resistance in this study was lower than reported from other settings. © 2012 Minh Ha et al; licensee BioMed Central Ltd. Hide abstract

Thao VP, Le T, Toeroek EM, Yen NTB, Chau TTH, Jurriaans S, van Doorn HR, de Jong MD, Farrar JJ, Dunstan SJ. 2012. HIV-1 drug resistance in antiretroviral-naive individuals with HIV-1-associated tuberculous meningitis initiating antiretroviral therapy in Vietnam (vol 17, pg 905, 2012) ANTIVIRAL THERAPY, 17 (5), pp. 937-937. Read abstract | Read more

Background: Access to antiretroviral therapy (ART) for Human Immunodeficiency Virus (HIV)-infected individuals in Viet Nam is rapidly expanding, but there are limited data on HIV drug resistance (HIVDR) to guide ART strategies. Methods: We retrospectively conducted HIVDR testing in 220 ART-naive individuals recruited to a randomized controlled trial of immediate versus deferred ART in individuals with HIV-associated tuberculous meningitis in Ho Chi Minh City (HCMC) from 2005-2008. HIVDR mutations were identified by population sequencing of the HIV pol gene and were defined based on 2009 WHO surveillance drug resistance mutations (SDRMs). Results: We successfully sequenced 219/220 plasma samples of subjects prior to ART. 218 were subtype CRF-01AE; one was subtype B. SDRMs were identified in 14/219 (6.4%) subjects. 8/14 were resistant to nucleoside/tide reverse transcriptase inhibitors [(NRTI) T69D, L74V, V75M, M184V/I, K219R], 5/14 to non-nucleoside reverse transcriptase inhibitors [(NNRTI) K103N, V106M, Y181C, Y188C, G190A], 1/14 to both NRTI and NNRTI (D67N, Y181C), and none to protease inhibitors. After 6 months of ART, 8 developed protocol-defined virological failure. HIVDR mutations were identified in 5/8 subjects. All 5 had mutations with high level resistance to NNRTI; 3 had mutations with high level resistance to NRTI. Due to a high early mortality rate (58%), the effect of pre-existing HIVDR mutations on treatment outcome could not be accurately assessed. Conclusions: The prevalence of WHO SDRMs in ART-naive individuals with HIV-associated tuberculous meningitis in HCMC from 2005-2008 is 6.4%. The SDRMs identified conferred resistance to NRTI and/or NNRTI reflecting the standard first-line ART regimens in Viet Nam. Hide abstract

Tobin DM, Roca FJ, Oh SF, McFarland R, Vickery TW, Ray JP, Ko DC, Zou Y et al. 2012. Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections. Cell, 148 (3), pp. 434-446. Read abstract | Read more

Susceptibility to tuberculosis is historically ascribed to an inadequate immune response that fails to control infecting mycobacteria. In zebrafish, we find that susceptibility to Mycobacterium marinum can result from either inadequate or excessive acute inflammation. Modulation of the leukotriene A(4) hydrolase (LTA4H) locus, which controls the balance of pro- and anti-inflammatory eicosanoids, reveals two distinct molecular routes to mycobacterial susceptibility converging on dysregulated TNF levels: inadequate inflammation caused by excess lipoxins and hyperinflammation driven by excess leukotriene B(4). We identify therapies that specifically target each of these extremes. In humans, we identify a single nucleotide polymorphism in the LTA4H promoter that regulates its transcriptional activity. In tuberculous meningitis, the polymorphism is associated with inflammatory cell recruitment, patient survival and response to adjunctive anti-inflammatory therapy. Together, our findings suggest that host-directed therapies tailored to patient LTA4H genotypes may counter detrimental effects of either extreme of inflammation. Hide abstract

Shah JA, Vary JC, Chau TT, Bang ND, Yen NT, Farrar JJ, Dunstan SJ, Hawn TR. 2012. Human TOLLIP regulates TLR2 and TLR4 signaling and its polymorphisms are associated with susceptibility to tuberculosis. J Immunol, 189 (4), pp. 1737-1746. Read abstract | Read more

Tuberculosis, one of the leading causes of death worldwide, stimulates inflammatory responses with beneficial and pathologic consequences. The regulation and nature of an optimal inflammatory response to Mycobacterium tuberculosis remains poorly understood in humans. Insight into mechanisms of negative regulation of the TLR-mediated innate immune response to M. tuberculosis could provide significant breakthroughs in the design of new vaccines and drugs. We hypothesized that TOLLIP and its common variants negatively regulate TLR signaling in human monocytes and are associated with susceptibility to tuberculosis. Using short hairpin RNA knockdown of TOLLIP in peripheral blood human monocytes, we found that TOLLIP suppresses TNF and IL-6 production after stimulation with TLR2 and TLR4 ligands. In contrast, secretion of the anti-inflammatory cytokine IL-10 was induced by TOLLIP. We also discovered two common polymorphisms that are associated with either decreased levels of mRNA expression (rs3750920) or increased IL-6 production (rs5743899) in a sample of 56 healthy volunteers. Furthermore, in a case-population study in Vietnam with 760 cord blood samples and 671 TB case patients, we found that SNPs rs3750920 and rs5743899 were associated with susceptibility to tuberculosis (p = 7.03 × 10(-16) and 6.97 × 10(-7), respectively). These data demonstrate that TOLLIP has an anti-inflammatory effect on TLR signaling in humans and that TOLLIP deficiency is associated with an increased risk of tuberculosis. To our knowledge, these data also show the first associations of TOLLIP polymorphisms with any infectious disease. These data also implicate an unexpected mechanism of negative regulation of TLR signaling in human tuberculosis pathogenesis. Hide abstract

Ross AG, Gray DJ, McManus DP, Li Y-S, Farrar J, Hunstman RJ. 2012. Neuroschistosomiasis Journal of Neurology, 259 (1), pp. 22-32. Read abstract | Read more

Schistosomiasis (bilharzia) is a neglected tropical disease caused by digenetic trematode platyhelminths of the genus Schistosoma. Neuroschistosomiasis is one of the most severe clinical outcomes associated with schistosome infection. Neurological complications early during the course of infection are thought to occur through in situ egg deposition following aberrant migration of adult worms to the brain or spinal cord. The presence of eggs in the CNS induces a cell-mediated Th2-driven periovular granulomatous reaction. The mass effect of thousands of eggs and the large granulomas concentrated within the brain or spinal cord explain the signs and symptoms of increased intracranial pressure, myelopathy, radiculopathy and subsequent clinical sequelae. Myelopathy (acute transverse myelitis and subacute myeloradiculopathy) of the lumbosacral region is the most common neurological manifestation of S. mansoni or S. haematobium infection, whereas acute encephalitis of the cortex, subcortical white matter, basal ganglia or internal capsule is typical of S. japonicum infection. Cerebral complications include encephalopathy with headache, visual impairment, delirium, seizures, motor deficits and ataxia, whereas spinal symptoms include lumbar pain, lower limb radicular pain, muscle weakness, sensory loss and bladder dysfunction. The finding of eggs in the stool or a positive serology, provides supportive but not direct evidence of neuroschistosomiasis. A definitive diagnosis can only be made with histopathological study showing Schistosoma eggs and granulomas. Schistosomicidal drugs (notably praziquantel), steroids and surgery are currently used for the treatment of neuroschistosomiasis. During the 'acute phase' of the disease, neuroschistosomiasis is treated with corticosteroids which are augmented with a course of praziquantel once female worm ovipositioning commences. Surgery should be reserved for special cases such as in those with evidence of medullary compression and in those who deteriorate despite clinical management. © 2011 Springer-Verlag. Hide abstract

Pan H, Cui B, Zhang D, Farrar J, Law F, Ba-Thein W. 2012. Prior knowledge, older age, and higher allowance are risk factors for self-medication with antibiotics among university students in southern China. PLoS One, 7 (7), pp. e41314. Read abstract | Read more

Self-medication with antibiotics (SMA) has been reported among university students in many countries, but little research has been done on this issue in China. The objective of this study was to evaluate knowledge and behaviors of university students and risk factors concerning SMA. Hide abstract

Horstick O, Farrar J, Lum L, Martinez E, San Martin JL, Ehrenberg J, Velayudhan R, Kroeger A. 2012. Reviewing the development, evidence base, and application of the revised dengue case classification. Pathog Glob Health, 106 (2), pp. 94-101. Read abstract | Read more

With the example of dengue, an evidence-based approach to prospectively develop a case classification is described, gathering evidence for identifying strength and weaknesses of the existing model, collecting new data describing the disease as it occurs globally, further developing a new model that can be applied in practice and field testing the newly developed model in comparison to the previous model. For each step in this process, the highest available level of evidence has been applied. This process has been initiated by the World Health Organization's (WHO) Special Programme for Research and Training in Tropical Diseases (TDR) and WHO's Department for Control of Neglected Tropical Diseases (NTD), developing the following for dengue. Since the early 1970s, dengue has been classified into dengue fever, dengue haemorrhagic fever grades I and II and dengue shock syndrome grades III and IV (DF/DHF/DSS). However, in recent years, a growing number of dengue clinicians have questioned the shortcomings of this scheme. The issues have revolved around the complexity of confirming DHF in clinical practice, misclassifying severe cases as DF, and the emphasis on haemorrhage rather than plasma leakage as the underlying problem in most severe dengue cases. Step 1: A systematic literature review highlighted the shortcomings of the DF/DHF/DSS scheme: (1) difficulties in applying the criteria for DHF/DSS; (2) the tourniquet test has a low sensitivity for distinguishing between DHF and DF; and (3) most DHF criteria had a large variability in frequency of occurrence. Step 2: An analysis of regional and national dengue guidelines and their application in the clinical practice showed a need to re-evaluate and standardize guidelines as the actual ones showed a large variation of definitions, an inconsistent application by medical staff, and a lack of diagnostic facilities necessary for the DHF diagnosis in frontline services. Step 3: A prospective cohort study in seven countries, confirmed the difficulties in applying the DF/DHF/DSS criteria even in tertiary care hospitals, that DF/DHF/DSS do not represent levels of disease severity and that a clear distinction between severe dengue (defined by plasma leakage and/or severe haemorrhage, and/or organ failure) and (non-severe) dengue can be made using highly sensitive and specific criteria. In contrast, the sub-grouping of (non-severe) dengue into two further severity levels was only possible with criteria that gave approximately 70% sensitivity and specificity. Step 4: Three regional expert consensus groups in the Americas and Asia concluded that 'dengue is one disease entity with different clinical presentations and often with unpredictable clinical evolution and outcome' and that, revising the results of Step 3, DF/DHF/DSS is not related to disease severity. Step 5: In a global expert consensus meeting at WHO in Geneva/Switzerland the evidence collected in Steps 1-4 was reviewed and a revised scheme was developed and accepted, distinguishing: dengue with or without warning signs and severe dengue; the further field testing and acquisition of further prospective evidence of the revised scheme was recommended. Step 6: In 18 countries, the usefulness and applicability of the revised classification compared to the DF/DHF/DSS scheme were tested showing clear results in favour of the revised classification. Step 7: Studies are under way on the predictive value of warning signs for severe dengue and on criteria for the clinical diagnosis of dengue which will complete the evidence foundation of the revised classification. The analysis has shown that the revised dengue case classification is better able to standardize clinical management, raise awareness about unnecessary interventions, match patient categories with specific treatment instructions, and make the key messages of patient management understandable for all health care staff dealing with dengue patients. Furthermore, the evidence-based approach to develop prospectively the dengue case classification could be a model approach for other disease classifications. Hide abstract

Loan HT, Parry J, Nga NTN, Yen LM, Binh NT, Thuy TTD, Duong NM, Campbell JI, Thwaites L, Farrar JJ, Parry CM. 2012. Semi-recumbent body position fails to prevent healthcare-associated pneumonia in Vietnamese patients with severe tetanus Transactions of the Royal Society of Tropical Medicine and Hygiene, 106 (2), pp. 90-97. Read abstract | Read more

Healthcare-associated pneumonia (HCAP) is a common complication in patients with severe tetanus. Nursing tetanus patients in a semi-recumbent body position could reduce the incidence of HCAP. In a randomised controlled trial we compared the occurrence of HCAP in patients with severe tetanus nursed in a semi-recumbent (30°) or supine position. A total of 229 adults and children (aged ≥1 year) with severe tetanus admitted to hospital in Vietnam, were randomly assigned to a supine (n = 112) or semi-recumbent (n = 117) position. For patients maintaining their assigned positions and in hospital for > 48. h there was no significant difference between the two groups in the frequency of clinically suspected pneumonia [22/106 (20.8%) vs 26/104 (25.0%); p = 0.464], pneumonia rate/1000 intensive care unit days (13.9 vs 14.6; p = 0.48) and pneumonia rate/1000 ventilated days (39.2 vs 38.1; p = 0.72). Mortality in the supine patients was 11/112 (9.8%) compared with 17/117 (14.5%) in the semi-recumbent patients (p = 0.277). The overall complication rate [57/112 (50.9%) vs 76/117 (65.0%); p = 0.03] and need for tracheostomy [51/112 (45.5%) vs 69/117 (58.9%); p = 0.04) was greater in semi-recumbent patients. Semi-recumbent body positioning did not prevent the occurrence of HCAP in severe tetanus patients. [Clinical Trials.gov Identifier: NCT01331252]. © 2011 Royal Society of Tropical Medicine and Hygiene. Hide abstract

Fox A, Le NM, Horby P, van Doorn HR, Nguyen VT, Nguyen HH, Nguyen TC, Vu DP et al. 2012. Severe pandemic H1N1 2009 infection is associated with transient NK and T deficiency and aberrant CD8 responses. PLoS One, 7 (2), pp. e31535. Read abstract | Read more

It is unclear why the severity of influenza varies in healthy adults or why the burden of severe influenza shifts to young adults when pandemic strains emerge. One possibility is that cross-protective T cell responses wane in this age group in the absence of recent infection. We therefore compared the acute cellular immune response in previously healthy adults with severe versus mild pandemic H1N1 infection. Hide abstract

Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A, Yu J, Sangal V, Brown DJ et al. 2012. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet, 44 (9), pp. 1056-1059. Read abstract | Read more

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery(1,2), spreading efficiently via low-dose fecal-oral transmission(3,4). Historically, S. sonnei has been predominantly responsible for dysentery in developed countries but is now emerging as a problem in the developing world, seeming to replace the more diverse Shigella flexneri in areas undergoing economic development and improvements in water quality(4-6). Classical approaches have shown that S. sonnei is genetically conserved and clonal(7). We report here whole-genome sequencing of 132 globally distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and that diversified into several distinct lineages with unique characteristics. Our analysis suggests that the majority of this diversification occurred in Europe and was followed by more recent establishment of local pathogen populations on other continents, predominantly due to the pandemic spread of a single, rapidly evolving, multidrug-resistant lineage. Hide abstract

Holt KE, Baker S, Farrar JJ, Weill F-X, Holmes EC, Kitchen A, Yu J, Sangal V et al. 2012. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe Nature Genetics, 44 (9), pp. 1056-1059. Read abstract | Read more

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery, spreading efficiently via low-dose fecal-oral transmission. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries but is now emerging as a problem in the developing world, seeming to replace the more diverse Shigella flexneri in areas undergoing economic development and improvements in water quality. Classical approaches have shown that S. sonnei is genetically conserved and clonal. We report here whole-genome sequencing of 132 globally distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and that diversified into several distinct lineages with unique characteristics. Our analysis suggests that the majority of this diversification occurred in Europe and was followed by more recent establishment of local pathogen populations on other continents, predominantly due to the pandemic spread of a single, rapidly evolving, multidrug-resistant lineage. © 2012 Nature America, Inc. All rights reserved. Hide abstract

Vien LETM, Minh NN, Thuong TC, Khuong HD, Nga TV, Thompson C, Campbell JI, de Jong M et al. 2012. The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children. PLoS One, 7 (8), pp. e42919. Read abstract | Read more

Antimicrobial consumption is one of the major contributing factors facilitating the development and maintenance of bacteria exhibiting antimicrobial resistance. Plasmid-mediated quinolone resistance (PMQR) genes, such as the qnr family, can be horizontally transferred and contribute to reduced susceptibility to fluoroquinolones. We performed an observational study, investigating the copy number of PMQR after antimicrobial therapy. We enrolled 300 children resident in Ho Chi Minh City receiving antimicrobial therapy for acute respiratory tract infections (ARIs). Rectal swabs were taken on enrollment and seven days subsequently, counts for Enterobacteriaceae were performed and qnrA, qnrB and qnrS were quantified by using real-time PCR on metagenomic stool DNA. On enrollment, we found no association between age, gender or location of the participants and the prevalence of qnrA, qnrB or qnrS. Yet, all three loci demonstrated a proportional increase in the number of samples testing positive between day 0 and day 7. Furthermore, qnrB demonstrated a significant increase in copy number between paired samples (p<0.001; Wilcoxon rank-sum), associated with non-fluoroquinolone combination antimicrobial therapy. To our knowledge, this is the first study describing an association between the use of non-fluoroquinolone antimicrobials and the increasing relative prevalence and quantity of qnr genes. Our work outlines a potential mechanism for the selection and maintenance of PMQR genes and predicts a strong effect of co-selection of these resistance determinants through the use of unrelated and potentially unnecessary antimicrobial regimes. Hide abstract

Nga TV, Parry CM, Le T, Lan NP, Diep TS, Campbell JI, Hoang NV, Dung LET et al. 2012. The decline of typhoid and the rise of non-typhoid salmonellae and fungal infections in a changing HIV landscape: bloodstream infection trends over 15 years in southern Vietnam. Trans R Soc Trop Med Hyg, 106 (1), pp. 26-34. Read abstract | Read more

The etiological spectrum of bloodstream infections is variable between industrialized and developing countries and even within a defined location over time. We investigated trends in bloodstream infections at an infectious disease hospital in Ho Chi Minh City, Vietnam, from 1994-2008. Amongst 66,111 blood cultures performed, a clinically relevant pathogen was isolated in 7645 episodes (positivity rate; 116/1000 cultures). Salmonella Typhi was the predominant pathogen until 2002; however, a considerable annual decline in the proportion of S. Typhi was observed (OR 0.6993, 95% CI [0.6885, 0.7103], p<0.0001). Conversely, there was a significant increase in the proportions of non-typhoidal Salmonella (NTS), Cryptococcus neoformans and Penicillium marneffei, concurrent with increasing HIV prevalence. These data document a substantial longitudinal shift in bloodstream infection etiology in southern Vietnam. We propose such changes are related to increasing economic prosperity and HIV prevalence, and this pattern marks a substantial change in the epidemiology of invasive salmonellosis in Southeast Asia. Hide abstract

Horby P, Mai LQ, Fox A, Thai PQ, Thi Thu Yen N, Thanh LT, Le Khanh Hang N, Duong TN et al. 2012. The epidemiology of interpandemic and pandemic influenza in Vietnam, 2007-2010 American Journal of Epidemiology, 175 (10), pp. 1062-1074. Read abstract | Read more

Prospective community-based studies have provided fundamental insights into the epidemiology of influenza in temperate regions, but few comparable studies have been undertaken in the tropics. The authors conducted prospective influenza surveillance and intermittent seroprevalence surveys in a household-based cohort in Vietnam between December 2007 and April 2010, resulting in 1,793 person-seasons of influenza surveillance. Age-and sex-standardized estimates of the risk of acquiring any influenza infection per season in persons 5 years of age or older were 21.1% (95% confidence interval: 17.4, 24.7) in season 1, 26.4% (95% confidence interval: 22.6, 30.2) in season 2, and 17.0% (95% confidence interval: 13.6, 20.4) in season 3. Some individuals experienced multiple episodes of infection with different influenza types/subtypes in the same season (n = 27) or reinfection with the same subtype in different seasons (n = 22). The highest risk of influenza infection was in persons 5-9 years old, in whom the risk of influenza infection per season was 41.8%. Although the highest infection risk was in school-aged children, there were important heterogeneities in the age of infection by subtype and season. These heterogeneities could influence the impact of school closure and childhood vaccination on influenza transmission in tropical areas, such as Vietnam. © The Author 2012. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.2012This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. © The Author 2012. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. Hide abstract

Taylor WR, Nguyen K, Nguyen D, Nguyen H, Horby P, Nguyen HL, Lien T, Tran G et al. 2012. The spectrum of central nervous system infections in an adult referral hospital in Hanoi, Vietnam. PLoS One, 7 (8), pp. e42099. Read abstract | Read more

To determine prospectively the causative pathogens of central nervous system (CNS) infections in patients admitted to a tertiary referral hospital in Hanoi, Vietnam. Hide abstract

Brancusi F, Farrar J, Heemskerk D. 2012. Tuberculous meningitis in adults: a review of a decade of developments focusing on prognostic factors for outcome. Future Microbiol, 7 (9), pp. 1101-1116. Read abstract | Read more

Tuberculous meningitis (TBM) is the most severe form of TB. Despite treatment, mortality and long-term disability remain unacceptably high. Prevention, early recognition, diagnosis and treatment are fundamental to improving outcomes. However, an effective vaccine remains elusive, initial symptoms are nonspecific, and sensitive diagnostic tests are not available. There has been progress in our understanding of the immunopathology of TBM, and several factors have been found to be associated with susceptibility to infection, disease progression and clinical outcome. However, these have not yet impacted on treatment. Early treatment initiation and uninterrupted continuation, severity on presentation, seizures, stroke, cranial nerve involvement, cerebrospinal fluid cell count and lactate levels, hyponatreamia and coinfection with HIV are all found to be important prognostic factors for outcome. Pathogen lineage (Beijing genotype) and host genetics (polymorphisms in TLR2, TIRAP and LTA4H genes) can influence susceptibility to TBM. However, these findings have not yet impacted on treatment. Progress in vaccine development, opportunities for better diagnostic tests, novel insights into pathogenesis and an increasing evidence base for improving treatment should impact the current high mortality and morbidity, if translated to global and local guidelines. Hide abstract

Schut ES, Brouwer MC, Scarborough M, Mai NT, Thwaites GE, Farrar JJ, Reitsma JB, van de Beek D. 2012. Validation of a Dutch risk score predicting poor outcome in adults with bacterial meningitis in Vietnam and Malawi. PLoS One, 7 (3), pp. e34311. Read abstract | Read more

We have previously developed and validated a prognostic model to predict the risk for unfavorable outcome in Dutch adults with bacterial meningitis. The aim of the current study was to validate this model in adults with bacterial meningitis from two developing countries, Vietnam and Malawi. Demographic and clinical characteristics of Vietnamese (n = 426), Malawian patients (n = 465) differed substantially from those of Dutch patients (n = 696). The Dutch model underestimated the risk of poor outcome in both Malawi and Vietnam. The discrimination of the original model (c-statistic [c] 0.84; 95% confidence interval 0.81 to 0.86) fell considerably when re-estimated in the Vietnam cohort (c = 0.70) or in the Malawian cohort (c = 0.68). Our validation study shows that new prognostic models have to be developed for these countries in a sufficiently large series of unselected patients. Hide abstract

Thuong NT, Hawn TR, Chau TT, Bang ND, Yen NT, Thwaites GE, Teo YY, Seielstad M et al. 2012. Epiregulin (EREG) variation is associated with susceptibility to tuberculosis. Genes Immun, 13 (3), pp. 275-281. Read abstract | Read more

Although host genetics influences susceptibility to Mycobacterium tuberculosis, the human genes regulating pathogenesis remain largely unknown. We used M. tuberculosis-stimulated macrophage gene expression profiling in conjunction with a case-control genetic association study to discover epiregulin (EREG), as a novel candidate tuberculosis (TB) susceptibility gene. Using a genome-wide association study dataset, we found that among the 21 genes with greater than 50-fold induction, EREG had the most polymorphisms associated with TB. We genotyped haplotype-tagging polymorphisms in discovery (N = 337 cases, N = 380 controls) and validation (N = 332 cases) datasets and an EREG polymorphism (rs7675690) was associated with susceptibility to TB (genotypic comparison; corrected P = 0.00007). rs7675690 was also associated more strongly with infections caused by the Beijing lineage of M. tuberculosis when compared with non-Beijing strains (controls vs Beijing, OR 7.81, P = 8.7 × 10(-5); non-Beijing, OR 3.13, P = 0.074). Furthermore, EREG expression was induced in monocytes and peripheral blood mononuclear cells stimulated with M. tuberculosis as well as TLR4 and TLR2/1/6 ligands. In murine macrophages, EREG expression induced by M. tuberculosis was MYD88- and TLR2-dependent. Together, these data provide the first evidence for an important role for EREG as a susceptibility gene for human TB. Hide abstract

Toeroek ME, Bang ND, Chau TTH, Yen NTB, Thwaites GE, Quy HT, Dung NH, Hien TT et al. 2011. Dexamethasone and Long-Term Outcome of Tuberculous Meningitis in Vietnamese Adults and Adolescents PLOS ONE, 6 (12), | Read more

Do LA, van Doorn HR, Bryant JE, Nghiem MN, Nguyen Van VC, Vo CK, Nguyen MD, Tran TH, Farrar J, de Jong MD. 2012. A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus. J Virol Methods, 179 (1), pp. 250-255. Read abstract | Read more

Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0×10(1) and 6.0×10(2)copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV. Hide abstract

Thai KT, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L et al. 2012. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. J Virol, 86 (2), pp. 835-843. Read abstract | Read more

Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this diversity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of sampling and/or experimental methods that do not fully account for errors generated through amplification and sequencing of viral RNAs. We investigated the extent and pattern of genetic diversity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma samples (n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from amplification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence diversities of viral populations were very low, with conservative estimates of the average levels of genetic diversity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic diversity and disease severity, immune status, or level of viremia. Hide abstract

Powell TJ, Fox A, Peng Y, Quynh Mai LET, Lien VT, Hang NL, Wang L, Lee LY et al. 2012. Identification of H5N1-specific T-cell responses in a high-risk cohort in vietnam indicates the existence of potential asymptomatic infections. J Infect Dis, 205 (1), pp. 20-27. Read abstract | Read more

Most reported human H5N1 viral infections have been severe and were detected after hospital admission. A case ascertainment bias may therefore exist, with mild cases or asymptomatic infections going undetected. We sought evidence of mild or asymptomatic H5N1 infection by examining H5N1-specific T-cell and antibody responses in a high-risk cohort in Vietnam. Hide abstract

Török ME, Farrar JJ. 2011. When to start antiretroviral therapy in HIV-associated tuberculosis. N Engl J Med, 365 (16), pp. 1538-1540. | Read more

Khor CC, Chau TN, Pang J, Davila S, Long HT, Ong RT, Dunstan SJ, Wills B et al. 2011. Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1. Nat Genet, 43 (11), pp. 1139-1141. Read abstract | Read more

Hypovolemic shock (dengue shock syndrome (DSS)) is the most common life-threatening complication of dengue. We conducted a genome-wide association study of 2,008 pediatric cases treated for DSS and 2,018 controls from Vietnam. Replication of the most significantly associated markers was carried out in an independent Vietnamese sample of 1,737 cases and 2,934 controls. SNPs at two loci showed genome-wide significant association with DSS. We identified a susceptibility locus at MICB (major histocompatibility complex (MHC) class I polypeptide-related sequence B), which was within the broad MHC region on chromosome 6 but outside the class I and class II HLA loci (rs3132468, P(meta) = 4.41 × 10(-11), per-allele odds ratio (OR) = 1.34 (95% confidence interval: 1.23-1.46)). We identified associated variants within PLCE1 (phospholipase C, epsilon 1) on chromosome 10 (rs3765524, P(meta) = 3.08 × 10(-10), per-allele OR = 0.80 (95% confidence interval: 0.75-0.86)). We identify two loci associated with susceptibility to DSS in people with dengue, suggesting possible mechanisms for this severe complication of dengue. Hide abstract

Baker S, Holt KE, Clements AC, Karkey A, Arjyal A, Boni MF, Dongol S, Hammond N et al. 2011. Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission. Open Biol, 1 (2), pp. 110008. Read abstract | Read more

Typhoid is a systemic infection caused by Salmonella Typhi and Salmonella Paratyphi A, human-restricted bacteria that are transmitted faeco-orally. Salmonella Typhi and S. Paratyphi A are clonal, and their limited genetic diversity has precluded the identification of long-term transmission networks in areas with a high disease burden. To improve our understanding of typhoid transmission we have taken a novel approach, performing a longitudinal spatial case-control study for typhoid in Nepal, combining single-nucleotide polymorphism genotyping and case localization via global positioning. We show extensive clustering of typhoid occurring independent of population size and density. For the first time, we demonstrate an extensive range of genotypes existing within typhoid clusters, and even within individual households, including some resulting from clonal expansion. Furthermore, although the data provide evidence for direct human-to-human transmission, we demonstrate an overwhelming contribution of indirect transmission, potentially via contaminated water. Consistent with this, we detected S. Typhi and S. Paratyphi A in water supplies and found that typhoid was spatially associated with public water sources and low elevation. These findings have implications for typhoid-control strategies, and our innovative approach may be applied to other diseases caused by other monophyletic or emerging pathogens. Hide abstract

Simmons CP, Farrar JJ, Nguyen VV, Wills B. 2012. Dengue. N Engl J Med, 366 (15), pp. 1423-1432. | Read more

Tra My PV, Rabaa MA, Vinh H, Holmes EC, Hoang NV, Vinh NT, Phuong LET, Tham NT et al. 2011. The emergence of rotavirus G12 and the prevalence of enteric viruses in hospitalized pediatric diarrheal patients in southern Vietnam. Am J Trop Med Hyg, 85 (4), pp. 768-775. Read abstract | Read more

Diarrhea is a major cause of childhood morbidity and mortality in developing countries, and the majority of infections are of viral etiology. We aimed to compare the etiological prevalence of the major enteric viruses in an urban and a rural setting in southern Vietnam. We simultaneously screened fecal specimens from 362 children in Ho Chi Minh City and Dong Thap province that were hospitalized with acute diarrhea over a 1-month-long period for four viral gastrointestinal pathogens. Rotavirus was the most common pathogen identified, but there was a differential prevalence of rotavirus and norovirus between the urban and rural locations. Furthermore, rotavirus genotyping and phylogenetic analysis again differentiated the genotypes by the sampling location. Our data show a disproportional distribution of enteric viral pathogens in urban and rural locations, and we provide evidence of continual importation of new rotavirus strains into southern Vietnam and report the emergence of rotavirus genotype G12. Hide abstract

Yacoub S, Griffiths A, Chau TT, Simmons CP, Wills B, Hien TT, Henein M, Farrar J. 2012. Cardiac function in Vietnamese patients with different dengue severity grades. Crit Care Med, 40 (2), pp. 477-483. Read abstract | Read more

Dengue continues to cause significant global morbidity and mortality. Severe disease is characterized by cardiovascular compromise from capillary leakage. Cardiac involvement in dengue has also been reported but has not been adequately studied. Hide abstract

Tricou V, Minh NN, Farrar J, Tran HT, Simmons CP. 2011. Kinetics of viremia and NS1 antigenemia are shaped by immune status and virus serotype in adults with dengue. PLoS Negl Trop Dis, 5 (9), pp. e1309. Read abstract | Read more

Dengue is a major public health problem in tropical and subtropical countries. Exploring the relationships between virological features of infection with patient immune status and outcome may help to identify predictors of disease severity and enable rational therapeutic strategies. Hide abstract

Nguyen-Pouplin J, Pouplin T, Van TP, The TD, Thi DN, Farrar J, Tinh HT, Wills B. 2011. Dextran fractional clearance studies in acute dengue infection. PLoS Negl Trop Dis, 5 (8), pp. e1282. Read abstract | Read more

Although increased capillary permeability is the major clinical feature associated with severe dengue infections the mechanisms underlying this phenomenon remain unclear. Dextran clearance methodology has been used to investigate the molecular sieving properties of the microvasculature in clinical situations associated with altered permeability, including during pregnancy and in various renal disorders. In order to better understand the characteristics of the vascular leak associated with dengue we undertook formal dextran clearance studies in Vietnamese dengue patients and healthy volunteers. Hide abstract

Nga TV, Nghia HD, Tu LETP, Diep TS, Mai NT, Chau TT, Sinh DX, Phu NH et al. 2011. Real-time PCR for detection of Streptococcus suis serotype 2 in cerebrospinal fluid of human patients with meningitis. Diagn Microbiol Infect Dis, 70 (4), pp. 461-467. Read abstract | Read more

Streptococcus suis serotype 2 is an emerging zoonotic pathogen and is the main cause of acute bacterial meningitis in adult patients in Vietnam. We developed an internally controlled real-time PCR for detection of S. suis serotype 2 in cerebrospinal fluid (CSF) samples targeted at the cps2J gene. Sensitivity and specificity in culture-confirmed clinical samples were 100%. The PCR detected S. suis serotype 2 infection in 101 of 238 (42.4%) prospectively collected CSF samples, of which 55 (23%) were culture positive. Culture-negative but PCR-positive CSF samples were significantly associated with the use of antimicrobial agents before admission. S. suis serotype 2 infection was more common than infections with Streptococcus pneumoniae and Neisseria meningitidis combined. Our results strikingly illustrate the additional diagnostic value of PCR in patients who are pretreated with antimicrobial agents and demonstrate the extremely high prevalence of S. suis infections among Vietnamese adult patients with bacterial meningitis. Hide abstract

Duong V, Simmons C, Gavotte L, Viari A, Ong S, Chantha N, Lennon NJ, Birren BW et al. 2013. Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia. Infect Genet Evol, 15 pp. 59-68. Read abstract | Read more

In Cambodia, dengue virus (DENV) was first isolated in 1963 and has become endemic with peak epidemic during raining season. Since 2000, the Dengue National Control Program has reported from 10,000 to 40,000 cases per year with fatality rates ranging from 0.7 to 1.7. All four dengue serotypes are found circulating in Cambodia with alternative predominance of serotypes DENV-2 and DENV-3. The DENV-1 represents from 5% to 20% of all circulating viruses, depending upon the year. In this work, 79 clinical strains of DENV-1 were isolated between 2000 and 2009 and their genome fully sequenced. Four distinct lineages with different dynamics were identified. The main evolutionary drive was negative selective pressure but each lineage was characterized by the presence of specific mutations acquired through evolution. Coexistence, extinction and replacement of lineages occurred over the 10-year period. Lineages 1, 2 and 3 were all detected since 2000-2002 and disappeared in 2003, 2004-2005 and 2007, respectively. Lineages 1 and 2 displayed different dynamics. Lineage 1 was very diverse whereas lineage 2 was very homogeneous. Lineage 4 which derived from lineage 3 in 2003 remained the only one at the end of the sampling period in 2008-2009 owing to a selective sweep. The lineages dynamic of DENV-1 viruses and consequences for molecular epidemiology are discussed. Hide abstract

Ross AG, McManus DP, Farrar J, Hunstman RJ, Gray DJ, Li YS. 2012. Neuroschistosomiasis. J Neurol, 259 (1), pp. 22-32. Read abstract | Read more

Schistosomiasis (bilharzia) is a neglected tropical disease caused by digenetic trematode platyhelminths of the genus Schistosoma. Neuroschistosomiasis is one of the most severe clinical outcomes associated with schistosome infection. Neurological complications early during the course of infection are thought to occur through in situ egg deposition following aberrant migration of adult worms to the brain or spinal cord. The presence of eggs in the CNS induces a cell-mediated Th2-driven periovular granulomatous reaction. The mass effect of thousands of eggs and the large granulomas concentrated within the brain or spinal cord explain the signs and symptoms of increased intracranial pressure, myelopathy, radiculopathy and subsequent clinical sequelae. Myelopathy (acute transverse myelitis and subacute myeloradiculopathy) of the lumbosacral region is the most common neurological manifestation of S. mansoni or S. haematobium infection, whereas acute encephalitis of the cortex, subcortical white matter, basal ganglia or internal capsule is typical of S. japonicum infection. Cerebral complications include encephalopathy with headache, visual impairment, delirium, seizures, motor deficits and ataxia, whereas spinal symptoms include lumbar pain, lower limb radicular pain, muscle weakness, sensory loss and bladder dysfunction. The finding of eggs in the stool or a positive serology, provides supportive but not direct evidence of neuroschistosomiasis. A definitive diagnosis can only be made with histopathological study showing Schistosoma eggs and granulomas. Schistosomicidal drugs (notably praziquantel), steroids and surgery are currently used for the treatment of neuroschistosomiasis. During the 'acute phase' of the disease, neuroschistosomiasis is treated with corticosteroids which are augmented with a course of praziquantel once female worm ovipositioning commences. Surgery should be reserved for special cases such as in those with evidence of medullary compression and in those who deteriorate despite clinical management. Hide abstract

Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP. 2011. Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLoS Pathog, 7 (6), pp. e1002064. Read abstract | Read more

Dengue is one of the most important infectious diseases of humans and has spread throughout much of the tropical and subtropical world. Despite this widespread dispersal, the determinants of dengue transmission in endemic populations are not well understood, although essential for virus control. To address this issue we performed a phylogeographic analysis of 751 complete genome sequences of dengue 1 virus (DENV-1) sampled from both rural (Dong Thap) and urban (Ho Chi Minh City) populations in southern Viet Nam during the period 2003-2008. We show that DENV-1 in Viet Nam exhibits strong spatial clustering, with likely importation from Cambodia on multiple occasions. Notably, multiple lineages of DENV-1 co-circulated in Ho Chi Minh City. That these lineages emerged at approximately the same time and dispersed over similar spatial regions suggests that they are of broadly equivalent fitness. We also observed an important relationship between the density of the human host population and the dispersion rate of dengue, such that DENV-1 tends to move from urban to rural populations, and that densely populated regions within Ho Chi Minh City act as major transmission foci. Despite these fluid dynamics, the dispersion rates of DENV-1 are relatively low, particularly in Ho Chi Minh City where the virus moves less than an average of 20 km/year. These low rates suggest a major role for mosquito-mediated dispersal, such that DENV-1 does not need to move great distances to infect a new host when there are abundant susceptibles, and imply that control measures should be directed toward the most densely populated urban environments. Hide abstract

Tho DQ, Lan NT, Chau NV, Farrar J, Caws M. 2011. Multiplex allele-specific polymerase chain reaction for detection of isoniazid resistance in Mycobacterium tuberculosis. Int J Tuberc Lung Dis, 15 (6), pp. 799-803. Read abstract | Read more

Pham Ngoc Thach Tuberculosis Reference Hospital, Ho Chi Minh City, Viet Nam. Hide abstract

Parry CM, Vinh H, Chinh NT, Wain J, Campbell JI, Hien TT, Farrar JJ, Baker S. 2011. The influence of reduced susceptibility to fluoroquinolones in Salmonella enterica serovar Typhi on the clinical response to ofloxacin therapy. PLoS Negl Trop Dis, 5 (6), pp. e1163. Read abstract | Read more

Infection with Salmonella enterica serovar Typhi (S. Typhi) with reduced susceptibility to fluoroquinolones has been associated with fluoroquinolone treatment failure. We studied the relationship between ofloxacin treatment response and the ofloxacin minimum inhibitory concentration (MIC) of the infecting isolate. Individual patient data from seven randomised controlled trials of antimicrobial treatment in enteric fever conducted in Vietnam in which ofloxacin was used in at least one of the treatment arms was studied. Data from 540 patients randomised to ofloxacin treatment was analysed to identify an MIC of the infecting organism associated with treatment failure. Hide abstract

Török ME, Yen NT, Chau TT, Mai NT, Phu NH, Mai PP, Dung NT, Chau NV et al. 2011. Timing of initiation of antiretroviral therapy in human immunodeficiency virus (HIV)--associated tuberculous meningitis. Clin Infect Dis, 52 (11), pp. 1374-1383. Read abstract | Read more

The optimal time to initiate antiretroviral therapy (ART) in human immunodeficiency virus (HIV)-associated tuberculous meningitis is unknown. Hide abstract

Fisher D, Hui DS, Gao Z, Lee C, Oh MD, Cao B, Hien TT, Patlovich K, Farrar J. 2011. Pandemic response lessons from influenza H1N1 2009 in Asia. Respirology, 16 (6), pp. 876-882. Read abstract | Read more

During April 2009, a novel H1N1 influenza A virus strain was identified in Mexico and the USA. Within weeks the virus had spread globally and the first pandemic of the 21st Century had been declared. It is unlikely to be the last and it is crucial that real lessons are learned from the experience. Asia is considered a hot spot for the emergence of new pathogens including past influenza pandemics. On this occasion while preparing for an avian, highly virulent influenza virus (H5N1 like) originating in Asia in fact the pandemic originated from swine, and was less virulent. This discrepancy between what was planned for and what emerged created its own challenges. The H1N1 pandemic has tested national health-care infrastructures and exposed shortcomings in our preparedness as a region. Key health challenges include communication throughout the region, surge capacity, access to reliable information and access to quality care, health-care worker skills, quality, density and distribution, access to essential medicines and lack of organizational infrastructure for emergency response. Despite years of preparation the public health and clinical research community were not ready to respond and opportunities for an immediate research response were missed. Despite warm words and pledges efforts to engage the international community to ensure equitable sharing of limited resources such as antivirals and vaccines fell short and stockpiles in the main remained in the rich world. This manuscript with authors from across the region describes some of the major challenges faced by Asia in response to the pandemic and draws lessons for the future. Hide abstract

Pouplin T, Pouplin JN, Van Toi P, Lindegardh N, Rogier van Doorn H, Hien TT, Farrar J, Török ME, Chau TT. 2011. Valacyclovir for herpes simplex encephalitis. Antimicrob Agents Chemother, 55 (7), pp. 3624-3626. Read abstract | Read more

The recommended treatment for herpes simplex encephalitis (HSE) remains intravenous acyclovir. In resource-poor countries, however, intravenous formulations are usually unavailable or unaffordable. We report the penetration of acyclovir into the cerebrospinal fluid (CSF) in patients with HSE, treated with the oral prodrug valacyclovir at 1,000 mg three times daily. The oral therapy achieved adequate acyclovir concentrations in the CSF and may be an acceptable early treatment for suspected HSE in resource-limited settings. Hide abstract

Hien TT, Hanpithakpong W, Truong NT, Dung NT, Toi PV, Farrar J, Lindegardh N, Tarning J, Ashton M. 2011. Orally formulated artemisinin in healthy fasting Vietnamese male subjects: a randomized, four-sequence, open-label, pharmacokinetic crossover study. Clin Ther, 33 (5), pp. 644-654. Read abstract | Read more

Artemisinin derivatives are used in antimalarial drug combination therapy. Artemisinin and piperaquine have recently been proven to be prospective candidates for combination therapy in the treatment of uncomplicated Plasmodium falciparum malaria. Hide abstract

Arjyal A, Basnyat B, Koirala S, Karkey A, Dongol S, Agrawaal KK, Shakya N, Shrestha K et al. 2011. Gatifloxacin versus chloramphenicol for uncomplicated enteric fever: an open-label, randomised, controlled trial. Lancet Infect Dis, 11 (6), pp. 445-454. Read abstract | Read more

We aimed to investigate whether gatifloxacin, a new generation and affordable fluoroquinolone, is better than chloramphenicol for the treatment of uncomplicated enteric fever in children and adults. Hide abstract

Barniol J, Gaczkowski R, Barbato EV, da Cunha RV, Salgado D, Martínez E, Segarra CS, Pleites Sandoval EB et al. 2011. Usefulness and applicability of the revised dengue case classification by disease: multi-centre study in 18 countries. BMC Infect Dis, 11 (1), pp. 106. Read abstract | Read more

In view of the long term discussion on the appropriateness of the dengue classification into dengue fever (DF), dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS), the World Health Organization (WHO) has outlined in its new global dengue guidelines a revised classification into levels of severity: dengue fever with an intermediary group of "dengue fever with warning sings", and severe dengue. The objective of this paper was to compare the two classification systems regarding applicability in clinical practice and surveillance, as well as user-friendliness and acceptance by health staff. Hide abstract

Le T, Wolbers M, Chi NH, Quang VM, Chinh NT, Lan NP, Lam PS, Kozal MJ, Shikuma CM, Day JN, Farrar J. 2011. Epidemiology, seasonality, and predictors of outcome of AIDS-associated Penicillium marneffei infection in Ho Chi Minh City, Viet Nam. Clin Infect Dis, 52 (7), pp. 945-952. Read abstract | Read more

Penicillium marneffei is an important human immunodeficiency virus (HIV)-associated opportunistic pathogen in Southeast Asia. The epidemiology and the predictors of penicilliosis outcome are poorly understood. Hide abstract

Le T, Farrar J, Shikuma C. 2011. Rebound of plasma viremia following cessation of antiretroviral therapy despite profoundly low levels of HIV reservoir: implications for eradication. AIDS, 25 (6), pp. 871-872. | Read more

Duyen HT, Ngoc TV, Ha DOT, Hang VT, Kieu NT, Young PR, Farrar JJ, Simmons CP, Wolbers M, Wills BA. 2011. Kinetics of plasma viremia and soluble nonstructural protein 1 concentrations in dengue: differential effects according to serotype and immune status. J Infect Dis, 203 (9), pp. 1292-1300. Read abstract | Read more

We describe the magnitude and kinetics of plasma viremia and nonstructural protein 1 (sNS1) levels in sequential samples from 167 children with acute dengue, enrolled early in a community study in Vietnam. All children recovered fully, and only 5 required hospitalization. Among those with dengue virus type 1 (DENV-1), plasma viremia was significantly greater in primary (49) than secondary (44) infections and took longer to resolve. In primary DENV-2 and 3 infections, viremia was significantly lower than among primary DENV-1 infections. Concentrations of sNS1 were significantly higher for DENV-1 than for DENV-2 after adjusting for viremia, with marked differences in the kinetic profiles between primary and secondary infections. Secondary infection and higher viremia were independent predictors of more severe thrombocytopenia, and higher viremia was associated with a small increase in hemoconcentration. Our findings identify clear serotype and immune-status related effects on the dynamics of dengue viremia and sNS1 responses, together with associations with important clinical parameters. Hide abstract

Heemskerk D, Day J, Chau TT, Dung NH, Yen NT, Bang ND, Merson L, Olliaro P et al. 2011. Intensified treatment with high dose rifampicin and levofloxacin compared to standard treatment for adult patients with tuberculous meningitis (TBM-IT): protocol for a randomized controlled trial. Trials, 12 (1), pp. 25. Read abstract | Read more

Tuberculous meningitis is the most severe form of tuberculosis. Mortality for untreated tuberculous meningitis is 100%. Despite the introduction of antibiotic treatment for tuberculosis the mortality rate for tuberculous meningitis remains high; approximately 25% for HIV-negative and 67% for HIV positive patients with most deaths occurring within one month of starting therapy. The high mortality rate in tuberculous meningitis reflects the severity of the condition but also the poor antibacterial activity of current treatment regimes and relatively poor penetration of these drugs into the central nervous system. Improving the antitubercular activity in the central nervous system of current therapy may help improve outcomes. Increasing the dose of rifampicin, a key drug with known poor cerebrospinal fluid penetration may lead to higher drug levels at the site of infection and may improve survival. Of the second generation fluoroquinolones, levofloxacin may have the optimal pharmacological features including cerebrospinal fluid penetration, with a ratio of Area Under the Curve (AUC) in cerebrospinal fluid to AUC in plasma of >75% and strong bactericidal activity against Mycobacterium tuberculosis. We propose a randomized controlled trial to assess the efficacy of an intensified anti-tubercular treatment regimen in tuberculous meningitis patients, comparing current standard tuberculous meningitis treatment regimens with standard treatment intensified with high-dose rifampicin and additional levofloxacin. Hide abstract

Wolbers M, Heemskerk D, Chau TT, Yen NT, Caws M, Farrar J, Day J. 2011. Sample size requirements for separating out the effects of combination treatments: randomised controlled trials of combination therapy vs. standard treatment compared to factorial designs for patients with tuberculous meningitis. Trials, 12 (1), pp. 26. Read abstract | Read more

In certain diseases clinical experts may judge that the intervention with the best prospects is the addition of two treatments to the standard of care. This can either be tested with a simple randomized trial of combination versus standard treatment or with a 2 x 2 factorial design. Hide abstract

Vien LETM, Abuoun M, Morrison V, Thomson N, Campbell JI, Woodward MJ, Van Vinh Chau N, Farrar J, Schultsz C, Baker S. 2011. Differential phenotypic and genotypic characteristics of qnrS1-harboring plasmids carried by hospital and community commensal enterobacteria. Antimicrob Agents Chemother, 55 (4), pp. 1798-1802. Read abstract | Read more

The qnrS1 gene induces reduced susceptibility to fluoroquinolones in enterobacteria. We investigated the structure, antimicrobial susceptibility phenotype, and antimicrobial resistance gene characteristics of qnrS1 plasmids from hospitalized patients and community controls in southern Vietnam. We found that the antimicrobial susceptibilities, resistance gene characteristics, and plasmid structures of qnrS1 plasmids from the hospital differed from those from the community. Our data imply that the characteristics of the two plasmid groups are indicative of distinct selective pressures in the differing environments. Hide abstract

Vinh H, Anh VT, Anh ND, Campbell JI, Hoang NV, Nga TV, Nhu NT, Minh PV et al. 2011. A multi-center randomized trial to assess the efficacy of gatifloxacin versus ciprofloxacin for the treatment of shigellosis in Vietnamese children. PLoS Negl Trop Dis, 5 (8), pp. e1264. Read abstract | Read more

The bacterial genus Shigella is the leading cause of dysentery. There have been significant increases in the proportion of Shigella isolated that demonstrate resistance to nalidixic acid. While nalidixic acid is no longer considered as a therapeutic agent for shigellosis, the fluoroquinolone ciprofloxacin is the current recommendation of the World Health Organization. Resistance to nalidixic acid is a marker of reduced susceptibility to older generation fluoroquinolones, such as ciprofloxacin. We aimed to assess the efficacy of gatifloxacin versus ciprofloxacin in the treatment of uncomplicated shigellosis in children. Hide abstract

Green JA, Thi Hong Chau T, Farrar JJ, Friedland JS, Thwaites GE. 2011. CNS infection, CSF matrix metalloproteinase concentrations, and clinical/laboratory features. Neurology, 76 (6), pp. 577-579. | Read more

Baker S, Boni MF, Duy PT, Nga TVT, Campbell JI, Dolecek C, Farrar JJ, Karkey A et al. 2011. Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission Open Biology, 1 (OCTOBER), Read abstract | Read more

Typhoid is a systemic infection caused by Salmonella Typhi and Salmonella Paratyphi A, human-restricted bacteria that are transmitted faeco-orally. Salmonella Typhi and S. Paratyphi A are clonal, and their limited genetic diversity has precluded the identification of long-term transmission networks in areas with a high disease burden. To improve our understanding of typhoid transmission we have taken a novel approach, performing a longitudinal spatial case-control study for typhoid in Nepal, combining single-nucleotide polymorphism genotyping and case localization via global positioning. We show extensive clustering of typhoid occurring independent of population size and density. For the first time, we demonstrate an extensive range of genotypes existing within typhoid clusters, and even within individual households, including some resulting from clonal expansion. Furthermore, although the data provide evidence for direct human-to-human transmission, we demonstrate an overwhelming contribution of indirect transmission, potentially via contaminated water. Consistent with this, we detected S. Typhi and S. Paratyphi A in water supplies and found that typhoid was spatially associated with public water sources and low elevation. These findings have implications for typhoid-control strategies, and our innovative approach may be applied to other diseases caused by other monophyletic or emerging pathogens. © 2011 The Authors. Hide abstract

Török ME, Nguyen DB, Tran TH, Nguyen TB, Thwaites GE, Hoang TQ, Nguyen HD, Tran TH et al. 2011. Dexamethasone and long-term outcome of tuberculous meningitis in Vietnamese adults and adolescents. PLoS One, 6 (12), pp. e27821. Read abstract | Read more

Dexamethasone has been shown to reduce mortality in patients with tuberculous meningitis but the long-term outcome of the disease is unknown. Hide abstract

Anders KL, Nguyet NM, Chau NV, Hung NT, Thuy TT, Lien LEB, Farrar J, Wills B, Hien TT, Simmons CP. 2011. Epidemiological factors associated with dengue shock syndrome and mortality in hospitalized dengue patients in Ho Chi Minh City, Vietnam. Am J Trop Med Hyg, 84 (1), pp. 127-134. Read abstract | Read more

Understanding trends in dengue disease burden and risk factors for severe disease can inform health service allocation, clinical management, and planning for vaccines and therapeutics. Dengue admissions at three tertiary hospitals in Ho Chi Minh City, Vietnam, increased between 1996 and 2009, peaking at 22,860 in 2008. Children aged 6-10 years had highest risk of dengue shock syndrome (DSS); however, mortality was highest in younger children and decreased with increasing age (odds ratio [OR] = 0.52, 95% confidence interval [CI] = 0.36-0.75 in 6- to 10- year-old children and OR = 0.27, 95% CI = 0.16-0.44 in 11- to 15-year-old children compared with 1- to 5-year-old children). Males were overrepresented among dengue cases; however, girls had higher risk of DSS (OR = 1.19, 95% CI = 1.14-1.24) and death (OR = 1.57, 95% CI = 1.14-2.17). Young children with dengue had greatest risk of death and should be targeted in dengue vaccine and drug trials. The increased risk of severe outcomes in girls warrants further attention in studies of pathogenesis, health-seeking behavior, and clinical care. Hide abstract

Khor CC, Pang J, Long HT, Hibberd ML, Davila S, Ong RTH, Chau TNB, Dunstan SJ et al. 2011. Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1 Nature Genetics, 43 (11), pp. 1139-1141. Read abstract | Read more

Hypovolemic shock (dengue shock syndrome (DSS)) is the most common life-threatening complication of dengue. We conducted a genome-wide association study of 2,008 pediatric cases treated for DSS and 2,018 controls from Vietnam. Replication of the most significantly associated markers was carried out in an independent Vietnamese sample of 1,737 cases and 2,934 controls. SNPs at two loci showed genome-wide significant association with DSS. We identified a susceptibility locus at MICB (major histocompatibility complex (MHC) class I polypeptide-related sequence B), which was within the broad MHC region on chromosome 6 but outside the class I and class II HLA loci (rs3132468, P = 4.41 × 10 , per-allele odds ratio (OR) = 1.34 (95% confidence interval: 1.23-1.46)). We identified associated variants within PLCE1 (phospholipase C, epsilon 1) on chromosome 10 (rs3765524, P = 3.08 × 10 , per-allele OR = 0.80 (95% confidence interval: 0.75-0.86)). We identify two loci associated with susceptibility to DSS in people with dengue, suggesting possible mechanisms for this severe complication of dengue. © 2011 Nature America, Inc. All rights reserved. Hide abstract

Fox A, Le NM, Simmons CP, Wolbers M, Wertheim HF, Pham TK, Tran TH, Trinh TM et al. 2011. Immunological and viral determinants of dengue severity in hospitalized adults in Ha Noi, Viet Nam. PLoS Negl Trop Dis, 5 (3), pp. e967. Read abstract | Read more

The relationships between the infecting dengue serotype, primary and secondary infection, viremia and dengue severity remain unclear. This cross-sectional study examined these interactions in adult patients hospitalized with dengue in Ha Noi. Hide abstract

Lam SK, Burke D, Capeding MR, Chong CK, Coudeville L, Farrar J, Gubler D, Hadinegoro SR et al. 2011. Preparing for introduction of a dengue vaccine: Recommendations from the 1st Dengue v2V Asia-Pacific Meeting Vaccine,

Lam SK, Burke D, Capeding MR, Chong CK, Coudeville L, Farrar J, Gubler D, Hadinegoro SR et al. 2011. Preparing for introduction of a dengue vaccine: recommendations from the 1st Dengue v2V Asia-Pacific Meeting. Vaccine, 29 (51), pp. 9417-9422. Read abstract | Read more

Infection with dengue virus is a major public health problem in the Asia-Pacific region and throughout tropical and sub-tropical regions of the world. Vaccination represents a major opportunity to control dengue and several candidate vaccines are in development. Experts in dengue and in vaccine introduction gathered for a two day meeting during which they examined the challenges inherent to the introduction of a dengue vaccine into the national immunisation programmes of countries of the Asia-Pacific. The aim was to develop a series of recommendations to reduce the delay between vaccine licensure and vaccine introduction. Major recommendations arising from the meeting included: ascertaining and publicising the full burden and cost of dengue; changing the perception of dengue in non-endemic countries to help generate global support for dengue vaccination; ensuring high quality active surveillance systems and diagnostics; and identifying sustainable sources of funding, both to support vaccine introduction and to maintain the vaccination programme. The attendees at the meeting were in agreement that with the introduction of an effective vaccine, dengue is a disease that could be controlled, and that in order to ensure a vaccine is introduced as rapidly as possible, there is a need to start preparing now. Hide abstract

Lindegardh N, Hanpithakpong W, Kamanikom B, Farrar J, Hien TT, Singhasivanon P, White NJ, Day NP. 2011. Quantification of the anti-influenza drug zanamivir in plasma using high-throughput HILIC-MS/MS. Bioanalysis, 3 (2), pp. 157-165. Read abstract | Read more

parenteral zanamivir is a promising drug for the treatment of severe influenza. However, quantification of this polar drug in biological matrices has traditionally been difficult and the methods developed have been relatively insensitive. Hide abstract

Cuong HQ, Hien NT, Duong TN, Phong TV, Cam NN, Farrar J, Nam VS, Thai KT, Horby P. 2011. Quantifying the emergence of dengue in Hanoi, Vietnam: 1998-2009. PLoS Negl Trop Dis, 5 (9), pp. e1322. Read abstract | Read more

An estimated 2.4 billion people live in areas at risk of dengue transmission, therefore the factors determining the establishment of endemic dengue in areas where transmission suitability is marginal is of considerable importance. Hanoi, Vietnam is such an area, and following a large dengue outbreak in 2009, we set out to determine if dengue is emerging in Hanoi. Hide abstract

Tan LEV, Van Doorn HR, Van der Hoek L, Minh Hien V, Jebbink MF, Quang Ha D, Farrar J, Van Vinh Chau N, de Jong MD. 2011. Random PCR and ultracentrifugation increases sensitivity and throughput of VIDISCA for screening of pathogens in clinical specimens. J Infect Dev Ctries, 5 (2), pp. 142-148. Read abstract

Virus discovery based on cDNA-AFLP (VIDISCA) is a sequence-independent virus discovery method that was recently developed and successfully used to characterize unknown viruses in cell cultures. Its applicability, however, is limited by its low sensitivity. Hide abstract

Thwaites GE, Bhavnani SM, Chau TT, Hammel JP, Török ME, Van Wart SA, Mai PP, Reynolds DK et al. 2011. Randomized pharmacokinetic and pharmacodynamic comparison of fluoroquinolones for tuberculous meningitis. Antimicrob Agents Chemother, 55 (7), pp. 3244-3253. Read abstract | Read more

Tuberculous meningitis (TBM) is the most lethal form of tuberculosis, and new treatments that improve outcomes are required. We randomly assigned adults with TBM to treatment with standard antituberculosis treatment alone or in combination with ciprofloxacin (750 mg/12 h), levofloxacin (500 mg/12 h), or gatifloxacin (400 mg/24 h) for the first 60 days of therapy. Fluoroquinolone concentrations were measured with plasma and cerebrospinal fluid (CSF) specimens taken at predetermined, randomly assigned times throughout treatment. We aimed to describe the pharmacokinetics of each fluoroquinolone during TBM treatment and evaluate the relationship between drug exposure and clinical response over 270 days of therapy (Controlled Trials number ISRCTN07062956). Sixty-one patients with TBM were randomly assigned to treatment with no fluoroquinolone (n = 15), ciprofloxacin (n = 16), levofloxacin (n = 15), or gatifloxacin (n = 15). Cerebrospinal fluid penetration, measured by the ratio of the plasma area under the concentration-time curve from 0 to 24 h (AUC(0-24)) to the cerebrospinal fluid AUC(0-24), was greater for levofloxacin (median, 0.74; range, 0.58 to 1.03) than for gatifloxacin (median, 0.48; range, 0.47 to 0.50) or ciprofloxacin (median, 0.26; range, 0.11 to 0.77). Univariable and multivariable analyses of fluoroquinolone exposure against a range of different treatment responses revealed worse outcomes among patients with lower and higher plasma and CSF exposures than for patients with intermediate exposures (a U-shaped exposure-response). TBM patients most likely to benefit from fluoroquinolone therapy were identified, along with exposure-response relationships associated with improved outcomes. Fluoroquinolones add antituberculosis activity to the standard treatment regimen, but to improve outcomes of TBM, they must be started early, before the onset of coma. Hide abstract

Nghia HD, Tu LETP, Wolbers M, Thai CQ, Hoang NV, Nga TV, Thao LETP, Phu NH et al. 2011. Risk factors of Streptococcus suis infection in Vietnam. A case-control study. PLoS One, 6 (3), pp. e17604. Read abstract | Read more

Streptococcus suis infection, an emerging zoonosis, is an increasing public health problem across South East Asia and the most common cause of acute bacterial meningitis in adults in Vietnam. Little is known of the risk factors underlying the disease. Hide abstract

Loan HT, Parry J, Nga NT, Yen LM, Binh NT, Thuy TT, Duong NM, Campbell JI, Thwaites L, Farrar JJ, Parry CM. 2012. Semi-recumbent body position fails to prevent healthcare-associated pneumonia in Vietnamese patients with severe tetanus. Trans R Soc Trop Med Hyg, 106 (2), pp. 90-97. Read abstract | Read more

Healthcare-associated pneumonia (HCAP) is a common complication in patients with severe tetanus. Nursing tetanus patients in a semi-recumbent body position could reduce the incidence of HCAP. In a randomised controlled trial we compared the occurrence of HCAP in patients with severe tetanus nursed in a semi-recumbent (30°) or supine position. A total of 229 adults and children (aged ≥1 year) with severe tetanus admitted to hospital in Vietnam, were randomly assigned to a supine (n=112) or semi-recumbent (n=117) position. For patients maintaining their assigned positions and in hospital for>48h there was no significant difference between the two groups in the frequency of clinically suspected pneumonia [22/106 (20.8%) vs 26/104 (25.0%); p=0.464], pneumonia rate/1000 intensive care unit days (13.9 vs 14.6; p=0.48) and pneumonia rate/1000 ventilated days (39.2 vs 38.1; p=0.72). Mortality in the supine patients was 11/112 (9.8%) compared with 17/117 (14.5%) in the semi-recumbent patients (p=0.277). The overall complication rate [57/112 (50.9%) vs 76/117 (65.0%); p=0.03] and need for tracheostomy [51/112 (45.5%) vs 69/117 (58.9%); p=0.04) was greater in semi-recumbent patients. Semi-recumbent body positioning did not prevent the occurrence of HCAP in severe tetanus patients. Hide abstract

Ngo TH, Tran TB, Tran TT, Nguyen VD, Campbell J, Pham HA, Huynh HT, Nguyen VV et al. 2011. Slaughterhouse pigs are a major reservoir of Streptococcus suis serotype 2 capable of causing human infection in southern Vietnam. PLoS One, 6 (3), pp. e17943. Read abstract | Read more

Streptococcus suis is a pathogen of major economic significance to the swine industry and is increasingly recognized as an emerging zoonotic agent in Asia. In Vietnam, S. suis is the leading cause of bacterial meningitis in adult humans. Zoonotic transmission is most frequently associated with serotype 2 strains and occupational exposure to pigs or consumption of infected pork. To gain insight into the role of pigs for human consumption as a reservoir for zoonotic infection in southern Vietnam, we determined the prevalence and diversity of S. suis carriage in healthy slaughterhouse pigs. Nasopharyngeal tonsils were sampled from pigs at slaughterhouses serving six provinces in southern Vietnam and Ho Chi Minh City area from September 2006 to November 2007. Samples were screened by bacterial culture. Isolates of S. suis were serotyped and characterized by multi locus sequence typing (MLST) and pulse field gel electrophoresis (PFGE). Antibiotic susceptibility profiles and associated genetic resistance determinants, and the presence of putative virulence factors were determined. 41% (222/542) of pigs carried S. suis of one or multiple serotypes. 8% (45/542) carried S. suis serotype 2 which was the most common serotype found (45/317 strains, 14%). 80% of serotype 2 strains belonged to the MLST clonal complex 1,which was previously associated with meningitis cases in Vietnam and outbreaks of severe disease in China in 1998 and 2005. These strains clustered with representative strains isolated from patients with meningitis in PFGE analysis, and showed similar antimicrobial resistance and virulence factor profiles. Slaughterhouse pigs are a major reservoir of S. suis serotype 2 capable of causing human infection in southern Vietnam. Strict hygiene at processing facilities, and health education programs addressing food safety and proper handling of pork should be encouraged. Hide abstract

Basnyat B, Holck PS, Pun M, Halverson S, Szawarski P, Gertsch J, Steif M, Powell S et al. 2011. Spironolactone does not prevent acute mountain sickness: a prospective, double-blind, randomized, placebo-controlled trial by SPACE Trial Group (spironolactone and acetazolamide trial in the prevention of acute mountain sickness group). Wilderness Environ Med, 22 (1), pp. 15-22. Read abstract | Read more

Over the last 20 years a number of small trials have reported that spironolactone effectively prevents acute mountain sickness (AMS), but to date there have been no large randomized trials investigating the efficacy of spironolactone in prevention of AMS. Hence, a prospective, double-blind, randomized, placebo-controlled trial was conducted to evaluate the efficacy of spironolactone in the prevention of AMS. Hide abstract

Holt KE, Dolecek C, Chau TT, Duy PT, La TT, Hoang NV, Nga TV, Campbell JI et al. 2011. Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam. PLoS Negl Trop Dis, 5 (1), pp. e929. Read abstract | Read more

typhoid fever remains a public health problem in Vietnam, with a significant burden in the Mekong River delta region. Typhoid fever is caused by the bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi), which is frequently multidrug resistant with reduced susceptibility to fluoroquinolone-based drugs, the first choice for the treatment of typhoid fever. We used a GoldenGate (Illumina) assay to type 1,500 single nucleotide polymorphisms (SNPs) and analyse the genetic variation of S. Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005. Hide abstract

Hoa NT, Chieu TT, Nghia HD, Mai NT, Anh PH, Wolbers M, Baker S, Campbell JI et al. 2011. The antimicrobial resistance patterns and associated determinants in Streptococcus suis isolated from humans in southern Vietnam, 1997-2008. BMC Infect Dis, 11 (1), pp. 6. Read abstract | Read more

Streptococcus suis is an emerging zoonotic pathogen and is the leading cause of bacterial meningitis in adults in Vietnam. Systematic data on the antimicrobial susceptibility profiles of S. suis strains isolated from human cases are lacking. We studied antimicrobial resistance and associated resistance determinants in S. suis isolated from patients with meningitis in southern Vietnam. Hide abstract

Tran CB, Nguyen HT, Phan HT, Tran NV, Wills B, Farrar J, Santangelo JD, Simmons CP. 2011. The seroprevalence and seroincidence of enterovirus71 infection in infants and children in Ho Chi Minh City, Viet Nam. PLoS One, 6 (7), pp. e21116. Read abstract | Read more

Enterovirus 71 (EV71)-associated hand, foot and mouth disease has emerged as a serious public health problem in South East Asia over the last decade. To better understand the prevalence of EV71 infection, we determined EV71 seroprevalence and seroincidence amongst healthy infants and children in Ho Chi Minh City, Viet Nam. In a cohort of 200 newborns, 55% of cord blood samples contained EV71 neutralizing antibodies and these decayed to undetectable levels by 6 months of age in 98% of infants. The EV71 neutralizing antibody seroconversion rate was 5.6% in the first year and 14% in the second year of life. In children 5-15 yrs of age, seroprevalence of EV71 neutralizing antibodies was 84% and in cord blood it was 55%. Taken together, these data suggest EV71 force of infection is high and highlights the need for more research into its epidemiology and pathogenesis in high disease burden countries. Hide abstract

Do AH, van Doorn HR, Nghiem MN, Bryant JE, Hoang TH, Do QH, Van TL, Tran TT et al. 2011. Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City, 2004-2008. PLoS One, 6 (3), pp. e18176. Read abstract | Read more

The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized children in resource-limited tropical countries where morbidity and mortality caused by ARIs are highest. Improved etiological insight is needed to improve clinical management and prevention. Hide abstract

Day JN, Hoang TN, Duong AV, Hong CT, Diep PT, Campbell JI, Sieu TP, Hien TT et al. 2011. Most cases of cryptococcal meningitis in HIV-uninfected patients in Vietnam are due to a distinct amplified fragment length polymorphism-defined cluster of Cryptococcus neoformans var. grubii VN1. J Clin Microbiol, 49 (2), pp. 658-664. Read abstract | Read more

Cryptococcal disease most commonly occurs in patients with an underlying immune deficit, most commonly HIV infection, and is due to Cryptococcus neoformans var. grubii. Occasionally disease due to this variety occurs in apparently immunocompetent patients. The relationship between strains infecting immunosuppressed and immunocompetent patients is not clear. Amplified fragment length polymorphism (AFLP) analysis was used to characterize the relationship between strains infecting HIV-infected and uninfected patients. Isolates from 51 HIV-uninfected patients and 100 HIV-infected patients with cryptococcal meningitis were compared. C. neoformans var. grubii VNI was responsible for infections in 73% of HIV-uninfected and 100% of HIV-infected patients. AFLP analysis defined two distinct clusters, VNIγ and VNIδ. The majority (84%) of isolates from HIV-uninfected patients were VNIγ, compared with only 38% of isolates from HIV-infected patients (odds ratio, 8.30; 95% confidence interval [CI], 3.04 to 26.6; P < 0.0001). In HIV-uninfected patients, underlying disease was less frequent in those with VNIγ infections. Two clusters of C. neoformans var. grubii VN1 are responsible for the majority of cases of cryptococcal meningitis in Vietnam. The distribution of these clusters differs according to the immune status of the host. Hide abstract

Guzman MG, Halstead SB, Artsob H, Buchy P, Farrar J, Gubler DJ, Hunsperger E, Kroeger A et al. 2010. Dengue: a continuing global threat. Nat Rev Microbiol, 8 (12 Suppl), pp. S7-16. Read abstract | Read more

Dengue fever and dengue haemorrhagic fever are important arthropod-borne viral diseases. Each year, there are ∼50 million dengue infections and ∼500,000 individuals are hospitalized with dengue haemorrhagic fever, mainly in Southeast Asia, the Pacific and the Americas. Illness is produced by any of the four dengue virus serotypes. A global strategy aimed at increasing the capacity for surveillance and outbreak response, changing behaviours and reducing the disease burden using integrated vector management in conjunction with early and accurate diagnosis has been advocated. Antiviral drugs and vaccines that are currently under development could also make an important contribution to dengue control in the future. Hide abstract

Hoang LT, Lynn DJ, Henn M, Birren BW, Lennon NJ, Le PT, Duong KT, Nguyen TT et al. 2010. The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. J Virol, 84 (24), pp. 12982-12994. Read abstract | Read more

Dengue is a pantropic public health problem. In children, dengue shock syndrome (DSS) is the most common life-threatening complication. The ability to predict which patients may develop DSS may improve triage and treatment. To this end, we conducted a nested case-control comparison of the early host transcriptional features in 24 DSS patients and 56 sex-, age-, and virus serotype-matched uncomplicated (UC) dengue patients. In the first instance, we defined the "early dengue" profile. The transcriptional signature in acute rather than convalescent samples (≤72 h post-illness onset) was defined by an overabundance of interferon-inducible transcripts (31% of the 551 overabundant transcripts) and canonical gene ontology terms that included the following: response to virus, immune response, innate immune response, and inflammatory response. Pathway and network analyses identified STAT1, STAT2, STAT3, IRF7, IRF9, IRF1, CEBPB, and SP1 as key transcriptional factors mediating the early response. Strikingly, the only difference in the transcriptional signatures of early DSS and UC dengue cases was the greater abundance of several neutrophil-associated transcripts in patients who progressed to DSS, a finding supported by higher plasma concentrations of several canonical proteins associated with neutrophil degranulation (bactericidal/permeability-increasing protein [BPI], elastase 2 [ELA2], and defensin 1 alpha [DEF1A]). Elevated levels of neutrophil-associated transcripts were independent of the neutrophil count and also of the genotype of the infecting virus, as genome-length sequences of dengue virus serotype 1 (DENV-1) (n = 15) and DENV-2 (n = 3) sampled from DSS patients were phylogenetically indistinguishable from those sampled from uncomplicated dengue patients (32 DENV-1 and 9 DENV-2 sequences). Collectively, these data suggest a hitherto unrecognized association between neutrophil activation, pathogenesis, and the development of DSS and point to future strategies for guiding prognosis. Hide abstract

Le T, Huu Chi N, Kim Cuc NT, Manh Sieu TP, Shikuma CM, Farrar J, Day JN. 2010. AIDS-associated Penicillium marneffei infection of the central nervous system. Clin Infect Dis, 51 (12), pp. 1458-1462. Read abstract | Read more

Penicillium marneffei is an important human immunodeficiency virus-associated opportunistic infection endemic in Southeast Asia. Central nervous system infection has not been described. We report the first case series of 21 human immunodeficiency virus-infected patients who presented with a syndrome consistent with acute central nervous system infection and who had Penicillium marneffei isolated from cerebrospinal fluid. Hide abstract

Ha DT, Lan NT, Kiet VS, Wolbers M, Hang HT, Day J, Hien NQ, Tien NA et al. 2010. Diagnosis of pulmonary tuberculosis in HIV-positive patients by microscopic observation drug susceptibility assay. J Clin Microbiol, 48 (12), pp. 4573-4579. Read abstract | Read more

The microscopic observation drug susceptibility assay (MODS) is a novel and promising test for the early diagnosis of tuberculosis (TB). We evaluated the MODS assay for the early diagnosis of TB in HIV-positive patients presenting to Pham Ngoc Thach Hospital for Tuberculosis and Lung Diseases in southern Vietnam. A total of 738 consecutive sputum samples collected from 307 HIV-positive individuals suspected of TB were tested by smear, MODS, and the mycobacteria growth indicator tube method (MGIT). The diagnostic sensitivity and specificity of MODS compared to the microbiological gold standard (either smear or MGIT) were 87 and 93%, respectively. The sensitivities of smear, MODS, and MGIT were 57, 71, and 75%, respectively, against clinical gold standard (MODS versus smear, P<0.001; MODS versus MGIT, P=0.03). The clinical gold standard was defined as patients who had a clinical examination and treatment consistent with TB, with or without microbiological confirmation. For the diagnosis of smear-negative patients, the sensitivities of MODS and MGIT were 38 and 45%, respectively (P=0.08). The median times to detection using MODS and MGIT were 8 and 11 days, respectively, and they were 11 and 17 days, respectively, for smear-negative samples. The original bacterial/fungal contamination rate of MODS was 1.1%, while it was 2.6% for MGIT. The cross-contamination rate of MODS was 4.7%. In conclusion, MODS is a sensitive, specific, and rapid test that is appropriate for the detection of HIV-associated TB; its cost and ease of use make it particularly useful in resource-limited settings. Hide abstract

Parry CM, Thuy CT, Dongol S, Karkey A, Vinh H, Chinh NT, Duy PT, Thieu Nga TV et al. 2010. Suitable disk antimicrobial susceptibility breakpoints defining Salmonella enterica serovar Typhi isolates with reduced susceptibility to fluoroquinolones. Antimicrob Agents Chemother, 54 (12), pp. 5201-5208. Read abstract | Read more

Infections with Salmonella enterica serovar Typhi isolates that have reduced susceptibility to ofloxacin (MIC ≥ 0.25 μg/ml) or ciprofloxacin (MIC ≥ 0.125 μg/ml) have been associated with a delayed response or clinical failure following treatment with these antimicrobials. These isolates are not detected as resistant using current disk susceptibility breakpoints. We examined 816 isolates of S. Typhi from seven Asian countries. Screening for nalidixic acid resistance (MIC ≥ 16 μg/ml) identified isolates with an ofloxacin MIC of ≥0.25 μg/ml with a sensitivity of 97.3% (253/260) and specificity of 99.3% (552/556). For isolates with a ciprofloxacin MIC of ≥0.125 μg/ml, the sensitivity was 92.9% (248/267) and specificity was 98.4% (540/549). A zone of inhibition of ≤28 mm around a 5-μg ofloxacin disc detected strains with an ofloxacin MIC of ≥0.25 μg/ml with a sensitivity of 94.6% (246/260) and specificity of 94.2% (524/556). A zone of inhibition of ≤30 mm detected isolates with a ciprofloxacin MIC of ≥0.125 μg/ml with a sensitivity of 94.0% (251/267) and specificity of 94.2% (517/549). An ofloxacin MIC of ≥0.25 μg/ml and a ciprofloxacin MIC of ≥0.125 μg/ml detected 74.5% (341/460) of isolates with an identified quinolone resistance-inducing mutation and 81.5% (331/406) of the most common mutant (carrying a serine-to-phenylalanine mutation at codon 83 in the gyrA gene). Screening for nalidixic acid resistance or ciprofloxacin and ofloxacin disk inhibition zone are suitable for detecting S. Typhi isolates with reduced fluoroquinolone susceptibility. Hide abstract

Guzman MG, Jaenisch T, Gaczkowski R, Ty Hang VT, Sekaran SD, Kroeger A, Vazquez S, Ruiz D et al. 2010. Multi-country evaluation of the sensitivity and specificity of two commercially-available NS1 ELISA assays for dengue diagnosis. PLoS Negl Trop Dis, 4 (8), pp. e811-e811. Read abstract | Read more

Early diagnosis of dengue can assist patient triage and management and prevent unnecessary treatments and interventions. Commercially available assays that detect the dengue virus protein NS1 in the plasma/serum of patients offers the possibility of early and rapid diagnosis. Hide abstract

Tran TH, Nguyen TD, Nguyen TT, Ninh TT, Tran NB, Nguyen VM, Tran TT, Cao TT et al. 2010. A randomised trial evaluating the safety and immunogenicity of the novel single oral dose typhoid vaccine M01ZH09 in healthy Vietnamese children. PLoS One, 5 (7), pp. e11778. Read abstract | Read more

The emergence of drug resistant typhoid fever is a major public health problem, especially in Asia. An oral single dose typhoid vaccine would have major advantages. M01ZH09 is a live oral single dose candidate typhoid vaccine containing Salmonella enterica serovar Typhi (Ty2 aroC(-)ssaV(-)) ZH9 with two independently attenuating deletions. Studies in healthy adults demonstrated immunogenicity and an acceptable safety profile. Hide abstract

Chau TT, Mai NH, Phu NH, Nghia HD, Chuong LV, Sinh DX, Duong VA, Diep PT et al. 2010. A prospective descriptive study of cryptococcal meningitis in HIV uninfected patients in Vietnam - high prevalence of Cryptococcus neoformans var grubii in the absence of underlying disease. BMC Infect Dis, 10 (1), pp. 199. Read abstract | Read more

Most cases of cryptococcal meningitis occur in patients with HIV infection: the course and outcome of disease in the apparently immunocompetent is much more poorly understood. We describe a cohort of HIV uninfected Vietnamese patients with cryptococcal meningitis in whom underlying disease is uncommon, and relate presenting features of patients and the characteristics of the infecting species to outcome. Hide abstract

Thai KT, Cazelles B, Nguyen NV, Vo LT, Boni MF, Farrar J, Simmons CP, van Doorn HR, de Vries PJ. 2010. Dengue dynamics in Binh Thuan province, southern Vietnam: periodicity, synchronicity and climate variability. PLoS Negl Trop Dis, 4 (7), pp. e747. Read abstract | Read more

Dengue is a major global public health problem with increasing incidence and geographic spread. The epidemiology is complex with long inter-epidemic intervals and endemic with seasonal fluctuations. This study was initiated to investigate dengue transmission dynamics in Binh Thuan province, southern Vietnam. Hide abstract

Rabaa MA, Ty Hang VT, Wills B, Farrar J, Simmons CP, Holmes EC. 2010. Phylogeography of recently emerged DENV-2 in southern Viet Nam. PLoS Negl Trop Dis, 4 (7), pp. e766. Read abstract | Read more

Revealing the dispersal of dengue viruses (DENV) in time and space is central to understanding their epidemiology. However, the processes that shape DENV transmission patterns at the scale of local populations are not well understood, particularly the impact of such factors as human population movement and urbanization. Herein, we investigated trends in the spatial dynamics of DENV-2 transmission in the highly endemic setting of southern Viet Nam. Through a phylogeographic analysis of 168 full-length DENV-2 genome sequences obtained from hospitalized dengue cases from 10 provinces in southern Viet Nam, we reveal substantial genetic diversity in both urban and rural areas, with multiple lineages identified in individual provinces within a single season, and indicative of frequent viral migration among communities. Focusing on the recently introduced Asian I genotype, we observed particularly high rates of viral exchange between adjacent geographic areas, and between Ho Chi Minh City, the primary urban center of this region, and populations across southern Viet Nam. Within Ho Chi Minh City, patterns of DENV movement appear consistent with a gravity model of virus dispersal, with viruses traveling across a gradient of population density. Overall, our analysis suggests that Ho Chi Minh City may act as a source population for the dispersal of DENV across southern Viet Nam, and provides further evidence that urban areas of Southeast Asia play a primary role in DENV transmission. However, these data also indicate that more rural areas are also capable of maintaining virus populations and hence fueling DENV evolution over multiple seasons. Hide abstract

Chau TT, Campbell JI, Schultsz C, Chau NV, Diep TS, Baker S, Chinh NT, Farrar JJ, van Doorn HR. 2010. Three adult cases of Listeria monocytogenes meningitis in Vietnam. PLoS Med, 7 (7), pp. e1000306. | Read more

Kiet VS, Lan NT, An DD, Dung NH, Hoa DV, van Vinh Chau N, Chinh NT, Farrar J, Caws M. 2010. Evaluation of the MTBDRsl test for detection of second-line-drug resistance in Mycobacterium tuberculosis. J Clin Microbiol, 48 (8), pp. 2934-2939. Read abstract | Read more

The MTBDRsl assay (Hain Lifescience GmbH, Germany) is a new line probe assay for the detection of extensively drug-resistant tuberculosis (XDR TB). The test simultaneously detects resistance to ethambutol, aminoglycosides/cyclic peptides, and fluoroquinolones through detection of mutations in the relevant genes. The assay format is identical to the MTBDR Hain assay. The assay was evaluated for the detection of second-line-drug resistance in Vietnamese isolates using two sample sets from the microbiology department of Pham Ngoc Thach Hospital, Ho Chi Minh City, Viet Nam, with existing conventional phenotypic drug susceptibility results for second-line drugs: 41 consecutive fluoroquinolone-resistant isolates and 21 consecutive multidrug-resistant but fluoroquinolone-sensitive isolates. The sensitivity for detection of fluoroquinolone resistance was 75.6% (31/41) (95% confidence interval [95% CI], 59.7% to 87.6%), and for kanamycin resistance, the sensitivity was 100% (5/5) (95% CI, 47.8% to 100%). The sensitivity of the test for detection of ethambutol resistance was low, consistent with previous reports, at 64.2% (34/53) (95% CI, 49.8% to 76.9%). The specificity of the test was 100% for all three drugs. These data suggest that the MTBDRsl assay is a rapid, specific test for the detection of XDR TB but should not be used exclusively to "rule out" second-line-drug resistance. Further operational evaluation is required and should be integrated with evaluations of the MTBDR test. Hide abstract

Nguyen NT, Ha V, Tran NV, Stabler R, Pham DT, Le TM, van Doorn HR, Cerdeño-Tárraga A et al. 2010. The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. PLoS Negl Trop Dis, 4 (6), pp. e702. Read abstract | Read more

Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem. The rise of CTX-M class extended spectrum beta lactamases (ESBLs) has been well documented in industrialized countries. Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges. Hide abstract

Holt KE, Baker S, Dongol S, Basnyat B, Adhikari N, Thorson S, Pulickal AS, Song Y et al. 2010. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. BMC Infect Dis, 10 (1), pp. 144. Read abstract | Read more

Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection. Hide abstract

O'Riordan S, Hien TT, Miles K, Allen A, Quyen NN, Hung NQ, Anh DOQ, Tuyen LN et al. 2010. Large scale screening for haemoglobin disorders in southern Vietnam: implications for avoidance and management. Br J Haematol, 150 (3), pp. 359-364. Read abstract | Read more

In order to obtain an approximate assessment of the public health burden that will be posed by the inherited disorders of haemoglobin in southern Vietnam, several thousand individuals were screened for these conditions. A smaller sample was screened for glucose-6-phosphate dehydrogenase (G6PD) deficiency. The important haemoglobin disorders identified were beta thalassaemia, haemoglobin E and a variety of different forms of alpha thalassaemia. There were sufficient G6PD-deficient individuals to materially affect malaria control programme design. The most remarkable finding was wide variation in the gene frequencies of these conditions among the ethnic groups sampled. The approximate number of babies expected to be born with clinically significant haemoglobin disorders in Vietnam was estimated from the gene-frequency data. This study emphasizes the importance of wide-scale population screening, including ethnic subgroups, to establish the requirements for inherited haemoglobin disorder programmes in resource-limited settings. Hide abstract

Dung NT, Duyen HT, Thuy NT, Ngoc TV, Chau NV, Hien TT, Rowland-Jones SL, Dong T, Farrar J, Wills B, Simmons CP. 2010. Timing of CD8+ T cell responses in relation to commencement of capillary leakage in children with dengue. J Immunol, 184 (12), pp. 7281-7287. Read abstract | Read more

Immune activation is a feature of dengue hemorrhagic fever (DHF) and CD8+ T cell responses in particular have been suggested as having a role in the vasculopathy that characterizes this disease. By phenotyping CD8+ T cells (CD38+/HLA-DR+, CD38+/Ki-67+, or HLA-DR+/Ki-67+) in serial blood samples from children with dengue, we found no evidence of increased CD8+ T cell activation prior to the commencement of resolution of viremia or hemoconcentration. Investigations with MHC class I tetramers to detect NS3(133-142)-specific CD8+ T cells in two independent cohorts of children suggested the commencement of hemoconcentration and thrombocytopenia in DHF patients generally begins before the appearance of measurable frequencies of NS3(133-142)-specific CD8+ T cells. The temporal mismatch between the appearance of measurable surface activated or NS3(133-142)-specific CD8+ T cells suggests that these cells are sequestered at sites of infection, have phenotypes not detected by our approach, or that other mechanisms independent of CD8+ T cells are responsible for early triggering of capillary leakage in children with DHF. Hide abstract

Ngaosuwankul N, Noisumdaeng P, Komolsiri P, Pooruk P, Chokephaibulkit K, Chotpitayasunondh T, Sangsajja C, Chuchottaworn C, Farrar J, Puthavathana P. 2010. Influenza A viral loads in respiratory samples collected from patients infected with pandemic H1N1, seasonal H1N1 and H3N2 viruses. Virol J, 7 (1), pp. 75. Read abstract | Read more

Nasopharyngeal aspirate (NPA), nasal swab (NS), and throat swab (TS) are common specimens used for diagnosis of respiratory virus infections based on the detection of viral genomes, viral antigens and viral isolation. However, there is no documented data regarding the type of specimen that yields the best result of viral detection. In this study, quantitative real time RT-PCR specific for M gene was used to determine influenza A viral loads present in NS, NPA and TS samples collected from patients infected with the 2009 pandemic H1N1, seasonal H1N1 and H3N2 viruses. Various copy numbers of RNA transcripts derived from recombinant plasmids containing complete M gene insert of each virus strain were assayed by RT-PCR. A standard curve for viral RNA quantification was constructed by plotting each Ct value against the log quantity of each standard RNA copy number. Hide abstract

Phu NH, Tuan PQ, Day N, Mai NT, Chau TT, Chuong LV, Sinh DX, White NJ, Farrar J, Hien TT. 2010. Randomized controlled trial of artesunate or artemether in Vietnamese adults with severe falciparum malaria. Malar J, 9 (1), pp. 97. Read abstract | Read more

Both artemether and artesunate have been shown to be superior to quinine for the treatment of severe falciparum malaria in Southeast Asian adults, although the magnitude of the superiority has been greater for artesunate than artemether. These two artemisinin derivatives had not been compared in a randomized trial. Hide abstract

Horby P, Sudoyo H, Viprakasit V, Fox A, Thai PQ, Yu H, Davila S, Hibberd M et al. 2010. What is the evidence of a role for host genetics in susceptibility to influenza A/H5N1? Epidemiol Infect, 138 (11), pp. 1550-1558. Read abstract | Read more

The apparent family clustering of avian influenza A/H5N1 has led several groups to postulate the existence of a host genetic influence on susceptibility to A/H5N1, yet the role of host factors on the risk of A/H5N1 disease has received remarkably little attention compared to the efforts focused on viral factors. We examined the epidemiological patterns of human A/H5N1 cases, their possible explanations, and the plausibility of a host genetic effect on susceptibility to A/H5N1 infection. The preponderance of familial clustering of cases and the relative lack of non-familial clusters, the occurrence of related cases separated by time and place, and the paucity of cases in some highly exposed groups such as poultry cullers, are consistent with a host genetic effect. Animal models support the biological plausibility of genetic susceptibility to A/H5N1. Although the evidence is circumstantial, host genetic factors are a parsimonious explanation for the unusual epidemiology of human A/H5N1 cases and warrant further investigation. Hide abstract

Thai KT, Phuong HL, Thanh Nga TT, Giao PT, Hung LEQ, Van Nam N, Binh TQ, Simmons C et al. 2010. Clinical, epidemiological and virological features of Dengue virus infections in Vietnamese patients presenting to primary care facilities with acute undifferentiated fever. J Infect, 60 (3), pp. 229-237. Read abstract | Read more

To explore clinical and virological characteristics and describe the epidemiology of dengue in patients who presented with acute undifferentiated fever (AUF) at primary health centers (PHC) in Binh Thuan Province, Vietnam. Hide abstract

Tricou V, Minh NN, Van TP, Lee SJ, Farrar J, Wills B, Tran HT, Simmons CP. 2010. A randomized controlled trial of chloroquine for the treatment of dengue in Vietnamese adults. PLoS Negl Trop Dis, 4 (8), pp. e785. Read abstract | Read more

There is currently no licensed antiviral drug for treatment of dengue. Chloroquine (CQ) inhibits the replication of dengue virus (DENV) in vitro. Hide abstract

Thanh TT, Pawestri HA, Ngoc NM, Hien VM, Syahrial H, Trung NV, van Doorn RH, Wertheim HF et al. 2010. A real-time RT-PCR for detection of clade 1 and 2 H5N1 influenza A virus using locked nucleic acid (LNA) TaqMan probes. Virol J, 7 (1), pp. 46. Read abstract | Read more

The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants. Hide abstract

van de Beek D, Farrar JJ, de Gans J, Mai NT, Molyneux EM, Peltola H, Peto TE, Roine I et al. 2010. Adjunctive dexamethasone in bacterial meningitis: a meta-analysis of individual patient data. Lancet Neurol, 9 (3), pp. 254-263. Read abstract | Read more

Dexamethasone improves outcome for some patients with bacterial meningitis, but not others. We aimed to identify which patients are most likely to benefit from dexamethasone treatment. Hide abstract

Chau TN, Anders KL, Lien LEB, Hung NT, Hieu LT, Tuan NM, Thuy TT, Phuong LET et al. 2010. Clinical and virological features of Dengue in Vietnamese infants. PLoS Negl Trop Dis, 4 (4), pp. e657. Read abstract | Read more

Infants account for a small proportion of the overall dengue case burden in endemic countries but can be clinically more difficult to manage. The clinical and laboratory features in infants with dengue have not been extensively characterised. Hide abstract

Lang TA, White NJ, Tran HT, Farrar JJ, Day NP, Fitzpatrick R, Angus BJ, Denis E et al. 2010. Clinical research in resource-limited settings: enhancing research capacity and working together to make trials less complicated. PLoS Negl Trop Dis, 4 (6), pp. e619. | Read more

Tricou V, Vu HT, Quynh NV, Nguyen CV, Tran HT, Farrar J, Wills B, Simmons CP. 2010. Comparison of two dengue NS1 rapid tests for sensitivity, specificity and relationship to viraemia and antibody responses. BMC Infect Dis, 10 (1), pp. 142. Read abstract | Read more

Dengue is a major public health problem in tropical and subtropical countries. Rapid and easy diagnosis of dengue can assist patient triage and care-management. The detection of DENV NS1 on rapid lateral flow tests offers a fast route to a presumptive dengue diagnosis but careful evaluations are urgently needed as more and more people use them. Hide abstract

Whitehorn J, Farrar J. 2010. Dengue. Br Med Bull, 95 (1), pp. 161-173. Read abstract | Read more

Dengue is a vector-borne viral infection that endangers an estimated 2.5 billion people. Disease caused by dengue ranges from a relatively minor febrile illness to a life-threatening condition characterized by extensive capillary leak. A greater understanding of dengue has the potential to improve both the clinical management of individual cases and the control of the disease. Hide abstract

Hien TT, Boni MF, Bryant JE, Ngan TT, Wolbers M, Nguyen TD, Truong NT, Dung NT et al. 2010. Early pandemic influenza (2009 H1N1) in Ho Chi Minh City, Vietnam: a clinical virological and epidemiological analysis. PLoS Med, 7 (5), pp. e1000277. Read abstract | Read more

To date, little is known about the initial spread and response to the 2009 pandemic of novel influenza A ("2009 H1N1") in tropical countries. Here, we analyse the early progression of the epidemic from 26 May 2009 until the establishment of community transmission in the second half of July 2009 in Ho Chi Minh City (HCMC), Vietnam. In addition, we present detailed systematic viral clearance data on 292 isolated and treated patients and the first three cases of selection of resistant virus during treatment in Vietnam. Hide abstract

Yu H, Liao Q, Zhou L, Xiang N, Huai Y, Feng Z, Yuan Y, Gao Z et al. 2010. Effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A H1N1: Opportunistic retrospective study of medical charts in China BMJ (Online), 341 (7775), pp. 714-714. Read abstract | Read more

Objective: To describe the clinical features and effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A(H1N1) virus infection. Design: Opportunistic retrospective review of medical charts of patients with confirmed 2009 H1N1 identified through the national surveillance system in China from May to July 2009. Setting: Under coordination of the Ministry of Health, local health departments were asked to collect medical records of confirmed patients and send them to the Chinese Centre for Disease Control and Prevention on a voluntary basis as part of the public health response. Population: 1291 patients with confirmed 2009 H1N1 infection and available data for chart review. Main outcome measures: Demographic characteristics, comorbidities, symptoms and signs, laboratory tests, findings on chest radiography, antiviral treatment, duration of fever, and duration of viral RNA shedding. Results: The median age of 1291 patients was 20 years (interquartile range 12-26); 701 (54%) were male. The most common symptoms were fever (820, 64%), cough (864, 67%), sore throat (425, 33%), sputum (239, 19%), and rhinorrhoea (228, 18%). Of 920 patients who underwent chest radiography, 110 (12%) had abnormal findings consistent with pneumonia. Some 983 (76%) patients were treated with oseltamivir from a median of the third day of symptoms (2-4). No patients required admission to the intensive care unit or mechanical ventilation. 2009 H1N1 was shed from one day before onset of symptoms to up to eight days after onset in most (91%) patients, with a median of 5 (3-6) days of shedding after onset. Treatment with oseltamivir significantly protected against subsequent development of radiographically confirmed pneumonia (odds ratio 0.12, 95% confidence interval 0.08 to 0.18), and treatment started within two days of symptom onset reduced the duration of fever and viral RNA shedding. Conclusions: Chinese patients with 2009 H1N1 infection predominantly presented with features of uncomplicated, self limiting acute respiratory illness. 2009 H1N1 might be shed longer than seasonal influenza virus. Treatment with oseltamivir was associated with a significantly reduced development of radiographically confirmed pneumonia and a shorter duration of fever and viral RNA shedding. Though these patients benefited from treatment, the findings should be interpreted with caution as the study was retrospective and not all patients underwent chest radiography. Hide abstract

Vu TT, Holmes EC, Duong V, Nguyen TQ, Tran TH, Quail M, Churcher C, Parkhill J et al. 2010. Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia. PLoS Negl Trop Dis, 4 (7), pp. e757. Read abstract | Read more

A better description of the extent and structure of genetic diversity in dengue virus (DENV) in endemic settings is central to its eventual control. To this end we determined the complete coding region sequence of 187 DENV-2 genomes and 68 E genes from viruses sampled from Vietnamese patients between 1995 and 2009. Strikingly, an episode of genotype replacement was observed, with Asian 1 lineage viruses entirely displacing the previously dominant Asian/American lineage viruses. This genotype replacement event also seems to have occurred within DENV-2 in Thailand and Cambodia, suggestive of a major difference in viral fitness. To determine the cause of this major evolutionary event we compared both the infectivity of the Asian 1 and Asian/American genotypes in mosquitoes and their viraemia levels in humans. Although there was little difference in infectivity in mosquitoes, we observed significantly higher plasma viraemia levels in paediatric patients infected with Asian 1 lineage viruses relative to Asian/American viruses, a phenotype that is predicted to result in a higher probability of human-to-mosquito transmission. These results provide a mechanistic basis to a marked change in the genetic structure of DENV-2 and more broadly underscore that an understanding of DENV evolutionary dynamics can inform the development of vaccines and anti-viral drugs. Hide abstract

Fox A, Horby P, Ha NH, Hoa LENM, Lam NT, Simmons C, Farrar J, Van Kinh N, Wertheim H. 2010. Influenza A H5N1 and HIV co-infection: case report. BMC Infect Dis, 10 (1), pp. 167. Read abstract | Read more

The role of adaptive immunity in severe influenza is poorly understood. The occurrence of influenza A/H5N1 in a patient with HIV provided a rare opportunity to investigate this. Hide abstract

Buchy P, Vong S, Chu S, Garcia JM, Hien TT, Hien VM, Channa M, Ha DOQ et al. 2010. Kinetics of neutralizing antibodies in patients naturally infected by H5N1 virus. PLoS One, 5 (5), pp. e10864. Read abstract | Read more

Little is known about the kinetics of anti-H5 neutralizing antibodies in naturally H5N1-infected patients with severe clinical illness or asymptomatic infection. Hide abstract

Wertheim HF, Puthavathana P, Nghiem NM, van Doorn HR, Nguyen TV, Pham HV, Subekti D, Harun S et al. 2010. Laboratory capacity building in Asia for infectious disease research: experiences from the South East Asia Infectious Disease Clinical Research Network (SEAICRN). PLoS Med, 7 (4), pp. e1000231. Read abstract | Read more

Enhancing laboratory capacity is essential for generating reliable and accurate data from clinical research, especially in resource-constrained settings. Local well-trained laboratory experts and scientists are important to research, and must participate actively in scientific activities and continuing education programs. Improving laboratory capacity is more than supplying new equipment and reagents; it also includes a long-term commitment to staff training, quality control, and biosafety. Improved laboratory capacity optimizes responses to an epidemic or an outbreak of a novel virulent pathogens, and can support international agendas to reduce the impact of pandemic influenza viruses. © 2010 Wertheim et al. Hide abstract

Flohr C, Tuyen LN, Quinnell RJ, Lewis S, Minh TT, Campbell J, Simmons C, Telford G et al. 2010. Reduced helminth burden increases allergen skin sensitization but not clinical allergy: a randomized, double-blind, placebo-controlled trial in Vietnam. Clin Exp Allergy, 40 (1), pp. 131-142. Read abstract | Read more

Observational evidence suggests that infection with helminths protects against allergic disease and allergen skin sensitization. It is postulated that such effects are mediated by helminth-induced cytokine responses, in particular IL-10. Hide abstract

Horby P, Wertheim H, Ha NH, Trung NV, Trinh DT, Taylor W, Ha NM, Lien TT, Farrar J, Van Kinh N. 2010. Stimulating the development of national Streptococcus suis guidelines in Viet Nam through a strategic research partnership. Bull World Health Organ, 88 (6), pp. 458-461. Read abstract | Read more

Streptococcus suis is a common cause of adult bacterial meningitis in Viet Nam, and possibly other parts of Asia, yet this disabling infection has been largely neglected. Prevention, diagnosis and treatment are relatively straightforward and affordable but, in early 2007, no national diagnostic, case management or prevention guidelines existed in Viet Nam. Hide abstract

Karkey A, Arjyal A, Anders KL, Boni MF, Dongol S, Koirala S, My PV, Nga TV et al. 2010. The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu. PLoS One, 5 (11), pp. e13988. Read abstract | Read more

Enteric fever, caused by Salmonella enterica serovars Typhi and Paratyphi A (S. Typhi and S. Paratyphi A) remains a major public health problem in many settings. The disease is limited to locations with poor sanitation which facilitates the transmission of the infecting organisms. Efficacious and inexpensive vaccines are available for S. Typhi, yet are not commonly deployed to control the disease. Lack of vaccination is due partly to uncertainty of the disease burden arising from a paucity of epidemiological information in key locations. We have collected and analyzed data from 3,898 cases of blood culture-confirmed enteric fever from Patan Hospital in Lalitpur Sub-Metropolitan City (LSMC), between June 2005 and May 2009. Demographic data was available for a subset of these patients (n = 527) that were resident in LSMC and who were enrolled in trials. We show a considerable burden of enteric fever caused by S. Typhi (2,672; 68.5%) and S. Paratyphi A (1,226; 31.5%) at this Hospital over a four year period, which correlate with seasonal fluctuations in rainfall. We found that local population density was not related to incidence and we identified a focus of infections in the east of LSMC. With data from patients resident in LSMC we found that the median age of those with S. Typhi (16 years) was significantly less than S. Paratyphi A (20 years) and that males aged 15 to 25 were disproportionately infected. Our findings provide a snapshot into the epidemiological patterns of enteric fever in Kathmandu. The uneven distribution of enteric fever patients within the population suggests local variation in risk factors, such as contaminated drinking water. These findings are important for initiating a vaccination scheme and improvements in sanitation. We suggest any such intervention should be implemented throughout the LSMC area. Hide abstract

Nga TV, Karkey A, Dongol S, Thuy HN, Dunstan S, Holt K, Tu LETP, Campbell JI et al. 2010. The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens. BMC Infect Dis, 10 (1), pp. 125. Read abstract | Read more

PCR amplification for the detection of pathogens in biological material is generally considered a rapid and informative diagnostic technique. Invasive Salmonella serovars, which cause enteric fever, can be commonly cultured from the blood of infected patients. Yet, the isolation of invasive Salmonella serovars from blood is protracted and potentially insensitive. Hide abstract

Le VT, Phan TQ, Do QH, Nguyen BH, Lam QB, Bach V, Truong H, Tran TH et al. 2010. Viral etiology of encephalitis in children in southern Vietnam: results of a one-year prospective descriptive study. PLoS Negl Trop Dis, 4 (10), pp. e854. Read abstract | Read more

Acute encephalitis is an important and severe disease in children in Vietnam. However, little is known about the etiology while such knowledge is essential for optimal prevention and treatment. To identify viral causes of encephalitis, in 2004 we conducted a one-year descriptive study at Children's Hospital Number One, a referral hospital for children in southern Vietnam including Ho Chi Minh City. Hide abstract

Ha DT, Lan NT, Wolbers M, Duong TN, Quang ND, Thi Van Thinh T, Thi Hong Ngoc L, Thi Ngoc Anh N et al. 2009. Microscopic observation drug susceptibility assay (MODS) for early diagnosis of tuberculosis in children. PLoS One, 4 (12), pp. e8341. Read abstract | Read more

MODS is a novel liquid culture based technique that has been shown to be effective and rapid for early diagnosis of tuberculosis (TB). We evaluated the MODS assay for diagnosis of TB in children in Viet Nam. 217 consecutive samples including sputum (n = 132), gastric fluid (n = 50), CSF (n = 32) and pleural fluid (n = 3) collected from 96 children with suspected TB, were tested by smear, MODS and MGIT. When test results were aggregated by patient, the sensitivity and specificity of smear, MGIT and MODS against "clinical diagnosis" (confirmed and probable groups) as the gold standard were 28.2% and 100%, 42.3% and 100%, 39.7% and 94.4%, respectively. The sensitivity of MGIT and MODS was not significantly different in this analysis (P = 0.5), but MGIT was more sensitive than MODS when analysed on the sample level using a marginal model (P = 0.03). The median time to detection of MODS and MGIT were 8 days and 13 days, respectively, and the time to detection was significantly shorter for MODS in samples where both tests were positive (P<0.001). An analysis of time-dependent sensitivity showed that the detection rates were significantly higher for MODS than for MGIT by day 7 or day 14 (P<0.001 and P = 0.04), respectively. MODS is a rapid and sensitive alternative method for the isolation of M.tuberculosis from children. Hide abstract

Vinh H, Nhu NT, Nga TV, Duy PT, Campbell JI, Hoang NV, Boni MF, My PV et al. 2009. A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation. BMC Infect Dis, 9 (1), pp. 204. Read abstract | Read more

Shigellosis remains considerable public health problem in some developing countries. The nature of Shigellae suggests that they are highly adaptable when placed under selective pressure in a human population. This is demonstrated by variation and fluctuations in serotypes and antimicrobial resistance profile of organisms circulating in differing setting in endemic locations. Antimicrobial resistance in the genus Shigella is a constant threat, with reports of organisms in Asia being resistant to multiple antimicrobials and new generation therapies. Hide abstract

Chau TN, Hieu NT, Anders KL, Wolbers M, Lien LEB, Hieu LT, Hien TT, Hung NT, Farrar J, Whitehead S, Simmons CP. 2009. Dengue virus infections and maternal antibody decay in a prospective birth cohort study of Vietnamese infants. J Infect Dis, 200 (12), pp. 1893-1900. Read abstract | Read more

Dengue hemorrhagic fever can occur in primary dengue virus (DENV) infection of infants. The decay of maternally derived DENV immunoglobulin (Ig) G and the incidence of DENV infection were determined in a prospectively studied cohort of 1244 Vietnamese infants. Higher concentrations of total IgG and DENV-reactive IgG were found in cord plasma relative to maternal plasma. Maternally derived DENV-neutralizing and E protein-reactive IgG titers declined to below measurable levels in >90% of infants by 6 months of age. In contrast, IgG reactive with whole DENV virions persisted until 12 months of age in 20% of infants. Serological surveillance identified 10 infants with asymptomatic DENV infection for an incidence of 1.7 cases per 100 person-years. DENV-neutralizing antibodies remained measurable for > or = 1 year after infection. These results suggest that whereas DENV infection in infants is frequently subclinical, there is a window between 4 and 12 months of age where virion-binding but nonneutralizing IgG could facilitate antibody-dependent enhancement. Hide abstract

Thompson LJ, Dunstan SJ, Dolecek C, Perkins T, House D, Dougan G, Nguyen TH, Tran TP et al. 2009. Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi. Proc Natl Acad Sci U S A, 106 (52), pp. 22433-22438. Read abstract | Read more

We used microarrays and transcriptional profiling of peripheral blood to investigate the host response of 29 individuals who contracted typhoid fever in the Mekong Delta region of Vietnam. Samples were taken over a nine month period encompassing acute disease, convalescence, and recovery. We found that typhoid fever induced a distinct and highly reproducible signature in the peripheral blood that changed during treatment and convalescence, returning in the majority of cases to the "normal" profile as measured in healthy uninfected controls. Unexpectedly, there was a strong, distinct signature of convalescence present at day 9 after infection that remained virtually unchanged one month after acute infection and in some cases persisted as long as nine months despite a complete clinical recovery in all patients. Patients who retain the convalescent signature may be genetically or temporarily incapable of developing an effective immune response and may be more susceptible to reinfection, relapse, or the establishment of a carrier state. Hide abstract

Dung NM, Turtle L, Chong WK, Mai NT, Thao TT, Thuy TT, Kneen R, Phu NH et al. 2009. An evaluation of the usefulness of neuroimaging for the diagnosis of Japanese encephalitis. J Neurol, 256 (12), pp. 2052-2060. Read abstract | Read more

Japanese encephalitis virus (JEV) is estimated to cause 30–50,000 cases of encephalitis every year. The disease occurs mainly in rural Asia and is transmitted to humans from birds and pigs by mosquitoes of the genus Culex. JE is diagnosed with antibody testing of the serum and CSF, but this is not available in many hospitals. Neuroimaging abnormalities, particularly thalamic hypodensity on computed tomography (CT) and hyperintensity on T2 weighted magnetic resonance imaging (MRI) have been described in case studies, but their usefulness for diagnosing JE is not known. We have therefore evaluated the usefulness of neuroimaging (CT and MRI) for the diagnosis of JE. The findings of thalamic lesions were compared with the final serological diagnosis in a cohort of 75 patients (children and adults) with suspected CNS infections in Southern Vietnam, a JEV endemic area. Thalamic lesions on CT and/or MRI combined had sensitivity 23% (95% confidence interval 12.9–33.1%), specificity 100%, positive predictive value 100% and negative predictive value 42.1% (95% confidence interval 30.2–53.8%) for a diagnosis of JE in this cohort. Over time, the thalamic lesions resolved in some patients. One patient showed disappearance of lesions on CT followed by reappearance of the lesions some time later, known as the fogging effect. In this setting, the presence of thalamic abnormalities suggested the diagnosis of JE, but their absence did not exclude it. Hide abstract

Le TM, Baker S, Le TP, Le TP, Cao TT, Tran TT, Nguyen VM, Campbell JI et al. 2009. High prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the Enterobacteriaceae in Ho Chi Minh City, Vietnam. J Med Microbiol, 58 (Pt 12), pp. 1585-1592. Read abstract | Read more

Antimicrobial-resistant pathogenic members of the Enterobacteriaceae are a well-defined global problem. We hypothesized that one of the main reservoirs of dissemination of antimicrobial resistance genes in Vietnam is non-pathogenic intestinal flora, and sought to isolate antimicrobial-resistant organisms from hospitalized patients and non-hospitalized healthy individuals in Ho Chi Minh City. The results identified substantial faecal carriage of gentamicin-, ceftazidime- and nalidixic acid-resistant members of the Enterobacteriaceae in both hospitalized patients and non-hospitalized healthy individuals. A high prevalence of quinolone resistance determinants was identified, particularly the qnrS gene, in both community- and hospital-associated strains. Furthermore, the results demonstrated that a combination of quinolone resistance determinants can confer resistance to nalidixic acid and ciprofloxacin, even in the apparent absence of additional chromosomal resistance mutations in wild-type strains and laboratory strains with transferred plasmids. These data suggest that intestinal commensal organisms are a significant reservoir for the dissemination of plasmid-mediated quinolone resistance in Ho Chi Minh City. Hide abstract

Duong DA, Nguyen TH, Nguyen TN, Dai VH, Dang TM, Vo SK, Do DA, Nguyen VV et al. 2009. Beijing genotype of Mycobacterium tuberculosis is significantly associated with high-level fluoroquinolone resistance in Vietnam. Antimicrob Agents Chemother, 53 (11), pp. 4835-4839. Read abstract | Read more

Consecutive fluoroquinolone (FQ)-resistant isolates (n = 109) identified at the Pham Ngoc Thach Hospital for Tuberculosis, Ho Chi Minh City, Vietnam, were sequenced in the quinolone resistance-determining regions of the gyrA and gyrB genes and typed by large sequence polymorphism typing and spoligotyping to identify the Beijing genotype of Mycobacterium tuberculosis. Beijing genotype prevalence was compared with 109 consecutive isolates from newly presenting patients with pulmonary tuberculosis from the hospital outpatient department. Overall, 82.6% (n = 90/109) of isolates had mutations in gyrAB. Nine novel mutations were identified in gyrB (S486F, N538T, T539P, D500A, D500H, D500N, G509A, E540V, and E540D). The influence of these novel gyrB mutations on FQ resistance is not proven. The Beijing genotype was significantly associated with FQ resistance (odds ratio [OR], 2.39 [95% confidence interval {CI}, 1.34 to 4.25]; P = 0.003). Furthermore, Beijing genotype FQ-resistant isolates were significantly more likely than FQ-resistant isolates of other genotypes to have gyrA mutations (OR, 7.75 [95% CI, 2.84 to 21.15]; P = 0.0001) and high-level (>8 microg/ml) FQ resistance (OR, 11.0 [95% CI, 2.6 to 47.0]; P = 0.001). The underlying mechanism of the association of the Beijing genotype with high-level FQ resistance in this setting remains to be determined. The association of the Beijing genotype with relatively high-level FQ resistance conferred by specific gyrA mutations reported here is of grave concern given the epidemic spread of the Beijing genotype and the current hopes for shorter first-line treatment regimens based on FQs. Hide abstract

Mai NT, Tuan TV, Wolbers M, Hoang DM, Nga TV, Chau TT, Chuong LV, Sinh DX et al. 2009. Immunological and biochemical correlates of adjunctive dexamethasone in Vietnamese adults with bacterial meningitis. Clin Infect Dis, 49 (9), pp. 1387-1392. Read abstract | Read more

Adjunctive treatment to improve outcome from bacterial meningitis has centered on dexamethasone. Among Vietnamese patients with bacterial meningitis, cerebrospinal fluid (CSF) opening pressure and CSF:plasma glucose ratios were significantly improved and levels of CSF cytokines interleukin (IL)-6, IL-8, and IL-10 and were all statistically significantly lower after treatment in patients who were randomized to dexamethasone, compared with levels in patients who received placebo. Hide abstract

Webster DP, Farrar J, Rowland-Jones S. 2009. Progress towards a dengue vaccine. Lancet Infect Dis, 9 (11), pp. 678-687. Read abstract | Read more

The spread of dengue virus throughout the tropics represents a major, rapidly growing public health problem with an estimated 2.5 billion people at risk of dengue fever and the life-threatening disease, severe dengue. A safe and effective vaccine for dengue is urgently needed. The pathogenesis of severe dengue results from a complex interaction between the virus, the host, and, at least in part, immune-mediated mechanisms. Vaccine development has been slowed by fears that immunisation might predispose individuals to the severe form of dengue infection. A pipeline of candidate vaccines now exists, including live attenuated, inactivated, chimeric, DNA, and viral-vector vaccines, some of which are at the stage of clinical testing. In this Review, we present what is understood about dengue pathogenesis and its implications for vaccine design, the progress that is being made in the development of a vaccine, and the future challenges. Hide abstract

Chen H, Wang Y, Liu W, Zhang J, Dong B, Fan X, de Jong MD, Farrar J, Riley S, Smith GJ, Guan Y. 2009. Serologic survey of pandemic (H1N1) 2009 virus, Guangxi Province, China. Emerg Infect Dis, 15 (11), pp. 1849-1850. | Read more

Wills B, Tran VN, Nguyen TH, Truong TT, Tran TN, Nguyen MD, Tran VD, Nguyen VV, Dinh TT, Farrar J. 2009. Hemostatic changes in Vietnamese children with mild dengue correlate with the severity of vascular leakage rather than bleeding. Am J Trop Med Hyg, 81 (4), pp. 638-644. Read abstract | Read more

The mechanisms underlying the bleeding manifestations and coagulopathy associated with dengue remain unclear, in part because of the focus of much previous work on severe disease without an appropriate comparison group. We describe detailed clinical and laboratory profiles for a large group of children with dengue of all severities, and a group with similar non-dengue febrile illnesses, all followed prospectively from early presentation through to recovery. Among the dengue-infected patients but not the controls, thrombocytopenia, increased partial thromboplastin times and reduced fibrinogen concentrations were apparent from an early stage, and these abnormalities correlated strongly with the severity and timing of vascular leakage but not bleeding. There was little evidence of procoagulant activation. The findings do not support a primary diagnosis of disseminated intravascular coagulation to explain the intrinsic coagulopathy. An alternative biologically plausible hypothesis is discussed. Hide abstract

Wertheim HFL, Farrar J, Horby P. 2009. Medicine and the Media Online video sharing and patients' privacy BRITISH MEDICAL JOURNAL, 339 (sep30 2), pp. b3991-b3991. | Read more

Bertozzi S, Kelso A, Tashiro M, Savy V, Farrar J, Osterholm M, Jameel S, Muller CP. 2009. Pandemic flu: from the front lines. Interviewed by Declan Butler. Nature, 461 (7260), pp. 20-21. | Read more

Simmons CP, Farrar J. 2009. Changing patterns of dengue epidemiology and implications for clinical management and vaccines. PLoS Med, 6 (9), pp. e1000129. | Read more

Jaenisch T, Wills B, Alexander N, Arana B, Balmaseda A, Jr SJB, Castelobranco I, Dimaano E et al. 2009. Evidence for a revised dengue classification: a multi-centre prospective study across Southeast Asia and Latin America TROPICAL MEDICINE & INTERNATIONAL HEALTH, 14 pp. 39-40.

Recker M, Blyuss KB, Simmons CP, Hien TT, Wills B, Farrar J, Gupta S. 2009. Immunological serotype interactions and their effect on the epidemiological pattern of dengue. Proc Biol Sci, 276 (1667), pp. 2541-2548. Read abstract | Read more

Long-term epidemiological data reveal multi-annual fluctuations in the incidence of dengue fever and dengue haemorrhagic fever, as well as complex cyclical behaviour in the dynamics of the four serotypes of the dengue virus. It has previously been proposed that these patterns are due to the phenomenon of the so-called antibody-dependent enhancement (ADE) among dengue serotypes, whereby viral replication is increased during secondary infection with a heterologous serotype; however, recent studies have implied that this positive reinforcement cannot account for the temporal patterns of dengue and that some form of cross-immunity or external forcing is necessary. Here, we show that ADE alone can produce the observed periodicities and desynchronized oscillations of individual serotypes if its effects are decomposed into its two possible manifestations: enhancement of susceptibility to secondary infections and increased transmissibility from individuals suffering from secondary infections. This decomposition not only lowers the level of enhancement necessary for realistic disease patterns but also reduces the risk of stochastic extinction. Furthermore, our analyses reveal a time-lagged correlation between serotype dynamics and disease incidence rates, which could have important implications for understanding the irregular pattern of dengue epidemics. Hide abstract

Tran TH, Ruiz-Palacios GM, Hayden FG, Farrar J. 2009. Patient-oriented pandemic influenza research. Lancet, 373 (9681), pp. 2085-2086. | Read more

Liem NT, Tung CV, Hien ND, Hien TT, Chau NQ, Long HT, Hien NT, Mai LEQ et al. 2009. Clinical features of human influenza A (H5N1) infection in Vietnam: 2004-2006. Clin Infect Dis, 48 (12), pp. 1639-1646. Read abstract | Read more

The first cases of avian influenza A (H5N1) in humans in Vietnam were detected in early 2004, and Vietnam has reported the second highest number of cases globally. Hide abstract

Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA et al. 2009. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet, 41 (6), pp. 657-665. Read abstract | Read more

We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations. Hide abstract

Campbell JI, Lam TM, Huynh TL, To SD, Tran TT, Nguyen VM, Le TS, Nguyen VV et al. 2009. Microbiologic characterization and antimicrobial susceptibility of Clostridium tetani isolated from wounds of patients with clinically diagnosed tetanus. Am J Trop Med Hyg, 80 (5), pp. 827-831. Read abstract

Clostridium tetani is the etiologic agent of the muscle-spasming disease tetanus. Despite an effective vaccine, tetanus is an ongoing problem in some developing countries. Diagnosis by bacterial culture is not done because it is generally unnecessary and the entry of route of the bacteria can be inapparent. We attempted to isolate and evaluate C. tetani from the wounds of 84 patients with tetanus. We effectively isolated C. tetani from 45 patients. All strains tested positive by polymerase chain reaction for the gene encoding tetanus neurotoxin. Antimicrobial susceptibilities were determined by disc diffusion and E-test. All C. tetani isolates were susceptible to penicillin and metronidazole but resistant to co-trimoxazole. Despite treatment with high doses of penicillin, C. tetani was isolated after 16 days of intravenous penicillin in two cases. These data show that the intravenous route for penicillin may be inadequate for clearing the infection and emphasizes wound debridement in the treatment of tetanus. Hide abstract

Khatri NS, Maskey P, Poudel S, Jaiswal VK, Karkey A, Koirala S, Shakya N, Agrawal K et al. 2009. Gallbladder carriage of Salmonella paratyphi A may be an important factor in the increasing incidence of this infection in South Asia. Ann Intern Med, 150 (8), pp. 567-568. | Read more

Lindegardh N, Tarning J, Toi PV, Hien TT, Farrar J, Singhasivanon P, White NJ, Ashton M, Day NP. 2009. Quantification of artemisinin in human plasma using liquid chromatography coupled to tandem mass spectrometry. J Pharm Biomed Anal, 49 (3), pp. 768-773. Read abstract | Read more

A liquid chromatographic tandem mass spectroscopy method for the quantification of artemisinin in human heparinised plasma has been developed and validated. The method uses Oasis HLB mu-elution solid phase extraction 96-well plates to facilitate a high throughput of 192 samples a day. Artesunate (internal standard) in a plasma-water solution was added to plasma (50 microL) before solid phase extraction. Artemisinin and its internal standard artesunate were analysed by liquid chromatography and MS/MS detection on a Hypersil Gold C18 (100 mm x 2.1 mm, 5 microm) column using a mobile phase containing acetonitrile-ammonium acetate 10mM pH 3.5 (50:50, v/v) at a flow rate of 0.5 mL/min. The method has been validated according to published FDA guidelines and showed excellent performance. The within-day, between-day and total precisions expressed as R.S.D., were lower than 8% at all tested quality control levels including the upper and lower limit of quantification. The limit of detection was 0.257 ng/mL for artemisinin and the calibration range was 1.03-762 ng/mL using 50 microL plasma. The method was free from matrix effects as demonstrated both graphically and quantitatively. Hide abstract

Wertheim HF, Nguyen TQ, Nguyen KA, de Jong MD, Taylor WR, Le TV, Nguyen HH, Nguyen HT, Farrar J, Horby P, Nguyen HD. 2009. Furious rabies after an atypical exposure. PLoS Med, 6 (3), pp. e44. | Read more

Long HT, Hibberd ML, Hien TT, Dung NM, Van Ngoc T, Farrar J, Wills B, Simmons CP. 2009. Patterns of gene transcript abundance in the blood of children with severe or uncomplicated dengue highlight differences in disease evolution and host response to dengue virus infection. J Infect Dis, 199 (4), pp. 537-546. Read abstract | Read more

DNA microarrays and specific reverse-transcription polymerase chain reaction assays were used to reveal transcriptional patterns in the blood of children presenting with dengue shock syndrome (DSS) and well-matched patients with uncomplicated dengue. The transcriptome of patients with acute uncomplicated dengue was characterized by a metabolically demanding "host-defense" profile; transcripts related to oxidative metabolism, interferon signaling, protein ubiquination, apoptosis, and cytokines were prominent. In contrast, the transcriptome of patients with DSS was surprisingly benign, particularly with regard to transcripts derived from apoptotic and type I interferon pathways. These data highlight significant heterogeneity in the type or timing of host transcriptional immune responses precipitated by dengue virus infection independent of the duration of illness. In particular, they suggest that, if transcriptional events in the blood compartment contribute to capillary leakage leading to hypovolemic shock, they occur before cardiovascular decompensation, a finding that has implications for rational adjuvant therapy in this syndrome. Hide abstract

Vinh H, Baker S, Campbell J, Hoang NV, Loan HT, Chinh MT, Anh VT, Diep TS, Phuong LET, Schultsz C, Farrar J. 2009. Rapid emergence of third generation cephalosporin resistant Shigella spp. in Southern Vietnam. J Med Microbiol, 58 (Pt 2), pp. 281-283. | Read more

Farrar J. 2009. Jeremy Farrar: When disaster strikes. Interview by Amy Maxmen. J Exp Med, 206 (1), pp. 4-5. Read abstract | Read more

Jeremy Farrar had not intended to be at the forefront of avian influenza research. But as the director of the Oxford University Clinical Research Unit in Ho Chi Minh City, the bird flu outbreak found him. Hide abstract

Green JA, Tran CT, Farrar JJ, Nguyen MT, Nguyen PH, Dinh SX, Ho ND, Ly CV, Tran HT, Friedland JS, Thwaites GE. 2009. Dexamethasone, cerebrospinal fluid matrix metalloproteinase concentrations and clinical outcomes in tuberculous meningitis. PLoS One, 4 (9), pp. e7277. Read abstract | Read more

Adjunctive dexamethasone reduces mortality from tuberculous meningitis, but how it produces this effect is not known. Matrix metalloproteinases (MMPs) are important in the immunopathology of many inflammatory CNS diseases thus we hypothesized that that their secretion is important in TBM and might be influenced by dexamethasone. Hide abstract

Hang VT, Nguyet NM, Trung DT, Tricou V, Yoksan S, Dung NM, Van Ngoc T, Hien TT, Farrar J, Wills B, Simmons CP. 2009. Diagnostic accuracy of NS1 ELISA and lateral flow rapid tests for dengue sensitivity, specificity and relationship to viraemia and antibody responses. PLoS Negl Trop Dis, 3 (1), pp. e360. Read abstract | Read more

Dengue is a public health problem in many countries. Rapid diagnosis of dengue can assist patient triage and management. Detection of the dengue viral protein, NS1, represents a new approach to dengue diagnosis. Hide abstract

Hue NT, Charlieu JP, Chau TT, Day N, Farrar JJ, Hien TT, Dunstan SJ. 2009. Glucose-6-phosphate dehydrogenase (G6PD) mutations and haemoglobinuria syndrome in the Vietnamese population. Malar J, 8 (1), pp. 152. Read abstract | Read more

In Vietnam the blackwater fever syndrome (BWF) has been associated with malaria infection, quinine ingestion and G6PD deficiency. The G6PD variants within the Vietnamese Kinh contributing to the disease risk in this population, and more generally to haemoglobinuria, are currently unknown. Hide abstract

Pulickal AS, Gautam S, Clutterbuck EA, Thorson S, Basynat B, Adhikari N, Makepeace K, Rijpkema S, Borrow R, Farrar JJ, Pollard AJ. 2009. Kinetics of the natural, humoral immune response to Salmonella enterica serovar Typhi in Kathmandu, Nepal. Clin Vaccine Immunol, 16 (10), pp. 1413-1419. Read abstract | Read more

Typhoid fever is a major public health problem in developing countries, conservatively estimated to occur in 17 million cases and be responsible for 200,000 deaths annually. We investigated the acquisition of natural immunity to Salmonella enterica serovar Typhi in a region where typhoid is endemic by testing sera from an age-stratified sample of 210 healthy participants in Kathmandu, Nepal, for bactericidal activity toward S. Typhi and for anti-Vi capsular polysaccharide antibodies. Bactericidal titers in children were significantly lower than those in newborns and adults (P < 0.0001). Anti-S. Typhi bactericidal geometric mean titers were age dependent, increasing 10-fold during childhood. Anti-Vi polysaccharide antibody geometric mean concentrations were also lower in children than in adults. Data presented here indicate the possibility of a relationship between low levels of bactericidal activity toward S. Typhi in serum and susceptibility to disease, as observed for other polysaccharide-encapsulated bacteria. Bactericidal antibody may be a marker of protective immunity against S. Typhi. Hide abstract

Boni MF, Manh BH, Thai PQ, Farrar J, Hien TT, Hien NT, Van Kinh N, Horby P. 2009. Modelling the progression of pandemic influenza A (H1N1) in Vietnam and the opportunities for reassortment with other influenza viruses. BMC Med, 7 (1), pp. 43. Read abstract | Read more

A novel variant of influenza A (H1N1) is causing a pandemic and, although the illness is usually mild, there are concerns that its virulence could change through reassortment with other influenza viruses. This is of greater concern in parts of Southeast Asia, where the population density is high, influenza is less seasonal, human-animal contact is common and avian influenza is still endemic. Hide abstract

Wertheim HF, Farrar J, Horby P. 2009. Online video sharing and patients' privacy. BMJ, 339 pp. b3991. | Read more

Schultsz C, Nguyen VD, Hai LET, Do QH, Peiris JS, Lim W, Garcia JM, Nguyen DT et al. 2009. Prevalence of antibodies against avian influenza A (H5N1) virus among Cullers and poultry workers in Ho Chi Minh City, 2005. PLoS One, 4 (11), pp. e7948. Read abstract | Read more

Between 2003 and 2005, highly pathogenic avian influenza A (H5N1) viruses caused large scale outbreaks in poultry in the Ho Chi Minh City area in Vietnam. We studied the prevalence of antibodies against H5N1 in poultry workers and cullers who were active in the program in Ho Chi Minh City in 2004 and 2005. Hide abstract

Wertheim HF, Nguyen HN, Taylor W, Lien TT, Ngo HT, Nguyen TQ, Nguyen BN, Nguyen HH et al. 2009. Streptococcus suis, an important cause of adult bacterial meningitis in northern Vietnam. PLoS One, 4 (6), pp. e5973. Read abstract | Read more

Streptococcus suis can cause severe systemic infection in adults exposed to infected pigs or after consumption of undercooked pig products. S. suis is often misdiagnosed, due to lack of awareness and improper testing. Here we report the first fifty cases diagnosed with S. suis infection in northern Viet Nam. Hide abstract

Nguyen TH, Mai NL, Le TP, Ha V, Nguyen TC, Tran TH, Nguyen TH, Farrar JJ, Dunstan SJ. 2009. Toll-like receptor 4 (TLR4) and typhoid fever in Vietnam. PLoS One, 4 (3), pp. e4800. Read abstract | Read more

Understanding the host genetic susceptibility to typhoid fever may provide a better understanding of pathogenesis and help in the development of new therapeutics and vaccines. Here we determine the genetic variation within the human TLR4 gene encoding the principal receptor for bacterial endotoxin recognition in typhoid fever patients. It is possible that genetic variants of TLR4 could detrimentally affect the innate immune response against S. typhi infection. Mutation detection and genotyping of TLR4 was performed on DNA from 414 Vietnamese typhoid fever patients and 372 population controls. dHPLC detected a total of 10 polymorphisms within the upstream and exonic regions of TLR4, of which 7 are novel. Two SNPs, T4025A and C4215G, were more frequent in typhoid cases than in controls however due to their low allele frequencies they showed borderline significance (T4025A: OR 1.9, 95%CI 0.9-4.3, P 0.07 and C4215G: OR 6.7, 95%CI 0.8-307, P 0.04). Six missense mutations were identified, with 5/6 positioned in the ectoplasmic domain. Four missense mutations and one promoter SNP (A-271G) were only present in typhoid cases, albeit at low allele frequencies. Here we determined the extent of genetic variation within TLR4 in a Vietnamese population and suggest that TLR4 may be involved in defense against typhoid fever in this population. Hide abstract

Bethell D, Farrar J, Hien TT. 2009. Diphtheria pp. 436-440. | Read more

Lindegardh N, Hanpithakpong W, Phakdeeraj A, Singhasivanon P, Farrar J, Hien TT, White NJ, Day NP. 2008. Development and validation of a high-throughput zwitterionic hydrophilic interaction liquid chromatography solid-phase extraction-liquid chromatography-tandem mass spectrometry method for determination of the anti-influenza drug peramivir in plasma. J Chromatogr A, 1215 (1-2), pp. 145-151. Read abstract | Read more

An assay for the analysis for the quantification of the anti-influenza drug peramivir in human plasma using high-throughput zwitterionic (ZIC) hydrophilic interaction liquid chromatography (HILIC) solid-phase extraction (SPE) in a 96-wellplate format and liquid chromatography coupled to positive tandem mass spectroscopy has been developed and validated. The ZIC-HILIC SPE efficiently removed sources of interference present in the supernatant after protein precipitation of plasma proteins. The main advantage of the ZIC-HILIC SPE sample preparation step was that it allowed load and elution conditions to be optimised to extract only peramivir and minimize co-extraction of lipophilic phospholipids. The method was validated according to published US Food and Drugs Administration guidelines and showed excellent performance. The assay was validated over two calibration ranges (0.952-500 and 50-50,000 ng/mL) to support analysis of peramivir after intra-venous administration. The lower limit of quantification for peramivir in plasma was 1 ng/mL and the upper limit of quantification was 50,000 ng/mL. The within-day and between-day precisions expressed as RSD, were lower than 8% at all tested quality control concentrations and below 11% at the lower limit of quantification. Validation of over-curve samples ensured that it would be possible with dilution if samples went outside the calibration range. Hide abstract

Tran TC, Campbell JI, Galindo C, Tran TH, Nguyen TC, Acosta CJ, Clemens JD, Farrar J, Dolecek C. 2008. Antimicrobial Drug Resistance of Salmonella Typhi in Asia INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E120-E120. | Read more

Tran NVT, Nguyen MH, Farrar J, Schultsz C. 2008. Bacterial DNA Load in Cerebrospinal Fluid During Treatment of Bacterial Meningitis INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E465-E465. | Read more

Caws M, An DD, Duyen NTH, Lan NTN, Hoa DV, Kiet VS, Thu DA, Chau NVV, Farrar JJ. 2008. Beijing Genotype of Mycobacterium tuberculosis is Significantly Associated with High-Level Fluoroquinolone Resistance in Vietnam INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E340-E340. | Read more

Nguyen H, Jamieson SE, Lanh MN, Phuong LT, Chinh NT, Hien TT, Blackwell JM, Farrar JJ, Dunstan SJ. 2008. Human Chromosome 17q11.2-q22 Contains Typhoid Fever Susceptibility Genes INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E50-E50. | Read more

Thuong NT, Dunstan SJ, Chau TT, Thorsson V, Simmons CP, Quyen NT, Thwaites GE, Thi Ngoc Lan N et al. 2008. Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles. PLoS Pathog, 4 (12), pp. e1000229. Read abstract | Read more

Although host genetics influences susceptibility to tuberculosis (TB), few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of Mycobacterium tuberculosis (Mtb) infection would have distinct gene expression profiles and that polymorphisms in these genes may also be associated with susceptibility to TB. We measured gene expression levels of >38,500 genes from ex vivo Mtb-stimulated macrophages in 12 subjects with 3 clinical phenotypes: latent, pulmonary, and meningeal TB (n = 4 per group). After identifying differentially expressed genes, we confirmed these results in 34 additional subjects by real-time PCR. We also used a case-control study design to examine whether polymorphisms in differentially regulated genes were associated with susceptibility to these different clinical forms of TB. We compared gene expression profiles in Mtb-stimulated and unstimulated macrophages and identified 1,608 and 199 genes that were differentially expressed by >2- and >5-fold, respectively. In an independent sample set of 34 individuals and a subset of highly regulated genes, 90% of the microarray results were confirmed by RT-PCR, including expression levels of CCL1, which distinguished the 3 clinical groups. Furthermore, 6 single nucleotide polymorphisms (SNPs) in CCL1 were found to be associated with TB in a case-control genetic association study with 273 TB cases and 188 controls. To our knowledge, this is the first identification of CCL1 as a gene involved in host susceptibility to TB and the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility. These results suggest that genome-wide studies can provide an unbiased method to identify critical macrophage response genes that are associated with different clinical outcomes and that variation in innate immune response genes regulate susceptibility to TB. Hide abstract

Tho DQ, Ha DM, Duy PM, Lan NTN, Hoa DV, Chau NVV, Farrar JJ, Caws M. 2008. MAS-PCR: A Quick Cheap Detection Test for Isoniazid Resistance in Mycobacterium tuberculosis INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E319-E319. | Read more

Le V, Le T, Cao T, Le L, Tran N, Le TP, Nguyen H, Campbell J, Baker S, Farrar J, Schultsz C. 2008. Prevalence of qnr and aac(6 ')-Ib-cr Genes in Community-Acquired Enterobacteriaceae Isolated in Healthy Volunteers in Hochiminh City INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E117-E118. | Read more

Nguyen QN, Dang MH, Do AT, Caws M, Torok E, Campbell J, Tran HC, Nguyen VC, Nguyen TC, Farrar J. 2008. Routine Diagnosis of Tuberculous Meningitis with MODS Assay INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 12 pp. E319-E320. | Read more

Tho DQ, Ha DT, Duy PM, Lan NT, Hoa DV, Chau NV, Farrar J, Caws M. 2008. Comparison of MAS-PCR and GenoType MTBDR assay for the detection of rifampicin-resistant Mycobacterium tuberculosis. Int J Tuberc Lung Dis, 12 (11), pp. 1306-1312. Read abstract

Pham Ngoc Thach Hospital for Tuberculosis and Lung Diseases, the tertiary referral hospital for tuberculosis (TB) in Southern Vietnam. Hide abstract

Baker S, Campbell JI, Stabler R, Nguyen HV, To DS, Nguyen DV, Farrar J. 2008. Fatal wound infection caused by Chromobacterium violaceum in Ho Chi Minh City, Vietnam. J Clin Microbiol, 46 (11), pp. 3853-3855. Read abstract | Read more

Chromobacterium violaceum is a proteobacterium found in soil and water in tropical regions which rarely causes infection in humans. Here, we report a fatal bacteremia caused by Chromobacterium violaceum in Vietnam. We describe a number of clinical, microbiological, and molecular aspects associated with this bacterial infection. Hide abstract

Simmons C, Farrar J. 2008. Insights into inflammation and influenza. N Engl J Med, 359 (15), pp. 1621-1623. | Read more

Lee LY, Ha DOLA, Simmons C, de Jong MD, Chau NV, Schumacher R, Peng YC, McMichael AJ et al. 2008. Memory T cells established by seasonal human influenza A infection cross-react with avian influenza A (H5N1) in healthy individuals. J Clin Invest, 118 (10), pp. 3478-3490. Read abstract | Read more

The threat of avian influenza A (H5N1) infection in humans remains a global health concern. Current influenza vaccines stimulate antibody responses against the surface glycoproteins but are ineffective against strains that have undergone significant antigenic variation. An alternative approach is to stimulate pre-existing memory T cells established by seasonal human influenza A infection that could cross-react with H5N1 by targeting highly conserved internal proteins. To determine how common cross-reactive T cells are, we performed a comprehensive ex vivo analysis of cross-reactive CD4+ and CD8+ memory T cell responses to overlapping peptides spanning the full proteome of influenza A/Viet Nam/CL26/2005 (H5N1) and influenza A/New York/232/2004 (H3N2) in healthy individuals from the United Kingdom and Viet Nam. Memory CD4+ and CD8+ T cells isolated from the majority of participants exhibited human influenza-specific responses and showed cross-recognition of at least one H5N1 internal protein. Participant CD4+ and CD8+ T cells recognized multiple synthesized influenza peptides, including peptides from the H5N1 strain. Matrix protein 1 (M1) and nucleoprotein (NP) were the immunodominant targets of cross-recognition. In addition, cross-reactive CD4+ and CD8+ T cells recognized target cells infected with recombinant vaccinia viruses expressing either H5N1 M1 or NP. Thus, vaccine formulas inducing heterosubtypic T cell-mediated immunity may confer broad protection against avian and human influenza A viruses. Hide abstract

Tan LEV, Ha DOQ, Hien VM, van der Hoek L, Farrar J, de Jong MD. 2008. Me Tri virus: a Semliki Forest virus strain from Vietnam? J Gen Virol, 89 (Pt 9), pp. 2132-2135. Read abstract | Read more

Me Tri virus (MTV) is a member of the Semliki Forest virus (SFV) complex in the genus Alphavirus, first isolated from Culex tritaeniorhynchus mosquitoes in Vietnam in 1971 and described as a newly recognized alphavirus, based on antigenic characterization. However, based on a partial nucleotide sequence of the E1 envelope glycoprotein gene, it has recently been argued that MTV may represent a variant of SFV rather than a separate species. To enable definitive classification, we determined the complete genome sequence of MTV from original virus stock. Nucleotide homology, as well as phylogenetic analyses based on whole and partial genome sequences confirmed that MTV is an isolate of SFV. Notable differences to other reported SFV sequences included a 122 nt insertion at the 5' non-translated region (NTR), likely resulting from homologous recombination of part of the nsP2 gene, and differences in the sequence length of the 3' NTR. To our knowledge, this is the first and only documentation of SFV isolation outside Africa. Further research is needed to clarify whether SFV continues to circulate in Vietnam. Hide abstract

Chau TN, Quyen NT, Thuy TT, Tuan NM, Hoang DM, Dung NT, Lien LEB, Quy NT et al. 2008. Dengue in Vietnamese infants--results of infection-enhancement assays correlate with age-related disease epidemiology, and cellular immune responses correlate with disease severity. J Infect Dis, 198 (4), pp. 516-524. Read abstract | Read more

The pathogenesis of severe dengue is not well understood. Maternally derived subneutralizing levels of dengue virus-reactive IgG are postulated to be a critical risk factor for severe dengue during infancy. In this study, we found that, in healthy Vietnamese infants, there was a strong temporal association between the Fc-dependent, dengue virus infection-enhancing activity of neat plasma and the age-related epidemiology of severe dengue. We then postulated that disease severity in infants with primary infections would be associated with a robust immune response, possibly as a consequence of higher viral burdens in vivo. Accordingly, in infants hospitalized with acute dengue, the activation phenotype of peripheral-blood NK cells and CD8+ and CD4+ T cells correlated with overall disease severity, but HLA-A*1101-restricted NS3(133-142)-specific CD8+ T cells were not measurable until early convalescence. Plasma levels of cytokines/chemokines were generally higher in infants with dengue shock syndrome. Collectively, these data support a model of dengue pathogenesis in infants whereby antibody-dependent enhancement of infection explains the age-related case epidemiology and could account for antigen-driven immune activation and its association with disease severity. These results also highlight potential risks in the use of live attenuated dengue vaccines in infants in countries where dengue is endemic. Hide abstract

Bird SM, Farrar J. 2008. Minimum dataset needed for confirmed human H5N1 cases. Lancet, 372 (9640), pp. 696-697. | Read more

Thwaites CL, Yen LM, Cordon SM, Thwaites GE, Loan HT, Thuy TT, White NJ, Soni N, Macdonald IA, Farrar JJ. 2008. Effect of magnesium sulphate on urinary catecholamine excretion in severe tetanus. Anaesthesia, 63 (7), pp. 719-725. Read abstract | Read more

Severe tetanus is characterised by muscle spasms and autonomic dysfunction. We recently reported the results of a randomised placebo controlled trial of magnesium sulphate infusions for the treatment of severe tetanus which showed magnesium was associated with improved muscle spasm and cardiovascular control. We hypothesised that magnesium controlled autonomic dysfunction by reducing catecholamine release and thus urinary excretion. Urinary adrenaline and noradrenaline concentrations were measured during the first 24 h of therapy in 180 adults with severe tetanus randomised to treatment with magnesium (n = 92) or placebo (n = 88). Magnesium therapy was associated with lower urinary adrenaline excretion and higher urinary noradrenaline excretion. High urinary adrenaline concentrations were associated with documented autonomic dysfunction. Patients given magnesium had significantly less autonomic dysfunction, required less cardiovascular stabilising drugs, and had lower urinary concentrations of adrenaline. These findings suggest adrenaline is important in the pathophysiology of severe tetanus and magnesium controls autonomic dysfunction by reducing adrenaline release. Hide abstract

van Doorn HR, An DD, de Jong MD, Lan NT, Hoa DV, Quy HT, Chau NV, Duy PM et al. 2008. Fluoroquinolone resistance detection in Mycobacterium tuberculosis with locked nucleic acid probe real-time PCR. Int J Tuberc Lung Dis, 12 (7), pp. 736-742. Read abstract

Pham Ngoc Thach Hospital for Tuberculosis and Lung Diseases, Ho Chi Minh City, Vietnam. Hide abstract

Baker S, Pickard D, Whitehead S, Farrar J, Dougan G. 2008. Mobilization of the incQ plasmid R300B with a chromosomal conjugation system in Salmonella enterica serovar typhi. J Bacteriol, 190 (11), pp. 4084-4087. Read abstract | Read more

Salmonella pathogenicity island 7 (SPI-7) in Salmonella enterica serovar Typhi appears to be related to other genomic islands. Evidence suggests that SPI-7 is susceptible to spontaneous circularization, loss, and transposition. Here, we demonstrate that a region within SPI-7 has the ability to mobilize the small incQ plasmid R300B. Hide abstract

Baker S, Holt K, van de Vosse E, Roumagnac P, Whitehead S, King E, Ewels P, Keniry A et al. 2008. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia. J Clin Microbiol, 46 (5), pp. 1741-1746. Read abstract | Read more

High-throughput epidemiological typing systems that provide phylogenetic and genotypic information are beneficial for tracking bacterial pathogens in the field. The incidence of Salmonella enterica serovar Typhi infection in Indonesia is high and is associated with atypical phenotypic traits such as expression of the j and the z66 flagellum antigens. Utilizing a high-throughput genotyping platform to investigate known nucleotide polymorphisms dispersed around the genome, we determined the haplotypes of 140 serovar Typhi isolates associated with Indonesia. We identified nine distinct serovar Typhi haplotypes circulating in Indonesia for more than 30 years, with eight of these present in a single Jakarta suburb within a 2-year period. One dominant haplotype, H59, is associated with j and z66 flagellum expression, representing a potential pathotype unique to Indonesia. Phylogenetic analysis suggests that H59 z66(+), j(+) isolates emerged relatively recently in terms of the origin of serovar Typhi and are geographically restricted. These data demonstrate the potential of high-throughput genotyping platforms for analyzing serovar Typhi populations in the field. The study also provides insight into the evolution of serovar Typhi and demonstrates the value of a molecular epidemiological technique that is exchangeable, that is internet friendly, and that has global utility. Hide abstract

Nguyen TH, Farrar J, Horby P. 2008. Person-to-person transmission of influenza A (H5N1). Lancet, 371 (9622), pp. 1392-1394. | Read more

Moran E, Simmons C, Vinh Chau N, Luhn K, Wills B, Dung NP, Thao LETT, Hien TT, Farrar J, Rowland-Jones S, Dong T. 2008. Preservation of a critical epitope core region is associated with the high degree of flaviviral cross-reactivity exhibited by a dengue-specific CD4+ T cell clone. Eur J Immunol, 38 (4), pp. 1050-1057. Read abstract | Read more

Dengue is a member of the Flaviviridae, a large group of related viruses some of which co-circulate in certain regions (e.g. dengue and Yellow fever in South America). Immune responses cross-reactive between different dengue serotypes are important in the pathogenesis of dengue disease but it is not known whether previous infection with one flavivirus might affect the clinical course of subsequent infections with other members of the family. CD4+ T cells have been shown to be important in the production of cytokines in response to dengue infection and can demonstrate significant epitope cross-reactivity. Here, we describe the generation and characterisation of CD4+ T cell clones from a patient experiencing acute dengue infection. These clones were DRB1*15+ and recognised epitope variants not only within other dengue viruses but certain other flaviviruses. This cross-reactivity was dependent upon the presence of a five-amino acid core region, consistent with structural observations of class II MHC binding to TCR demonstrating that only a subset of residues within an epitope bound to a class II molecule are "read out" by the TCR. This capacity of CD4+ T cell clones to recognise a given epitope despite considerable variation between viruses may be of pathological significance, particularly in regions where related viruses co-circulate. Hide abstract

Thwaites G, Caws M, Chau TT, D'Sa A, Lan NT, Huyen MN, Gagneux S, Anh PT et al. 2008. Relationship between Mycobacterium tuberculosis genotype and the clinical phenotype of pulmonary and meningeal tuberculosis. J Clin Microbiol, 46 (4), pp. 1363-1368. Read abstract | Read more

We used large sequence polymorphisms to determine the genotypes of 397 isolates of Mycobacterium tuberculosis from human immunodeficiency virus-uninfected Vietnamese adults with pulmonary (n = 235) or meningeal (n = 162) tuberculosis. We compared the pretreatment radiographic appearances of pulmonary tuberculosis and the presentation, response to treatment, and outcome of tuberculous meningitis between the genotypes. Multivariate analysis identified variables independently associated with genotype and outcome. A higher proportion of adults with pulmonary tuberculosis caused by the Euro-American genotype had consolidation on chest X-ray than was the case with disease caused by other genotypes (P = 0.006). Multivariate analysis revealed that meningitis caused by the East Asian/Beijing genotype was independently associated with a shorter duration of illness before presentation and fewer cerebrospinal fluid (CSF) leukocytes. Older age, fewer CSF leukocytes, and the presence of hemiplegia (but not strain lineage) were independently associated with death or severe disability, although the East Asian/Beijing genotype was strongly associated with drug-resistant tuberculosis. The genotype of M. tuberculosis influenced the presenting features of pulmonary and meningeal tuberculosis. The association between the East Asian/Beijing lineage and disease progression and CSF leukocyte count suggests the lineage may alter the presentation of meningitis by influencing the intracerebral inflammatory response. In addition, increased drug resistance among bacteria of the East Asian/Beijing lineage might influence the response to treatment. This study suggests the genetic diversity of M. tuberculosis has important clinical consequences. Hide abstract

Higgs ES, Hayden FG, Chotpitayasunondh T, Whitworth J, Farrar J. 2008. The Southeast Asian Influenza Clinical Research Network: development and challenges for a new multilateral research endeavor. Antiviral Res, 78 (1), pp. 64-68. Read abstract | Read more

The Southeast Asia Influenza Clinical Research Network (SEA ICRN) (www.seaclinicalresearch.org) is a recently developed multilateral, collaborative partnership that aims to advance scientific knowledge and management of human influenza through integrated clinical investigation. The partnership of hospitals and institutions in Indonesia, Thailand, United Kingdom, United States, and Viet Nam was established in late 2005 after agreement on the general principles and mission of the initiative and after securing initial financial support. The establishment of the SEA ICRN was both a response to the re-emergence of the highly pathogenic avian influenza A(H5N1) virus in Southeast Asia in late 2003 and an acknowledgment that clinical trials on emerging infectious diseases require prepared and coordinated research capacity. The objectives of the Network also include building sustainable research capacity in the region, compliance with international standards, and prompt dissemination of information and sharing of samples. The scope of research includes diagnosis, pathogenesis, treatment and prevention of human influenza due to seasonal or novel viruses. The Network has overcome numerous logistical and scientific challenges but has now successfully initiated several clinical trials. The establishment of a clinical research network is a vital part of preparedness and an important element during an initial response phase to a pandemic. Hide abstract

Mai NTH, Thwaites G, Farrar JJ. 2008. Corticosteroids for bacterial meningitis - Reply NEW ENGLAND JOURNAL OF MEDICINE, 358 (13), pp. 1400-1401.

Caws M, Thwaites G, Dunstan S, Hawn TR, Lan NT, Thuong NT, Stepniewska K, Huyen MN et al. 2008. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog, 4 (3), pp. e1000034. Read abstract | Read more

The factors that govern the development of tuberculosis disease are incompletely understood. We hypothesized that some strains of Mycobacterium tuberculosis (M. tuberculosis) are more capable of causing disseminated disease than others and may be associated with polymorphisms in host genes responsible for the innate immune response to infection. We compared the host and bacterial genotype in 187 Vietnamese adults with tuberculous meningitis (TBM) and 237 Vietnamese adults with uncomplicated pulmonary tuberculosis. The host genotype of tuberculosis cases was also compared with the genotype of 392 cord blood controls from the same population. Isolates of M. tuberculosis were genotyped by large sequence polymorphisms. The hosts were defined by polymorphisms in genes encoding Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP) and Toll-like receptor-2 (TLR-2). We found a significant protective association between the Euro-American lineage of M. tuberculosis and pulmonary rather than meningeal tuberculosis (Odds ratio (OR) for causing TBM 0.395, 95% confidence intervals (C.I.) 0.193-0.806, P = 0.009), suggesting these strains are less capable of extra-pulmonary dissemination than others in the study population. We also found that individuals with the C allele of TLR-2 T597C allele were more likely to have tuberculosis caused by the East-Asian/Beijing genotype (OR = 1.57 [95% C.I. 1.15-2.15]) than other individuals. The study provides evidence that M. tuberculosis genotype influences clinical disease phenotype and demonstrates, for the first time, a significant interaction between host and bacterial genotypes and the development of tuberculosis. Hide abstract

Achidi EA, Agbenyega T, Allen S, Amodu O, Bojang K, Conway D, Corran P, Deloukas P et al. 2008. A global network for investigating the genomic epidemiology of malaria Nature, 456 (7223), pp. 732-737. Read abstract | Read more

Large-scale studies of genomic variation could assist efforts to eliminate malaria. But there are scientific, ethical and practical challenges to carrying out such studies in developing countries, where the burden of disease is greatest. The Malaria Genomic Epidemiology Network (MalariaGEN) is now working to overcome these obstacles, using a consortial approach that brings together researchers from 21 countries. © 2008 Macmillan Publishers Limited. All rights reserved. Hide abstract

Dolecek C, Tran TP, Nguyen NR, Le TP, Ha V, Phung QT, Doan CD, Nguyen TB et al. 2008. A multi-center randomised controlled trial of gatifloxacin versus azithromycin for the treatment of uncomplicated typhoid fever in children and adults in Vietnam. PLoS One, 3 (5), pp. e2188. Read abstract | Read more

Drug resistant typhoid fever is a major clinical problem globally. Many of the first line antibiotics, including the older generation fluoroquinolones, ciprofloxacin and ofloxacin, are failing. Hide abstract

Pandit A, Arjyal A, Paudyal B, Campbell JC, Day JN, Farrar JJ, Basnyat B. 2008. A patient with paratyphoid A fever: an emerging problem in Asia and not always a benign disease. J Travel Med, 15 (5), pp. 364-365. Read abstract | Read more

A 15-year-old Nepalese boy with fever was thought to have enteric fever and started on cefixime. His blood culture grew Salmonella paratyphoid A. On the sixth day, he developed gastrointestinal bleeding, disseminated intravascular coagulation, and later, acute respiratory distress syndrome. He succumbed to his illness despite treatment in the intensive care unit with ceftriaxone, intravenous fluids, and mechanical ventilation. Salmonella paratyphoid A, for which there is no commercial vaccine, may not be a benign disease as perceived, and cefixime that is recommended for enteric fever may be an ineffective choice. Hide abstract

Hien TT, Truong NT, Minh NH, Dat HD, Dung NT, Hue NT, Dung TK, Tuan PQ, Campbell JI, Farrar JJ, Day JN. 2008. A randomized controlled pilot study of artesunate versus triclabendazole for human fascioliasis in central Vietnam. Am J Trop Med Hyg, 78 (3), pp. 388-392. Read abstract

Human fascioliasis caused by Fasciola hepatica or Fasciola gigantica is an increasing global problem. The mainstay of current treatment is triclabendazole, but resistance in animals has been described, and it is not available in many countries. The antimalarial artesunate has an excellent safety profile, and there is increasing evidence of its efficacy against other parasites both in vitro and in vivo. We performed a study to investigate the usefulness of artesunate in symptomatic human fascioliasis; 100 patients were enrolled. Patients treated with artesunate were significantly more likely to be free of abdominal pain at hospital discharge (50/50 versus 44/50, P = 0.027, relative risk 1.14, 95% confidence interval 1.03-1.26), but the complete response rate at 3 months was lower than for patients treated with triclabendazole (38/50 versus 46/50, P = 0.05, RR 0.83, 95% CI 0.69-0.98, artesunate versus triclabendazole). There may be a role for artesunate in fascioliasis. Hide abstract

Ochiai RL, Acosta CJ, Danovaro-Holliday MC, Baiqing D, Bhattacharya SK, Agtini MD, Bhutta ZA, Canh DOG et al. 2008. A study of typhoid fever in five Asian countries: disease burden and implications for controls. Bull World Health Organ, 86 (4), pp. 260-268. Read abstract | Read more

To inform policy-makers about introduction of preventive interventions against typhoid, including vaccination. Hide abstract

Basnyat B, Hargrove J, Holck PS, Srivastav S, Alekh K, Ghimire LV, Pandey K, Griffiths A et al. 2008. Acetazolamide fails to decrease pulmonary artery pressure at high altitude in partially acclimatized humans. High Alt Med Biol, 9 (3), pp. 209-216. Read abstract | Read more

In this randomized, double-blind placebo controlled trial our objectives were to determine if acetazolamide is capable of preventing high altitude pulmonary edema (HAPE) in trekkers traveling between 4250 m (Pheriche)\4350 m (Dingboche) and 5000 m (Lobuje) in Nepal; to determine if acetazolamide decreases pulmonary artery systolic pressures (PASP) at high altitude; and to determine if there is an association with PASP and signs and symptoms of HAPE. Participants received either acetazolamide 250 mg PO BID or placebo at Pheriche\Dingboche and were reassessed in Lobuje. The Lake Louise Consensus Criteria were used for the diagnosis of HAPE, and cardiac ultrasonography was used to measure the velocity of tricuspid regurgitation and estimate PASP. Complete measurements were performed on 339 of the 364 subjects (164 in the placebo group, 175 in the acetazolamide group). No cases of HAPE were observed in either study group nor were differences in the signs and symptoms of HAPE found between the two groups. Mean PASP values did not differ significantly between the acetazolamide and placebo groups (31.3 and 32.6 mmHg, respectively). An increasing number of signs and symptoms of HAPE was associated with elevated PASP (p < 0.01). The efficacy of acetazolamide against acute mountain sickness, however, was significant with a 21.9% incidence in the placebo group compared to 10.2 % in the acetazolamide group (p < 0.01). Given the lack of cases of HAPE in either group, we can draw no conclusions about the efficacy of acetazolamide in preventing HAPE, but the absence of effect on PASP suggests that any effect may be minor possibly owing to partial acclimatization during the trek up to 4200 m. Hide abstract

House D, Ho VA, Diep TS, Chinh NT, Bay PV, Vinh H, Duc M, Parry CM et al. 2008. Antibodies to the Vi capsule of Salmonella Typhi in the serum of typhoid patients and healthy control subjects from a typhoid endemic region. J Infect Dev Ctries, 2 (4), pp. 308-312. Read abstract

There is very little published data on the antibody response to the Vi capsular polysaccharide (Vi-CPS) of S. Typhi during naturally acquired typhoid fever in an endemic area. Hide abstract

Torok ME, Chau TT, Mai PP, Phong ND, Dung NT, Chuong LV, Lee SJ, Caws M, de Jong MD, Hien TT, Farrar JJ. 2008. Clinical and microbiological features of HIV-associated tuberculous meningitis in Vietnamese adults. PLoS One, 3 (3), pp. e1772. Read abstract | Read more

The aim of this prospective, observational cohort study was to determine the clinical and microbiological features, outcome, and baseline variables predictive of death, in Vietnamese adults with HIV-associated tuberculous meningitis (TBM). 58 patients were admitted to the Hospital for Tropical Diseases in Ho Chi Minh City and underwent routine clinical and laboratory assessments. Treatment was with standard antituberculous therapy and adjunctive dexamethasone; antiretroviral therapy was not routinely available. Patients were followed up until the end of TB treatment or death. Hide abstract

Maskey AP, Basnyat B, Thwaites GE, Campbell JI, Farrar JJ, Zimmerman MD. 2008. Emerging trends in enteric fever in Nepal: 9124 cases confirmed by blood culture 1993-2003. Trans R Soc Trop Med Hyg, 102 (1), pp. 91-95. Read abstract | Read more

This was a retrospective study in an urban hospital in Kathmandu, Nepal to determine the changing burden of salmonella septicaemia, the proportion of Salmonella paratyphi A, and the emergence of drug-resistant organisms. The participants were outpatients and inpatients over the period 1993-2003, and the main outcome measures were blood culture isolates and antibiotic sensitivity testing. The results showed that of 82467 blood cultures performed, a bacterium was isolated from 12252. Salmonella accounted for 9124 (74.5%) of the positive blood cultures: 6447 (70.7%) were Salmonella enterica serotype Typhi (S. typhi) and 2677 (29.3%) were Paratyphi A (S. paratyphi A). In comparing the period 1997-2000 to the period 2001-2003, we found that, as a proportion of total blood cultures taken, salmonella septicaemia more than doubled, from 6.2 to 13.6% (P<0.001). From the first half of the study (1993-1998) to the second half (1999-2003), S. paratyphi A as a proportion of all salmonella isolates rose from 23 to 34% (P<0.001), which paralleled its increased resistance to ciprofloxacin. Despite the introduction of new antibiotics, enteric fever continues to grow as a cause for hospital presentation in Nepal. Salmonella paratyphi A contributes an increasingly large proportion of cases, and ciprofloxacin resistance is also emerging more rapidly in S. paratyphi A. Hide abstract

Nghia HD, Hoa NT, Linh LED, Campbell J, Diep TS, Chau NV, Mai NT, Hien TT, Spratt B, Farrar J, Schultsz C. 2008. Human case of Streptococcus suis serotype 16 infection. Emerg Infect Dis, 14 (1), pp. 155-157. Read abstract | Read more

Streptococcus suis infection is an emerging zoonosis in Southeast Asia. We report a fatal case of S. suis serotype 16 infection in a Vietnamese man in 2001. Hide abstract

Thuong NTT, Dunstan SJ, Simmons CP, Quyen NTH, Farrar JJ, Chau TTH, Thorsson V, Aderem A et al. 2008. Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles PLoS Pathogens, 4 (12), Read abstract | Read more

Although host genetics influences susceptibility to tuberculosis (TB), few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of Mycobacterium tuberculosis (Mtb) infection would have distinct gene expression profiles and that polymorphisms in these genes may also be associated with susceptibility to TB. We measured gene expression levels of >38,500 genes from ex vivo Mtb-stimulated macrophages in 12 subjects with 3 clinical phenotypes: latent, pulmonary, and meningeal TB (n = 4 per group). After identifying differentially expressed genes, we confirmed these results in 34 additional subjects by real-time PCR. We also used a case-control study design to examine whether polymorphisms in differentially regulated genes were associated with susceptibility to these different clinical forms of TB. We compared gene expression profiles in Mtb-stimulated and unstimulated macrophages and identified 1,608 and 199 genes that were differentially expressed by >2- and >5-fold, respectively. In an independent sample set of 34 individuals and a subset of highly regulated genes, 90% of the microarray results were confirmed by RT-PCR, including expression levels of CCL1, which distinguished the 3 clinical groups. Furthermore, 6 single nucleotide polymorphisms (SNPs) in CCL1 were found to be associated with TB in a case-control genetic association study with 273 TB cases and 188 controls. To our knowledge, this is the first identification of CCL1 as a gene involved in host susceptibility to TB and the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility. These results suggest that genome-wide studies can provide an unbiased method to identify critical macrophage response genes that are associated with different clinical outcomes and that variation in innate immune response genes regulate susceptibility to TB. © 2008 Thuong et al. Hide abstract

Le MT, Wertheim HF, Nguyen HD, Taylor W, Hoang PV, Vuong CD, Nguyen HL, Nguyen HH et al. 2008. Influenza A H5N1 clade 2.3.4 virus with a different antiviral susceptibility profile replaced clade 1 virus in humans in northern Vietnam. PLoS One, 3 (10), pp. e3339. Read abstract | Read more

Prior to 2007, highly pathogenic avian influenza (HPAI) H5N1 viruses isolated from poultry and humans in Vietnam were consistently reported to be clade 1 viruses, susceptible to oseltamivir but resistant to amantadine. Here we describe the re-emergence of human HPAI H5N1 virus infections in Vietnam in 2007 and the characteristics of the isolated viruses. Hide abstract

Taylor WR, Thinh BN, Anh GT, Horby P, Wertheim H, Lindegardh N, de Jong MD, Stepniewska K et al. 2008. Oseltamivir is adequately absorbed following nasogastric administration to adult patients with severe H5N1 influenza. PLoS One, 3 (10), pp. e3410. Read abstract | Read more

In the absence of a parenteral drug, oral oseltamivir is currently recommended by the WHO for treating H5N1 influenza. Whether oseltamivir absorption is adequate in severe influenza is unknown. We measured the steady state, plasma concentrations of nasogastrically administered oseltamivir 150 mg bid and its active metabolite, oseltamivir carboxylate (OC), in three, mechanically ventilated patients with severe H5N1 (male, 30 yrs; pregnant female, 22 yrs) and severe H3N2 (female, 76 yrs). Treatments were started 6, 7 and 8 days after illness onset, respectively. Both females were sampled while on continuous venovenous haemofiltration. Admission and follow up specimens (trachea, nose, throat, rectum, blood) were tested for RNA viral load by reverse transcriptase PCR. In vitro virus susceptibility to OC was measured by a neuraminidase inhibition assay. Admission creatinine clearances were 66 (male, H5N1), 82 (female, H5N1) and 6 (H3N2) ml/min. Corresponding AUC(0-12) values (5932, 10,951 and 34,670 ng.h/ml) and trough OC concentrations (376, 575 and 2730 ng/ml) were higher than previously reported in healthy volunteers; the latter exceeded 545 to 3956 fold the H5N1 IC(50) (0.69 ng/ml) isolated from the H5N1 infected female. Two patients with follow-up respiratory specimens cleared their viruses after 5 (H5N1 male) and 5 (H3N2 female) days of oseltamivir. Both female patients died of respiratory failure; the male survived. 150 mg bid of oseltamivir was well absorbed and converted extensively to OC. Virus was cleared in two patients but two patients died, suggesting viral efficacy but poor clinical efficacy. Hide abstract

Wain J, Diep TS, Bay PV, Walsh AL, Vinh H, Duong NM, Ho VA, Hien TT et al. 2008. Specimens and culture media for the laboratory diagnosis of typhoid fever. J Infect Dev Ctries, 2 (6), pp. 469-474. Read abstract

Culture of S. Typhi is necessary for the definitive diagnosis of typhoid fever and provides isolates for antibiotic susceptibility testing and epidemiological studies. However, current methods are not fully optimised and sourcing culture media and bottles for culture media may be problematic. Hide abstract

Mai NT, Hoa NT, Nga TV, Linh LED, Chau TT, Sinh DX, Phu NH, Chuong LV et al. 2008. Streptococcus suis meningitis in adults in Vietnam. Clin Infect Dis, 46 (5), pp. 659-667. Read abstract | Read more

Streptococcus suis infection is an emerging zoonosis in Asia. We determined the detailed epidemiological, clinical, and microbiological characteristics of S. suis meningitis in adults. Hide abstract

Chau TT, Campbell JI, Galindo CM, Van Minh Hoang N, Diep TS, Nga TT, Van Vinh Chau N, Tuan PQ et al. 2007. Antimicrobial drug resistance of Salmonella enterica serovar typhi in asia and molecular mechanism of reduced susceptibility to the fluoroquinolones. Antimicrob Agents Chemother, 51 (12), pp. 4315-4323. Read abstract | Read more

This study describes the pattern and extent of drug resistance in 1,774 strains of Salmonella enterica serovar Typhi isolated across Asia between 1993 and 2005 and characterizes the molecular mechanisms underlying the reduced susceptibilities to fluoroquinolones of these strains. For 1,393 serovar Typhi strains collected in southern Vietnam, the proportion of multidrug resistance has remained high since 1993 (50% in 2004) and there was a dramatic increase in nalidixic acid resistance between 1993 (4%) and 2005 (97%). In a cross-sectional sample of 381 serovar Typhi strains from 8 Asian countries, Bangladesh, China, India, Indonesia, Laos, Nepal, Pakistan, and central Vietnam, collected in 2002 to 2004, various rates of multidrug resistance (16 to 37%) and nalidixic acid resistance (5 to 51%) were found. The eight Asian countries involved in this study are home to approximately 80% of the world's typhoid fever cases. These results document the scale of drug resistance across Asia. The Ser83-->Phe substitution in GyrA was the predominant alteration in serovar Typhi strains from Vietnam (117/127 isolates; 92.1%). No mutations in gyrB, parC, or parE were detected in 55 of these strains. In vitro time-kill experiments showed a reduction in the efficacy of ofloxacin against strains harboring a single-amino-acid substitution at codon 83 or 87 of GyrA; this effect was more marked against a strain with a double substitution. The 8-methoxy fluoroquinolone gatifloxacin showed rapid killing of serovar Typhi harboring both the single- and double-amino-acid substitutions. Hide abstract

Farrar J. 2007. Global health science: a threat and an opportunity for collaborative clinical science. Nat Immunol, 8 (12), pp. 1277-1279. | Read more

Dunstan SJ, Nguyen TH, Rockett K, Forton J, Morris AP, Diakite M, Mai NL, Le TP et al. 2007. A TNF region haplotype offers protection from typhoid fever in Vietnamese patients. Hum Genet, 122 (1), pp. 51-61. Read abstract | Read more

The genomic region surrounding the TNF locus on human chromosome 6 has previously been associated with typhoid fever in Vietnam (Dunstan et al. in J Infect Dis 183:261-268, 2001). We used a haplotypic approach to understand this association further. Eighty single nucleotide polymorphisms (SNPs) spanning a 150 kb region were genotyped in 95 Vietnamese individuals (typhoid case/mother/father trios). A subset of data from 33 SNPs with a minor allele frequency of >4.3% was used to construct haplotypes. Fifteen SNPs, which tagged the 42 constructed haplotypes were selected. The haplotype tagging SNPs (T1-T15) were genotyped in 380 confirmed typhoid cases and 380 Vietnamese ethnically matched controls. Allelic frequencies of seven SNPs (T1, T2, T3, T5, T6, T7, T8) were significantly different between typhoid cases and controls. Logistic regression results support the hypothesis that there is just one signal associated with disease at this locus. Haplotype-based analysis of the tag SNPs provided positive evidence of association with typhoid (posterior probability 0.821). The analysis highlighted a low-risk cluster of haplotypes that each carry the minor allele of T1 or T7, but not both, and otherwise carry the combination of alleles *12122*1111 at T1-T11, further supporting the one associated signal hypothesis. Finally, individuals that carry the typhoid fever protective haplotype *12122*1111 also produce a relatively low TNF-alpha response to LPS. Hide abstract

Simmons CP, Chau TN, Thuy TT, Tuan NM, Hoang DM, Thien NT, Lien LEB, Quy NT et al. 2007. Maternal antibody and viral factors in the pathogenesis of dengue virus in infants. J Infect Dis, 196 (3), pp. 416-424. Read abstract | Read more

The pathogenesis of dengue in infants is poorly understood. We postulated that dengue severity in infants would be positively associated with markers of viral burden and that maternally derived, neutralizing anti-dengue antibody would have decayed before the age at which infants with dengue presented to the hospital. In 75 Vietnamese infants with primary dengue, we found significant heterogeneity in viremia and NS1 antigenemia at hospital presentation, and these factors were independent of disease grade or continuous measures of disease severity. Neutralizing antibody titers, predicted in each infant at the time of their illness, suggested that the majority of infants (65%) experienced dengue hemorrhagic fever when the maternally derived neutralizing antibody titer had declined to <1 : 20. Collectively, these data have important implications for dengue vaccine research because they suggest that viral burden may not solely explain severe dengue in infants and that neutralizing antibody is a reasonable but not absolute marker of protective immunity in infants. Hide abstract

Farrar J. 2007. A personal perspective on clinical research in Enteric Fever. Clin Infect Dis, 45 Suppl 1 (Supplement 1), pp. S9-14. Read abstract | Read more

With the global spread of enteric fever, the emergence of Salmonella enterica serovar Paratyphi as a major pathogen (particularly in Asia), the spread of drug resistance, and the global increase in the incidence of non-Typhi salmonella, particularly in patients coinfected with human immunodeficiency virus, there is now more than ever a need for clinical research in enteric fever. The work of Ted Woodward 60 years ago remains relevant today, and his holistic approach to clinical research inspired many of us to follow in his footsteps. There remains healthy discussion among clinicians about the best treatment for enteric fever, and pragmatic, well-designed, randomized controlled trials are required to provide clear evidence. Vaccines and public health measures will have the greatest impact on the overall burden of disease; however, while we wait for these measures, prompt diagnosis and early treatment with the best available and affordable drug will help patients, reduce transmission within the community, and potentially help to contain the spread of drug resistance. Better integration of clinical medicine with epidemiology, public health, vaccine development, and modern laboratory science will help to yield tangible benefits for the vast number of people who have this disease. Hide abstract

Thuong NT, Hawn TR, Thwaites GE, Chau TT, Lan NT, Quy HT, Hieu NT, Aderem A, Hien TT, Farrar JJ, Dunstan SJ. 2007. A polymorphism in human TLR2 is associated with increased susceptibility to tuberculous meningitis. Genes Immun, 8 (5), pp. 422-428. Read abstract | Read more

Tuberculous meningitis (TBM) results from the haematogenous dissemination of Mycobacterium tuberculosis from the lung to the brain. Dissemination is believed to occur early during infection, before the development of adaptive immunity. Toll-like receptor 2 (TLR2) mediates recognition of M. tuberculosis and initiates the innate immune response to infection. We hypothesized that polymorphisms in the TLR2 gene influence bacterial dissemination and the development of TBM. A case-control study was designed to test the hypothesis. Cases of bacteriologically confirmed pulmonary tuberculosis (TB) (n=183) and TBM (n=175), and cord blood controls (n=389) were enrolled in Vietnam. TLR2 genotype 597CC was associated with susceptibility to TB (odds ratio (OR)=2.22, 95% confidence interval (CI): 1.23-3.99). The association was found with meningeal rather than pulmonary TB (TBM vs control, OR=3.26, 95% CI: 1.72-6.18), and was strongest when miliary TB was found on chest radiography (controls vs TBM with miliary TB, OR=5.28, 95% CI: 2.20-12.65). Furthermore, the association increased with the severity of neurologic symptoms (grade I TBM, OR=1.93, 95% CI: 0.54-6.92; grade II, OR=3.32, 95% CI: 0.84-13.2; and grade III, OR=5.70, 95% CI: 1.81-18.0). These results demonstrate a strong association of TLR2 SNP T597C with the development of TBM and miliary TB and indicate that TLR2 influences the dissemination of M. tuberculosis. Hide abstract

Pandit A, Arjyal A, Day JN, Paudyal B, Dangol S, Zimmerman MD, Yadav B, Stepniewska K et al. 2007. An Open Randomized Comparison of Gatifloxacin versus Cefixime for the Treatment of Uncomplicated Enteric Fever PLOS ONE, 2 (6), | Read more

Farrar J, Focks D, Gubler D, Barrera R, Guzman MG, Simmons C, Kalayanarooj S, Lum L et al. 2007. Editorial: Towards a global dengue research agenda TROPICAL MEDICINE & INTERNATIONAL HEALTH, 12 (6), pp. 695-699. | Read more

Caws M, Tho DQ, Duy PM, Lan NT, Hoa DV, Torok ME, Chau TT, Chau NV, Chinh NT, Farrar J. 2007. PCR-restriction fragment length polymorphism for rapid, low-cost identification of isoniazid-resistant Mycobacterium tuberculosis. J Clin Microbiol, 45 (6), pp. 1789-1793. Read abstract | Read more

PCR-restriction fragment length poymorphism (PCR-RFLP) is a simple, robust technique for the rapid identification of isoniazid-resistant Mycobacterium tuberculosis. One hundred consecutive isolates from a Vietnamese tuberculosis hospital were tested by MspA1I PCR-RFLP for the detection of isoniazid-resistant katG_315 mutants. The test had a sensitivity of 80% and a specificity of 100% against conventional phenotypic drug susceptibility testing. The positive and negative predictive values were 1 and 0.86, respectively. None of the discrepant isolates had mutant katG_315 codons by sequencing. The test is cheap (less than $1.50 per test), specific, and suitable for the rapid identification of isoniazid resistance in regions with a high prevalence of katG_315 mutants among isoniazid-resistant M. tuberculosis isolates. Hide abstract

Farrar J, Focks D, Gubler D, Barrera R, Guzman MG, Simmons C, Kalayanarooj S, Lum L et al. 2007. Towards a global dengue research agenda. Trop Med Int Health, 12 (6), pp. 695-699. | Read more

Lühn K, Simmons CP, Moran E, Dung NT, Chau TN, Quyen NT, Thao LETT, Van Ngoc T et al. 2007. Increased frequencies of CD4+ CD25(high) regulatory T cells in acute dengue infection. J Exp Med, 204 (5), pp. 979-985. Read abstract | Read more

Dengue virus infection is an increasingly important tropical disease, causing 100 million cases each year. Symptoms range from mild febrile illness to severe hemorrhagic fever. The pathogenesis is incompletely understood, but immunopathology is thought to play a part, with antibody-dependent enhancement and massive immune activation of T cells and monocytes/macrophages leading to a disproportionate production of proinflammatory cytokines. We sought to investigate whether a defective population of regulatory T cells (T reg cells) could be contributing to immunopathology in severe dengue disease. CD4(+)CD25(high)FoxP3(+) T reg cells of patients with acute dengue infection of different severities showed a conventional phenotype. Unexpectedly, their capacity to suppress T cell proliferation and to secrete interleukin-10 was not altered. Moreover, T reg cells suppressed the production of vasoactive cytokines after dengue-specific stimulation. Furthermore, T reg cell frequencies and also T reg cell/effector T cell ratios were increased in patients with acute infection. A strong indication that a relative rise of T reg cell/effector T cell ratios is beneficial for disease outcome comes from patients with mild disease in which this ratio is significantly increased (P < 0.0001) in contrast to severe cases (P = 0.2145). We conclude that although T reg cells expand and function normally in acute dengue infection, their relative frequencies are insufficient to control the immunopathology of severe disease. Hide abstract

Lindegardh N, Davies GR, Hien TT, Farrar J, Singhasivanon P, Day NP, White NJ. 2007. Importance of collection tube during clinical studies of oseltamivir. Antimicrob Agents Chemother, 51 (5), pp. 1835-1836. Read abstract | Read more

Ex vivo conversion of the anti-influenza drug oseltamivir to its active metabolite can be inhibited by the esterase inhibitor dichlorvos or by using commercial fluoride-oxalate tubes. Oseltamivir and its active metabolite remain intact in plasma samples during a proposed virus heat inactivation step: incubation at 60 degrees C for 45 min. Hide abstract

Schünemann HJ, Hill SR, Kakad M, Vist GE, Bellamy R, Stockman L, Wisløff TF, Del Mar C et al. 2007. Transparent development of the WHO rapid advice guidelines. PLoS Med, 4 (5), pp. e119. Read abstract | Read more

Emerging health problems require rapid advice. We describe the development and pilot testing of a systematic, transparent approach used by the World Health Organization (WHO) to develop rapid advice guidelines in response to requests from member states confronted with uncertainty about the pharmacological management of avian influenza A (H5N1) virus infection. We first searched for systematic reviews of randomized trials of treatment and prevention of seasonal influenza and for non-trial evidence on H5N1 infection, including case reports and animal and in vitro studies. A panel of clinical experts, clinicians with experience in treating patients with H5N1, influenza researchers, and methodologists was convened for a two-day meeting. Panel members reviewed the evidence prior to the meeting and agreed on the process. It took one month to put together a team to prepare the evidence profiles (i.e., summaries of the evidence on important clinical and policy questions), and it took the team only five weeks to prepare and revise the evidence profiles and to prepare draft guidelines prior to the panel meeting. A draft manuscript for publication was prepared within 10 days following the panel meeting. Strengths of the process include its transparency and the short amount of time used to prepare these WHO guidelines. The process could be improved by shortening the time required to commission evidence profiles. Further development is needed to facilitate stakeholder involvement, and evaluate and ensure the guideline's usefulness. Hide abstract

Simmons CP, Popper S, Dolocek C, Chau TN, Griffiths M, Dung NT, Long TH, Hoang DM et al. 2007. Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue hemorrhagic fever. J Infect Dis, 195 (8), pp. 1097-1107. Read abstract | Read more

Responses by peripheral blood leukocytes may contribute to the pathogenesis of dengue hemorrhagic fever (DHF). We used DNA microarrays to reveal transcriptional patterns in the blood of 14 adults with DHF. Acute DHF was defined by an abundance of transcripts from cell cycle- and endoplasmic reticulum (ER)-related genes, suggesting a proliferative response accompanied by ER stress. Transcript-abundance levels for immunoresponse-associated genes, including cell surface markers, immunoglobulin, and innate response elements, were also elevated. Twenty-four genes were identified for which transcript abundance distinguished patients with dengue shock syndrome (DSS) from those without DSS. All the gene transcripts associated with DSS, many of which are induced by type I interferons, were less abundant in patients with DSS than in those without DSS. To our knowledge, these data provide the first snapshot of gene-expression patterns in peripheral blood during acute dengue and suggest that DSS is associated with attenuation of selected aspects of the innate host response. Hide abstract

Molyneux M. 2007. UK doctors are already put off by changes in training. BMJ, 334 (7596), pp. 709-710. | Read more

Medana IM, Day NP, Hien TT, Mai NT, Bethell D, Phu NH, Turner GD, Farrar J, White NJ, Esiri MM. 2007. Cerebral calpain in fatal falciparum malaria. Neuropathol Appl Neurobiol, 33 (2), pp. 179-192. Read abstract | Read more

Disruption of axonal transport may represent a final common pathway leading to neurological dysfunction in cerebral malaria (CM). Calpains are calcium (Ca2+)-activated cysteine proteases which have been implicated in axonal injury in neurological diseases of various aetiologies. In this study we examined the association between mu- and m-calpain, the specific inhibitor calpastatin, and axonal injury in post mortem brain tissue from patients who died from severe malaria. Calpains were associated with axons labelled for the beta-amyloid precursor protein that detects impaired axonal transport. Elevated levels of calpastatin were rarely observed in injured axons. There were increased numbers of neurones with mu-calpain in the nuclear compartment in severe malaria cases compared with non-neurological controls, and increased numbers of glia with nuclear mu-calpain in CM patients compared with non-CM malaria cases and non-neurological controls. There was marked redistribution of calpastatin in the sequestered Plasmodium falciparum-infected erythrocytes. Responses specific to malaria infection were ascertained following analysis of brain samples from fatal cases with acute axonal injury, HIV encephalitis, and progressive multifocal leucoencephalopathy. Our findings implicate a role for calpains in the modulation of disease progression in CM. Hide abstract

Flohr C, Tuyen LN, Lewis S, Minh TT, Campbell J, Britton J, Williams H, Hien TT, Farrar J, Quinnell RJ. 2007. Low efficacy of mebendazole against hookworm in Vietnam: two randomized controlled trials. Am J Trop Med Hyg, 76 (4), pp. 732-736. Read abstract

Vietnam is participating in a global de-worming effort that aims to treat 650 million school children regularly by 2010. The treatment used in Vietnam is single dose oral mebendazole (Phardazone) 500 mg. We tested the efficacy of single dose mebendazole 500 mg in the therapy of hookworm infection in a randomized double-blind placebo-controlled trial among 271 Vietnamese schoolchildren. The treatment efficacy of single dose mebendazole in children did not differ significantly from placebo, with a reduction in mean eggs per gram of feces relative to placebo of 31% (95% CI -9 to 56%, P = 0.1). In light of these findings we then carried out a similar randomized trial comparing triple dose mebendazole, single dose albendazole, and triple dose albendazole against placebo in 209 adults in the same area. The estimated reduction in mean post-treatment eggs per gram of feces relative to placebo was 63% (95% CI 30-81%) for triple mebendazole, 75% (47-88%) for single albendazole, and 88% (58-97%) for triple albendazole. Our results suggest that single dose oral mebendazole has low efficacy against hookworm infection in Vietnam, and that it should be replaced by albendazole. These findings are of major public health relevance given the opportunity costs of treating entire populations with ineffective therapies. We recommend that efficacy of anti-helminth therapies is pilot tested before implementation of national gut worm control programs. Hide abstract

Thwaites GE, Macmullen-Price J, Tran TH, Pham PM, Nguyen TD, Simmons CP, White NJ, Tran TH, Summers D, Farrar JJ. 2007. Serial MRI to determine the effect of dexamethasone on the cerebral pathology of tuberculous meningitis: an observational study. Lancet Neurol, 6 (3), pp. 230-236. Read abstract | Read more

Adjunctive dexamethasone increases survival from tuberculous meningitis, but the underlying mechanism is unclear. We aimed to determine the effect of dexamethasone on cerebral MRI changes and their association with intracerebral inflammatory responses and clinical outcome in adults treated for tuberculous meningitis. Hide abstract

Nguyen-Pouplin J, Tran H, Tran H, Phan TA, Dolecek C, Farrar J, Tran TH, Caron P, Bodo B, Grellier P. 2007. Antimalarial and cytotoxic activities of ethnopharmacologically selected medicinal plants from South Vietnam. J Ethnopharmacol, 109 (3), pp. 417-427. Read abstract | Read more

Malaria is a major global public health problem and the alarming spread of drug resistance and limited number of effective drugs now available underline how important it is to discover new antimalarial compounds. An ethnopharmacological investigation was undertaken of medicinal plants traditionally used to treat malaria in the South Vietnam. Forty-nine plants were identified, 228 extracts were prepared and tested for their in vitro activity against Plasmodium falciparum, and assessed for any cytotoxicity against the human cancer cell line HeLa and the embryonic lung MRC5 cell line. In a first screening at a concentration of 10 microg/ml, 92 extracts from 46 plants showed antiplasmodial activity (parasite growth inhibition >30%). The IC(50) values of the most active extracts were determined as well as their selectivity towards Plasmodium falciparum in comparison to their cytotoxic effects against the human cell lines. Six plants showed interesting antiplasmodial activity (IC(50) ranging from 0.4 to 8.6 microg/ml) with a good selectivity: two Menispermaceae, Arcangelisia flava (L.) Merr. and Fibraurea tinctoria Lour., and also Harrisonia perforata (Blanco) Merr. (Simaroubaceae), Irvingia malayana Oliv. ex Benn. (Irvingiaceae), Elaeocarpus kontumensis Gagn. (Elaeocarpaceae) and Anneslea fragrans Wall. (Theaceae). Hide abstract

Caws M, Thwaites GE, Duy PM, Tho DQ, Lan NT, Hoa DV, Chau TT, Huyen MN et al. 2007. Molecular analysis of Mycobacterium tuberculosis causing multidrug-resistant tuberculosis meningitis. Int J Tuberc Lung Dis, 11 (2), pp. 202-208. Read abstract

Tertiary referral hospitals in southern Vietnam. Hide abstract

Hawn TR, Misch EA, Dunstan SJ, Thwaites GE, Lan NT, Quy HT, Chau TT, Rodrigues S et al. 2007. A common human TLR1 polymorphism regulates the innate immune response to lipopeptides. Eur J Immunol, 37 (8), pp. 2280-2289. Read abstract | Read more

Toll-like receptors (TLR) are critical mediators of the immune response to pathogens and human polymorphisms in this gene family regulate inflammatory pathways and are associated with susceptibility to infection. Lipopeptides are present in a wide variety of microbes and stimulate immune responses through TLR1/2 or TLR2/6 heterodimers. It is not currently known whether polymorphisms in TLR1 regulate the innate immune response. We stimulated human whole blood with triacylated lipopeptide, a ligand for TLR1/2 heterodimers, and found substantial inter-individual variation in the immune response. We sequenced the coding region of TLR1 and found a non-synonymous polymorphism, I602S (base pair T1805G), that regulated signalling. In comparison to TLR1_602S, the 602I variant mediated substantially greater basal and lipopeptide-induced NF-kappaB signalling in transfected HEK293 cells. These signalling differences among TLR1 variants were also found with stimulation by extracts of Mycobacterium tuberculosis. Furthermore, individuals with the 602II genotype produced substantially more IL-6 than those with the 602SS variant in a lipopeptide-stimulated whole-blood cytokine assay. Together, these observations demonstrate that variation in the inflammatory response to bacterial lipopeptides is regulated by a common TLR1 transmembrane domain polymorphism that could potentially impact the innate immune response and clinical susceptibility to a wide spectrum of pathogens. Hide abstract

Pandit A, Arjyal A, Day JN, Paudyal B, Dangol S, Zimmerman MD, Yadav B, Stepniewska K et al. 2007. An open randomized comparison of gatifloxacin versus cefixime for the treatment of uncomplicated enteric fever. PLoS One, 2 (6), pp. e542. Read abstract | Read more

To assess the efficacy of gatifloxacin versus cefixime in the treatment of uncomplicated culture positive enteric fever. Hide abstract

Tang CT, Nguyen DT, Ngo TH, Nguyen TM, Le VT, To SD, Lindsay J, Nguyen TD et al. 2007. An outbreak of severe infections with community-acquired MRSA carrying the Panton-Valentine leukocidin following vaccination. PLoS One, 2 (9), pp. e822. Read abstract | Read more

Infections with community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) are emerging worldwide. We investigated an outbreak of severe CA-MRSA infections in children following out-patient vaccination. Hide abstract

Schultsz C, Vien LEM, Campbell JI, Chau NV, Diep TS, Hoang NV, Nga TT, Savelkoul P et al. 2007. Changes in the nasal carriage of drug-resistant Streptococcus pneumoniae in urban and rural Vietnamese schoolchildren. Trans R Soc Trop Med Hyg, 101 (5), pp. 484-492. Read abstract | Read more

Studying the antimicrobial drug resistance of nasopharyngeal or nasal carriage isolates of Streptococcus pneumoniae in children is likely to have predictive potential for invasive isolates. Streptococcus pneumoniae nasal carriage was studied in 1422 Vietnamese children. Forty-six percent of 536 isolates showed reduced susceptibility to penicillin and 7% showed intermediate susceptibility to ceftriaxone; and 50% of 518 isolates showed resistance to erythromycin. All isolates were sensitive to levofloxacin and gatifloxacin. Urban and suburban children were significantly more likely to carry drug-resistant isolates than rural children. Rates of non-susceptibility to penicillin and erythromycin increased significantly in the rural province Khanh Hoa in 2003/2004 compared with rates obtained in 1997. An emerging clone of penicillin non-susceptible S. pneumoniae of serogroup 15 was identified, which was widely distributed in addition to the pandemic clones Spain(23F)-1 and Taiwan(19F)-14. Although resistance to fluoroquinolones was not observed, 6 (18%) of 34 isolates had a Lys137Asn mutation in the parC gene. This study shows that drug resistance is increasing in carriage isolates of S. pneumoniae in rural areas in Vietnam owing to spread of pandemic and emerging resistant clones. Hide abstract

Nguyen TH, Tran TH, Thwaites G, Ly VC, Dinh XS, Ho Dang TN, Dang QT, Nguyen DP et al. 2007. Dexamethasone in Vietnamese adolescents and adults with bacterial meningitis. N Engl J Med, 357 (24), pp. 2431-2440. Read abstract | Read more

It is uncertain whether all adults with bacterial meningitis benefit from treatment with adjunctive dexamethasone. Hide abstract

Caws M, Dang TM, Torok E, Campbell J, Do DA, Tran TH, Nguyen VV, Nguyen TC, Farrar J. 2007. Evaluation of the MODS culture technique for the diagnosis of tuberculous meningitis. PLoS One, 2 (11), pp. e1173. Read abstract | Read more

Tuberculous meningitis (TBM) is a devastating condition. The rapid instigation of appropraite chemotherapy is vital to reduce morbidity and mortality. However rapid diagnosis remains elusive; smear microscopy has extremely low sensitivity on cerebrospinal fluid (CSF) in most laboratories and PCR requires expertise with advanced infrastructure and has sensitivity of only around 60% under optimal conditions. Neither technique allows for the microbiological isolation of M. tuberculosis and subsequent drug susceptibility testing. We evaluated the recently developed microscopic observation drug susceptibility (MODS) assay format for speed and accuracy in diagnosing TBM. Hide abstract

Dong T, Moran E, Vinh Chau N, Simmons C, Luhn K, Peng Y, Wills B, Phuong Dung N et al. 2007. High pro-inflammatory cytokine secretion and loss of high avidity cross-reactive cytotoxic T-cells during the course of secondary dengue virus infection. PLoS One, 2 (12), pp. e1192. Read abstract | Read more

Dengue is one of the most important human diseases transmitted by an arthropod vector and the incidence of dengue virus infection has been increasing - over half the world's population now live in areas at risk of infection. Most infections are asymptomatic, but a subset of patients experience a potentially fatal shock syndrome characterised by plasma leakage. Severe forms of dengue are epidemiologically associated with repeated infection by more than one of the four dengue virus serotypes. Generally attributed to the phenomenon of antibody-dependent enhancement, recent observations indicate that T-cells may also influence disease phenotype. Hide abstract

Simmons CP, Bernasconi NL, Suguitan AL, Mills K, Ward JM, Chau NV, Hien TT, Sallusto F et al. 2007. Prophylactic and therapeutic efficacy of human monoclonal antibodies against H5N1 influenza. PLoS Med, 4 (5), pp. e178. Read abstract | Read more

New prophylactic and therapeutic strategies to combat human infections with highly pathogenic avian influenza (HPAI) H5N1 viruses are needed. We generated neutralizing anti-H5N1 human monoclonal antibodies (mAbs) and tested their efficacy for prophylaxis and therapy in a murine model of infection. Hide abstract

Parry CM, Ho VA, Phuong LET, Bay PV, Lanh MN, Tung LET, Tham NT, Wain J, Hien TT, Farrar JJ. 2007. Randomized controlled comparison of ofloxacin, azithromycin, and an ofloxacin-azithromycin combination for treatment of multidrug-resistant and nalidixic acid-resistant typhoid fever. Antimicrob Agents Chemother, 51 (3), pp. 819-825. Read abstract | Read more

Isolates of Salmonella enterica serovar Typhi that are multidrug resistant (MDR, resistant to chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) and have reduced susceptibility to fluoroquinolones (nalidixic acid resistant, Na(r)) are common in Asia. The optimum treatment for infections caused by such isolates is not established. This study compared different antimicrobial regimens for the treatment of MDR/Na(r) typhoid fever. Vietnamese children and adults with uncomplicated typhoid fever were entered into an open randomized controlled trial. Ofloxacin (20 mg/kg of body weight/day for 7 days), azithromycin (10 mg/kg/day for 7 days), and ofloxacin (15 mg/kg/day for 7 days) combined with azithromycin (10 mg/kg/day for the first 3 days) were compared. Of the 241 enrolled patients, 187 were eligible for analysis (186 S. enterica serovar Typhi, 1 Salmonella enterica serovar Paratyphi A). Eighty-seven percent (163/187) of the patients were children; of the S. enterica serovar Typhi isolates, 88% (165/187) were MDR and 93% (173/187) were Na(r). The clinical cure rate was 64% (40/63) with ofloxacin, 76% (47/62) with ofloxacin-azithromycin, and 82% (51/62) with azithromycin (P = 0.053). The mean (95% confidence interval [CI]) fever clearance time for patients treated with azithromycin (5.8 days [5.1 to 6.5 days]) was shorter than that for patients treated with ofloxacin-azithromycin (7.1 days [6.2 to 8.1 days]) and ofloxacin (8.2 days [7.2 to 9.2 days]) (P < 0.001). Positive fecal carriage immediately posttreatment was detected in 19.4% (12/62) of patients treated with ofloxacin, 6.5% (4/62) of those treated with the combination, and 1.6% (1/62) of those treated with azithromycin (P = 0.006). Both antibiotics were well tolerated. Uncomplicated typhoid fever due to isolates of MDR S. enterica serovar Typhi with reduced susceptibility to fluoroquinolones (Na(r)) can be successfully treated with a 7-day course of azithromycin. Hide abstract

Thwaites GE, Hien TT, Farrar JJ. 2007. Reply to "Dr D Dhasmana and Dr R Davidson: Multi-drug resistant tuberculous meningitis" JOURNAL OF INFECTION, 54 (2), pp. 206-206. | Read more

Török ME, Nghia HD, Chau TT, Mai NT, Thwaites GE, Stepniewska K, Farrar JJ. 2007. Validation of a diagnostic algorithm for adult tuberculous meningitis. Am J Trop Med Hyg, 77 (3), pp. 555-559. Read abstract

Tuberculous meningitis (TBM) remains difficult to diagnose. We prospectively evaluated a diagnostic algorithm for TBM in 205 HIV-negative patients with meningitis and a low CSF glucose. Patients were classified as having TBM or bacterial meningitis (BM) by two diagnostic methods: logistic regression method (LRM) and classification and regression tree (CART). We performed analyses of TBM versus BM and TBM versus non-TBM in all patients and in patients with microbiologically confirmed diagnoses. Diagnostic sensitivities for TBM were 99% (LRM) and 87% (CART). For BM, diagnostic sensitivities were 81.5% (LRM) and 86.5% (CART) in the primary analysis and 86.5% (LRM) and 74% (CART) in the secondary analysis. In microbiologically confirmed cases, similar rates were achieved. These figures are superior to microbiological confirmation rates in routine laboratories and support the use of this algorithm in high-prevalence TB settings with limited diagnostic facilities. Validation in an HIV-endemic setting is required. Hide abstract

Schünemann HJ, Hill SR, Kakad M, Bellamy R, Uyeki TM, Hayden FG, Yazdanpanah Y, Beigel J et al. 2007. WHO Rapid Advice Guidelines for pharmacological management of sporadic human infection with avian influenza A (H5N1) virus. Lancet Infect Dis, 7 (1), pp. 21-31. Read abstract | Read more

Recent spread of avian influenza A (H5N1) virus to poultry and wild birds has increased the threat of human infections with H5N1 virus worldwide. Despite international agreement to stockpile antivirals, evidence-based guidelines for their use do not exist. WHO assembled an international multidisciplinary panel to develop rapid advice for the pharmacological management of human H5N1 virus infection in the current pandemic alert period. A transparent methodological guideline process on the basis of the Grading Recommendations, Assessment, Development and Evaluation (GRADE) approach was used to develop evidence-based guidelines. Our development of specific recommendations for treatment and chemoprophylaxis of sporadic H5N1 infection resulted from the benefits, harms, burden, and cost of interventions in several patient and exposure groups. Overall, the quality of the underlying evidence for all recommendations was rated as very low because it was based on small case series of H5N1 patients, on extrapolation from preclinical studies, and high quality studies of seasonal influenza. A strong recommendation to treat H5N1 patients with oseltamivir was made in part because of the severity of the disease. Similarly, strong recommendations were made to use neuraminidase inhibitors as chemoprophylaxis in high-risk exposure populations. Emergence of other novel influenza A viral subtypes with pandemic potential, or changes in the pathogenicity of H5N1 virus strains, will require an update of these guidelines and WHO will be monitoring this closely. Hide abstract

German AC, Myint KS, Mai NT, Pomeroy I, Phu NH, Tzartos J, Winter P, Collett J et al. 2006. A preliminary neuropathological study of Japanese encephalitis in humans and a mouse model. Trans R Soc Trop Med Hyg, 100 (12), pp. 1135-1145. Read abstract | Read more

Japanese encephalitis virus is a mosquito-borne flavivirus that causes approximately 10000 deaths annually in Asia. After a brief viraemia, the virus enters the central nervous system, but the means of crossing the blood-brain barrier is uncertain. We used routine histological staining, immunohistology and electron microscopy to examine brain material from four fatal human cases, and made comparisons with material from a mouse model. In human material there was oedema, perivascular inflammation, haemorrhage, microglial nodules and acellular necrotic foci, as has been described previously. In addition, there was new evidence suggestive of viral replication in the vascular endothelium, with endothelial cell damage; this included occasional viral antigen staining, uneven binding of the vascular endothelial cells to Ulex europaeus agglutinin I and ultrastructural changes. Viral antigen was also found in neurons. There was an active astrocytic response, as shown by glial fibrillary acidic protein staining, and activation of microglial cells was demonstrated by an increase in major histocompatibility complex class II expression. Similar inflammatory infiltrates and a microglial reaction were observed in mouse brain tissue. In addition, beta-amyloid precursor protein staining indicated impaired axonal transport. Whether these findings are caused by viral replication in the vascular endothelium or the immune response merits further investigation. Hide abstract

Flohr C, Tuyen LN, Lewis S, Quinnell R, Minh TT, Liem HT, Campbell J, Pritchard D et al. 2006. Poor sanitation and helminth infection protect against skin sensitization in Vietnamese children: A cross-sectional study. J Allergy Clin Immunol, 118 (6), pp. 1305-1311. Read abstract | Read more

Geohelminth infection and poor hygiene may be protective against allergic sensitization. Hide abstract

Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S, Chinh NT, Le TA, Acosta CJ, Farrar J, Dougan G, Achtman M. 2006. Evolutionary history of Salmonella typhi. Science, 314 (5803), pp. 1301-1304. Read abstract | Read more

For microbial pathogens, phylogeographic differentiation seems to be relatively common. However, the neutral population structure of Salmonella enterica serovar Typhi reflects the continued existence of ubiquitous haplotypes over millennia. In contrast, clinical use of fluoroquinolones has yielded at least 15 independent gyrA mutations within a decade and stimulated clonal expansion of haplotype H58 in Asia and Africa. Yet, antibiotic-sensitive strains and haplotypes other than H58 still persist despite selection for antibiotic resistance. Neutral evolution in Typhi appears to reflect the asymptomatic carrier state, and adaptive evolution depends on the rapid transmission of phenotypic changes through acute infections. Hide abstract

Caws M, Thwaites G, Stepniewska K, Nguyen TN, Nguyen TH, Nguyen TP, Mai NT, Phan MD et al. 2006. Beijing genotype of Mycobacterium tuberculosis is significantly associated with human immunodeficiency virus infection and multidrug resistance in cases of tuberculous meningitis. J Clin Microbiol, 44 (11), pp. 3934-3939. Read abstract | Read more

Multidrug-resistant tuberculous meningitis is fatal without rapid diagnosis and use of second-line therapy. It is more common in human immunodeficiency virus (HIV)-positive patients. Beijing genotype strains of Mycobacterium tuberculosis are associated with drug resistance, particularly multidrug resistance, and their prevalence is increasing worldwide. The prevalence of Beijing genotype strains among Mycobacterium tuberculosis isolates from the cerebrospinal fluid of HIV-positive (n = 35) and HIV-negative (n = 187) patients in Ho Chi Minh City was determined. The Beijing genotype was significantly associated with HIV status (odds ratio [OR] = 2.95 [95% confidence interval {CI}, 1.38 to 6.44]; P = 0.016), resistance to any drug (OR = 3.34 [95% CI, 1.87 to 5.95]; P < 0.001) and multidrug resistance (Fisher's exact test; P = 0.001). The association of the Beijing genotype with drug resistance was independent of HIV status. This is the first report of Beijing genotype association with HIV status, which may be an association unique to tuberculous meningitis. Hide abstract

Popper S, Simmons CP, Dolecek C, Chau TNB, Griffiths M, Dung NTP, Long TH, Hoang DM et al. 2006. Gene expression programs in adults with acute dengue infections AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 75 (5), pp. 290-290.

Hoang LT, Hibberd ML, Farrar J, Simmons CP. 2006. Global gene expression profiles during acute dengue revealed by microarray analysis AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 75 (5), pp. 290-290.

Flohr C, Tuyen LN, Lewis S, Quinnell R, Minh TT, Liem HT, Campbell J, Pritchard D et al. 2006. Poor sanitation and helminth infection protect against skin sensitization in Vietnamese children: A cross-sectional study AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 75 (5), pp. 321-321.

Nguyen D, Dong T, Nguyen VVC, Nguyen MD, Wills B, Rowland-Jones S, Farrar J, Simmons C. 2006. Spectrum and kinetic of T cell responses to dengue virus epitopes and the influence of hla polymorphisms in dengue disease pathogenesis AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 75 (5), pp. 289-290.

Qureshi NR, Hien TT, Farrar J, Gleeson FV. 2006. The radiologic manifestations of H5N1 avian influenza. J Thorac Imaging, 21 (4), pp. 259-264. Read abstract | Read more

Avian influenza is caused by the H5N1 subtype of the influenza A virus. Human transmission is either directly through close contact with infected birds usually poultry or their secretions. To date 178 people throughout South East Asia have been infected with 85 deaths. Patients usually present with a rapidly progressive pneumonia that can result in respiratory failure and acute respiratory distress syndrome. The chest radiograph therefore remains the most convenient and accessible imaging modality. Studies have shown that most radiographs are abnormal at the time of presentation with multifocal consolidation the commonest radiographic finding. During the course of disease, pleural effusions and cavitation can also develop. Consolidation that involves > or = 4 zones on presentation or at day 7 after the onset of symptoms and subsequent development of acute respiratory distress syndrome are generally associated with an adverse outcome. Chest CT examinations performed during the convalescent period have demonstrated persistent ground glass attenuation and segmental consolidation. Additional features included pseudocavitation, pneumatocoele formation, lymphadenopathy, and centrilobular nodules. Overall the appearances are suggestive of mild fibrosis. Hide abstract

Thwaites CL, Yen LM, Loan HT, Thuy TT, Thwaites GE, Stepniewska K, Soni N, White NJ, Farrar JJ. 2006. Magnesium sulphate for treatment of severe tetanus: a randomised controlled trial. Lancet, 368 (9545), pp. 1436-1443. Read abstract | Read more

The most common cause of death in individuals with severe tetanus in the absence of mechanical ventilation is spasm-related respiratory failure, whereas in ventilated patients it is tetanus-associated autonomic dysfunction. Our aim was to determine whether continuous magnesium sulphate infusion reduces the need for mechanical ventilation and improves control of muscle spasms and autonomic instability. Hide abstract

Hawn TR, Dunstan SJ, Thwaites GE, Simmons CP, Thuong NT, Lan NT, Quy HT, Chau TT et al. 2006. A polymorphism in Toll-interleukin 1 receptor domain containing adaptor protein is associated with susceptibility to meningeal tuberculosis. J Infect Dis, 194 (8), pp. 1127-1134. Read abstract | Read more

Although meningitis is the most severe form of infection caused by Mycobacterium tuberculosis, the immunopathogenesis of this disease is poorly understood. We tested the hypothesis that polymorphisms in Toll-interleukin 1 receptor domain containing adaptor protein (TIRAP), an adaptor protein that mediates signals from Toll-like receptors activated by mycobacteria, are associated with susceptibility to tuberculosis (TB). Hide abstract

Lindegårdh N, Hien TT, Farrar J, Singhasivanon P, White NJ, Day NP. 2006. A simple and rapid liquid chromatographic assay for evaluation of potentially counterfeit Tamiflu. J Pharm Biomed Anal, 42 (4), pp. 430-433. Read abstract | Read more

A simple and rapid liquid chromatographic assay for the evaluation of potentially counterfeit oseltamivir (Tamiflu has been developed and assessed. The assay uses approximately 1mg Tamiflu powder when used for authentication and content estimate. The procedure was validated using 50 replicates analysed during five independent series with a total R.S.D. of 11.2%. The assay can also be used to monitor the exact content of oseltamivir in Tamiflu capsules. One Tamiflu capsule was transferred to a 250mL volumetric flask and 150mL water was added. The flask was placed in an ultrasonic bath at 40 degrees C for 20min to dissolve the capsule. The solution was allowed to cool to room temperature before the flask was filled up to the mark (250mL). A small aliquot was centrifuged and then directly injected into the LC-system for quantification. Oseltamivir was analysed by liquid chromatography with UV detection on a Hypersil Gold column (150mmx4.6mm) using a mobile phase containing methanol-phosphate buffer (pH 2.5; 0.1M) (50:50, v/v) at a flow rate of 1.0mL/min. The assay was implemented for the analysis of Tamiflu purchased over the Internet and at local pharmacies in Thailand and Vietnam. Hide abstract

de Jong MD, Simmons CP, Thanh TT, Hien VM, Smith GJ, Chau TN, Hoang DM, Chau NV et al. 2006. Fatal outcome of human influenza A (H5N1) is associated with high viral load and hypercytokinemia. Nat Med, 12 (10), pp. 1203-1207. Read abstract | Read more

Avian influenza A (H5N1) viruses cause severe disease in humans, but the basis for their virulence remains unclear. In vitro and animal studies indicate that high and disseminated viral replication is important for disease pathogenesis. Laboratory experiments suggest that virus-induced cytokine dysregulation may contribute to disease severity. To assess the relevance of these findings for human disease, we performed virological and immunological studies in 18 individuals with H5N1 and 8 individuals infected with human influenza virus subtypes. Influenza H5N1 infection in humans is characterized by high pharyngeal virus loads and frequent detection of viral RNA in rectum and blood. Viral RNA in blood was present only in fatal H5N1 cases and was associated with higher pharyngeal viral loads. We observed low peripheral blood T-lymphocyte counts and high chemokine and cytokine levels in H5N1-infected individuals, particularly in those who died, and these correlated with pharyngeal viral loads. Genetic characterization of H5N1 viruses revealed mutations in the viral polymerase complex associated with mammalian adaptation and virulence. Our observations indicate that high viral load, and the resulting intense inflammatory responses, are central to influenza H5N1 pathogenesis. The focus of clinical management should be on preventing this intense cytokine response, by early diagnosis and effective antiviral treatment. Hide abstract

Thuong NT, Dunstan SJ, Dung NM, Charlieu JP, Loan HT, Wills B, Solomon T, Farrar JJ. 2006. Polymorphisms of the gene coding for copper/zinc superoxide dismutase (SOD1) in patients with Japanese encephalitis. Ann Trop Med Parasitol, 100 (7), pp. 631-636. Read abstract | Read more

Japanese encephalitis is the commonest form of encephalitis globally. Most cases develop characteristic encephalitis but some also present with flaccid paralysis. The paralysis is secondary to damage at the alpha motor neurone, the site that is also damaged in amyotrophic lateral sclerosis (ALS). The gene coding for superoxide dismutase 1 (SOD1) is thought to be involved in ALS and may also be linked to susceptibility to Japanese encephalitis. To investigate this possibility, polymorphisms in the SOD1 gene were investigated, in 61 cases of Japanese encephalitis, 61 matched controls and 171 population controls, in Vietnam. Novel polymorphisms, found only in three of the cases and one of the population controls, may be involved with susceptibility to Japanese encephalitis and potentially to other flavivirus infections that lead to damage to the cells of the anterior horn. Further research on this possible association is required. Hide abstract

Lindegardh N, Davies GR, Tran TH, Farrar J, Singhasivanon P, Day NP, White NJ. 2006. Rapid degradation of oseltamivir phosphate in clinical samples by plasma esterases. Antimicrob Agents Chemother, 50 (9), pp. 3197-3199. Read abstract | Read more

The anti-influenza drug oseltamivir is an ester prodrug activated by hepatic carboxylesterases. Plasma esterases also convert up to 31.8% of the parent compound to the active metabolite after 4 h ex vivo, with wide interindividual variation. This source of error is removed by adding the esterase inhibitor dichlorvos to blood collection tubes. Hide abstract

Deen JL, Harris E, Wills B, Balmaseda A, Hammond SN, Rocha C, Dung NM, Hung NT, Hien TT, Farrar JJ. 2006. The WHO dengue classification and case definitions: time for a reassessment. Lancet, 368 (9530), pp. 170-173. | Read more

Smith GJ, Naipospos TS, Nguyen TD, de Jong MD, Vijaykrishna D, Usman TB, Hassan SS, Nguyen TV et al. 2006. Evolution and adaptation of H5N1 influenza virus in avian and human hosts in Indonesia and Vietnam. Virology, 350 (2), pp. 258-268. Read abstract | Read more

Highly pathogenic avian influenza virus H5N1 is endemic in poultry in East and Southeast Asia with disease outbreaks recently spreading to parts of central Asia, Europe and Africa. Continued interspecies transmission to humans has been reported in Vietnam, Thailand, Cambodia, Indonesia and China, causing pandemic concern. Here, we genetically characterize 82 H5N1 viruses isolated from poultry throughout Indonesia and Vietnam and 11 human isolates from southern Vietnam together with sequence data available in public databases to address questions relevant to virus introduction, endemicity and evolution. Phylogenetic analysis shows that all viruses from Indonesia form a distinct sublineage of H5N1 genotype Z viruses suggesting this outbreak likely originated from a single introduction that spread throughout the country during the past two years. Continued virus activities in Indonesia were attributed to transmission via poultry movement within the country rather than through repeated introductions by bird migration. Within Indonesia and Vietnam, H5N1 viruses have evolved over time into geographically distinct groups within each country. Molecular analysis of the H5N1 genotype Z genome shows that only the M2 and PB1-F2 genes were under positive selection, suggesting that these genes might be involved in adaptation of this virus to new hosts following interspecies transmission. At the amino acid level 12 residues were under positive selection in those genotype Z viruses, in the HA and PB1-F2 proteins. Some of these residues were more frequently observed in human isolates than in avian isolates and are related to viral antigenicity and receptor binding. Our study provides insight into the ongoing evolution of H5N1 influenza viruses that are transmitting in diverse avian species and at the interface between avian and human hosts. Hide abstract

Caws M, Duy PM, Tho DQ, Lan NT, Hoa DV, Farrar J. 2006. Mutations prevalent among rifampin- and isoniazid-resistant Mycobacterium tuberculosis isolates from a hospital in Vietnam. J Clin Microbiol, 44 (7), pp. 2333-2337. Read abstract | Read more

Vietnam is ranked 13th among the WHO list of 22 high-burden countries, based upon estimated total number of tuberculosis cases. Despite having a model national tuberculosis program, consistently achieving and exceeding WHO targets for detection and cure, drug-resistant and multidrug-resistant tuberculosis cases continue to rise. Rapid multidrug-resistant tests applicable in this setting, coupled with effective treatment regimens, would be a useful tool in reversing this trend, allowing early identification of patients with multidrug-resistant tuberculosis and avoiding resistance-amplifying regimens. Sequencing of consecutive isolates identified by the National Tuberculosis Program showed 89% of isoniazid-resistant isolates could be detected by targeting just 2 codons, katG 315 and -15C-->T in the inhA promoter, while rifampin resistance will be more complex to detect, with many different mutation and insertion events in rpoB. The most prevalent rifampin resistance-conferring mutations, as in other countries, were in rpoB codons 531 (43%), 526 (31%), and 516 (15%). However, a hybridization-based resistance test with probes targeting the 5 most common mutations would only detect 78% of rifampin-resistant isolates. Overall, these data suggest that rifampin resistance may be used as a surrogate marker for multidrug-resistant tuberculosis and that a sensitivity of between 70 to 80% may be possible for rapid molecular detection of multidrug-resistant tuberculosis in this setting. Hide abstract

Thwaites CL, Yen LM, Cordon SM, Binh NT, T N, Nga N, White NJ, Soni N, MacDonald IA, Farrar JJ. 2006. Urinary catecholamine excretion in tetanus. Anaesthesia, 61 (4), pp. 355-359. Read abstract | Read more

Imperfect understanding of the pathophysiology of tetanus has limited therapeutic advances. Autonomic disturbance is a major cause of mortality and is believed to be associated with catecholamine release, predominantly norepinephrine. We measured epinephrine and norepinephrine concentrations in 24-h urine collections from tetanus and critically ill patients suffering from other severe diseases. In patients with severe tetanus, mean (SD) epinephrine was 164.18 (129.37) nmol x day(-1) compared with 45.18 (37.74) nmol x day(-1) in mild-moderate disease (p = 0.008). In the severe group, mean (SD) norepinephrine was 411.64 (208.5), and 121.00 (81.81) nmol x day(-1) in moderately ill patients (p < 0.001). Compared with critically ill control patients, median epinephrine was 331.77 in tetanus patients and 89.70 nmol x day(-1) in controls (p < 0.001). Median norepinephrine concentration was 788.02 nmol x day(-1) in tetanus and 300.05 nmol x day(-1) in control patients, p = 0.006. The study finds a novel result of increased epinephrine excretion in tetanus and confirms that catecholamine excretion in tetanus exceeds that in other critically ill patients. These results should be considered in designing more effective therapeutic strategies. Hide abstract

de Jong MD, Hien TT, Farrar J. 2006. Oseltamivir resistance in influenza A (H5N1) infection - Reply NEW ENGLAND JOURNAL OF MEDICINE, 354 (13), pp. 1424-1424.

Hieu NT, Gainsborough M, Simpson JA, Thuy NT, Hang NN, Taylor AM, Ghebremeskel K, Crawford M, Golfetto I, Dubowitz L, Farrar J. 2006. Neurological status of low-risk Vietnamese newborns: a comparison with a British newborn cohort. J Health Popul Nutr, 24 (1), pp. 57-63. Read abstract

A shortened version of the Dubowitz newborn neurological examination, recently reassessed in rural Thailand, was applied to a group of 58 Vietnamese newborns. The aim was to establish the neurological status of newborns in this population for use in further studies and to compare with groups previously studied. Compared to the original British cohort, the Vietnamese newborns showed significantly lower scores in 10 of 25 items, including several related to truncal tone. Evidence was sought of thiamine and long-chain fatty acid deficiency as a possible cause for these findings, but no correlation was found between the neurological status and the maternal or infant blood levels of these nutritional indicators. The findings suggest that the neurological status of low-risk Vietnamese newborns appears to lie between that of British newborns and those ethnic minority Karen newborns in refugee camps on the Thai-Burmese border tested previously. Although no specific nutritional cause has been identified in the study, the findings may still reflect sub-optimal intake of some important nutrients. Hide abstract

Thwaites CL, Yen LM, Glover C, Tuan PQ, Nga NT, Parry J, Loan HT, Bethell D et al. 2006. Predicting the clinical outcome of tetanus: the tetanus severity score. Trop Med Int Health, 11 (3), pp. 279-287. Read abstract | Read more

To create a new tetanus score and compare it with the Phillips and Dakar scores. Hide abstract

Simmons CP, Thwaites GE, Quyen NT, Torok E, Hoang DM, Chau TT, Mai PP, Lan NT et al. 2006. Pretreatment intracerebral and peripheral blood immune responses in Vietnamese adults with tuberculous meningitis: diagnostic value and relationship to disease severity and outcome. J Immunol, 176 (3), pp. 2007-2014. Read abstract

Tuberculous meningitis (TBM) is the most devastating form of tuberculosis. Both intracerebral and peripheral blood immune responses may be relevant to pathogenesis, diagnosis, and outcome. In this study, the relationship between pretreatment host response, disease phenotype, and outcome in Vietnamese adults with TBM was examined. Before treatment, peripheral blood IFN-gamma ELISPOT responses to the Mycobacterium tuberculosis Ags ESAT-6, CFP-10, and purified protein derivative (PPD) were a poor diagnostic predictor of TBM. Cerebrospinal fluid IL-6 concentrations at presentation were independently associated with severe disease presentation, suggesting an immunological correlate of neurological damage before treatment. Surprisingly however, elevated cerebrospinal fluid inflammatory cytokines were not associated with death or disability in HIV-negative TBM patients at presentation. HIV coinfection attenuated multiple cerebrospinal fluid inflammatory indices. Low cerebrospinal fluid IFN-gamma concentrations were independently associated with death in HIV-positive TBM patients, implying that IFN-gamma contributes to immunity and survival. Collectively, these results reveal the effect of HIV coinfection on the pathogenesis of TBM and suggest that intracerebral immune responses, at least in HIV-negative cases, may not be as intimately associated with disease outcome as previously thought. Hide abstract

Canard B, Stephenson J, Hombach J, Keller T, Halstead S, Heinz FX, Evans TG, Gubler DJ, Farrar J, Zinkernagel R. 2006. Discussion Novartis Foundation Symposium, 277 pp. 201-205.

Evans TG, Holmes E, Young P, Gubler DJ, Harris E, Halstead S, Padmanabhan RP, Rice C et al. 2006. Discussion Novartis Foundation Symposium, 277 pp. 187-192.

Rice C, Hibberd M, Gu F, Harris E, Jans DA, Farrar J, Vasudevan S, Evans TG, Holmes E, Fairlie D, Keller T. 2006. Discussion Novartis Foundation Symposium, 277 pp. 214-217.

Harris E, Flamand M, Canard B, Stephenson J, Farrar J, Zinkernagel R, Satchidanandam V, Malasit P et al. 2006. Discussion Novartis Foundation Symposium, 277 pp. 247-250.

Young P, Keller T, Padmanabhan RP, Fairlie D, Hibberd M, Rice C, Canard B, Vasudevan S et al. 2006. Discussion Novartis Foundation Symposium, 277 pp. 114-119.

Harris E, Screaton G, Farrar J, Hombach J, Halstead S, Rice C, Holmes E, Satchidanandam V et al. 2006. Discussion Novartis Foundation Symposium, 277 pp. 171-176.

Pandit A, Arjyal A, Farrar J, Basnyat B. 2006. Nepal Practical Neurology, 6 (2), pp. 129-133. | Read more

Thuong NTT, Dunstan SJ, Dung NM, Charlieu J-P, Loan HT, Wills B, Solomon T, Farrar JJ. 2006. Polymorphisms of the gene coding for copper/zinc superoxide dismutase (SOD1) in patients with Japanese encephalitis Annals of Tropical Medicine and Parasitology, 100 (7), pp. 631-636. Read abstract | Read more

Japanese encephalitis is the commonest form of encephalitis globally. Most cases develop characteristic encephalitis but some also present with flaccid paralysis. The paralysis is secondary to damage at the alpha motor neurone, the site that is also damaged in amyotrophic lateral sclerosis (ALS). The gene coding for superoxide dismutase 1 (SOD1) is thought to be involved in ALS and may also be linked to susceptibility to Japanese encephalitis. To investigate this possibility, polymorphisms in the SOD1 gene were investigated, in 61 cases of Japanese encephalitis, 61 matched controls and 171 population controls, in Vietnam. Novel polymorphisms, found only in three of the cases and one of the population controls, may be involved with susceptibility to Japanese encephalitis and potentially to other flavivirus infections that lead to damage to the cells of the anterior horn. Further research on this possible association is required. © 2006 The Liverpool School of Tropical Medicine. Hide abstract

Maskey AP, Day JN, Phung QT, Thwaites GE, Campbell JI, Zimmerman M, Farrar JJ, Basnyat B. 2006. Salmonella enterica serovar Paratyphi A and S. enterica serovar Typhi cause indistinguishable clinical syndromes in Kathmandu, Nepal. Clin Infect Dis, 42 (9), pp. 1247-1253. Read abstract | Read more

Enteric fever is a major global problem. Emergence of antibacterial resistance threatens to render current treatments ineffective. There is little research or public health effort directed toward Salmonella enterica serovar Paratyphi A, because it is assumed to cause less severe enteric fever than does S. enterica serovar Typhi. There are few data on which to base this assumption, little is known of the serovar's antibacterial susceptibilities, and there is no readily available tolerable vaccination. Hide abstract

De Jong MD, Tran TH, Farrar J. 2006. The authors reply [4] New England Journal of Medicine, 354 (13), pp. 1424-1424. | Read more

de Jong MD, Tran TT, Truong HK, Vo MH, Smith GJ, Nguyen VC, Bach VC, Phan TQ et al. 2005. Oseltamivir resistance during treatment of influenza A (H5N1) infection. N Engl J Med, 353 (25), pp. 2667-2672. Read abstract | Read more

Influenza A (H5N1) virus with an amino acid substitution in neuraminidase conferring high-level resistance to oseltamivir was isolated from two of eight Vietnamese patients during oseltamivir treatment. Both patients died of influenza A (H5N1) virus infection, despite early initiation of treatment in one patient. Surviving patients had rapid declines in the viral load to undetectable levels during treatment. These observations suggest that resistance can emerge during the currently recommended regimen of oseltamivir therapy and may be associated with clinical deterioration and that the strategy for the treatment of influenza A (H5N1) virus infection should include additional antiviral agents. Hide abstract

Thwaites GE, Duc Bang N, Huy Dung N, Thi Quy H, Thi Tuong Oanh D, Thi Cam Thoa N, Quang Hien N, Tri Thuc N et al. 2005. The influence of HIV infection on clinical presentation, response to treatment, and outcome in adults with Tuberculous meningitis. J Infect Dis, 192 (12), pp. 2134-2141. Read abstract | Read more

Tuberculous meningitis occurs more commonly in human immunodeficiency virus (HIV)-infected individuals than in HIV-uninfected individuals, but whether HIV infection alters the presentation and outcome of tuberculous meningitis is unknown. Hide abstract

Wills BA, Dung NM, Farrar JJ. 2005. Fluid solutions in dengue shock syndrome - Reply NEW ENGLAND JOURNAL OF MEDICINE, 353 (23), pp. 2511-2511.

Wills B, Dung NM, Loan HT, Tam DT, Thu TT, Minh LT, Diet TV, Hao NT et al. 2005. Fluid resuscitation for dengue shock syndrome - The evidence from formal randomised and blinded intervention trials in Vietnam AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 73 (6), pp. 361-361.

Tran CT, Dolecek C, Ochiai RLR, Campbell JI, Yang Y, Nguyen HMV, Bhutta ZA, Bhattacharya SK et al. 2005. Investigating the molecular mechanisms of nalidixic acid resistance and reduced susceptibility to fluoroquinolones in Salmonella typhi AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 73 (6), pp. 191-191.

Wills BA, Nguyen MD, Ha TL, Dong TH, Tran TN, Le TT, Tran VD, Nguyen TH et al. 2005. Comparison of three fluid solutions for resuscitation in dengue shock syndrome. N Engl J Med, 353 (9), pp. 877-889. Read abstract | Read more

Dengue shock syndrome is characterized by severe vascular leakage and disordered hemostasis and progresses to death in 1 to 5 percent of cases. Although volume replacement is recognized as the critical therapeutic intervention, World Health Organization management guidelines remain empirical rather than evidence-based. Hide abstract

House D, Chinh NT, Diep TS, Parry CM, Wain J, Dougan G, White NJ, Hien TT, Farrar JJ. 2005. Use of paired serum samples for serodiagnosis of typhoid fever. J Clin Microbiol, 43 (9), pp. 4889-4890. Read abstract | Read more

Using an enzyme-linked immunosorbent assay we demonstrate that, in adult patients with typhoid fever, the sensitivity of a serological test based on the detection of anti-lipopolysaccharide immunoglobulin G is increased when used with paired serum samples taken 1 week apart. Hide abstract

Medana IM, Lindert RB, Wurster U, Hien TT, Day NP, Phu NH, Mai NT, Chuong LV et al. 2005. Cerebrospinal fluid levels of markers of brain parenchymal damage in Vietnamese adults with severe malaria. Trans R Soc Trop Med Hyg, 99 (8), pp. 610-617. Read abstract | Read more

A retrospective study of cerebrospinal fluid (CSF) markers of brain parenchymal damage was conducted in Vietnamese adults with severe malaria. Three markers were analysed by immunoassays: the microtubule-associated protein tau, for degenerated axons; neuron-specific enolase (NSE), for neurons; and S100B for astrocytes. The mean concentration of tau proteins in the CSF was significantly raised in patients with severe malaria compared with controls (P=0.0003) as reported for other central nervous system diseases. By contrast, the mean concentration of NSE and S100B remained within the normal range. Tau levels were associated with duration of coma (P=0.004) and S100B was associated with convulsions (P=0.006). Concentrations of axonal and astrocyte degeneration markers also were associated with vital organ dysfunction. No association was found between the level of markers of brain parenchymal damage on admission and a fatal outcome. On admission to hospital, patients with severe malaria had biochemical evidence of brain parenchymal damage predominantly affecting axons. Hide abstract

Schultsz C, Dong VC, Chau NV, Le NT, Lim W, Thanh TT, Dolecek C, de Jong MD, Hien TT, Farrar J. 2005. Avian influenza H5N1 and healthcare workers. Emerg Infect Dis, 11 (7), pp. 1158-1159. | Read more

Thwaites GE, Lan NT, Dung NH, Quy HT, Oanh DT, Thoa NT, Hien NQ, Thuc NT et al. 2005. Effect of antituberculosis drug resistance on response to treatment and outcome in adults with tuberculous meningitis. J Infect Dis, 192 (1), pp. 79-88. Read abstract | Read more

Tuberculous meningitis (TBM) caused by Mycobacterium tuberculosis resistant to 1 or more antituberculosis drugs is an increasingly common clinical problem, although the impact on outcome is uncertain. Hide abstract

Simmons CP, Thwaites GE, Quyen NT, Chau TT, Mai PP, Dung NT, Stepniewska K, White NJ, Hien TT, Farrar J. 2005. The clinical benefit of adjunctive dexamethasone in tuberculous meningitis is not associated with measurable attenuation of peripheral or local immune responses. J Immunol, 175 (1), pp. 579-590. Read abstract

Outcome from tuberculous meningitis (TBM) is believed to be dependent on the severity of the intracerebral inflammatory response. We have recently shown that dexamethasone improved survival in adults with TBM and postulated that the clinical effect would be associated with a measurable systemic and intracerebral impact on immunological markers of inflammation. Prolonged inflammatory responses were detected in all TBM patients irrespective of treatment assignment (placebo or dexamethasone). The inflammatory response in the cerebrospinal fluid was characterized by a leukocytosis (predominantly CD3(+)CD4(+) T lymphocytes, phenotypically distinct from those in the peripheral blood), elevated concentrations of inflammatory and anti-inflammatory cytokines, chemokines, and evidence of prolonged blood-brain barrier dysfunction. Dexamethasone significantly modulated acute cerebrospinal fluid protein concentrations and marginally reduced IFN-gamma concentrations; other immunological and routine biochemical indices of inflammation were unaffected. Peripheral blood monocyte and T cell responses to Mycobacterium tuberculosis Ags were also unaffected. Dexamethasone does not appear to improve survival from TBM by attenuating immunological mediators of inflammation in the subarachnoid space or by suppressing peripheral T cell responses to mycobacterial Ags. These findings challenge previously held theories of corticosteroid action in this disease. An understanding of how dexamethasone acts in TBM may suggest novel and more effective treatment strategies. Hide abstract

Simmons CP, Dong T, Chau NV, Dung NT, Chau TN, Thao LETT, Dung NT, Hien TT, Rowland-Jones S, Farrar J. 2005. Early T-cell responses to dengue virus epitopes in Vietnamese adults with secondary dengue virus infections. J Virol, 79 (9), pp. 5665-5675. Read abstract | Read more

T-cell responses to dengue viruses may be important in both protective immunity and pathogenesis. This study of 48 Vietnamese adults with secondary dengue virus infections defined the breadth and magnitude of peripheral T-cell responses to 260 overlapping peptide antigens derived from a dengue virus serotype 2 (DV2) isolate. Forty-seven different peptides evoked significant gamma interferon enzyme-linked immunospot (ELISPOT) assay responses in 39 patients; of these, 34 peptides contained potentially novel T-cell epitopes. NS3 and particularly NS3200-324 were important T-cell targets. The breadth and magnitude of ELISPOT responses to DV2 peptides were independent of the infecting dengue virus serotype, suggesting that cross-reactive T cells dominate the acute response during secondary infection. Acute ELISPOT responses were weakly correlated with the extent of hemoconcentration in individual patients but not with the nadir of thrombocytopenia or overall clinical disease grade. NS3556-564 and Env414-422 were identified as novel HLA-A*24 and B*07-restricted CD8+ T-cell epitopes, respectively. Acute T-cell responses to natural variants of Env414-422 and NS3556-564 were largely cross-reactive and peaked during disease convalescence. The results highlight the importance of NS3 and cross-reactive T cells during acute secondary infection but suggest that the overall breadth and magnitude of the T-cell response is not significantly related to clinical disease grade. Hide abstract

Bishop AL, Baker S, Jenks S, Fookes M, Gaora PO, Pickard D, Anjum M, Farrar J, Hien TT, Ivens A, Dougan G. 2005. Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX). J Bacteriol, 187 (7), pp. 2469-2482. Read abstract | Read more

The divergence of Salmonella enterica and Escherichia coli is estimated to have occurred approximately 140 million years ago. Despite this evolutionary distance, the genomes of these two species still share extensive synteny and homology. However, there are significant differences between the two species in terms of genes putatively acquired via various horizontal transfer events. Here we report on the composition and distribution across the Salmonella genus of a chromosomal region designated SPI-10 in Salmonella enterica serovar Typhi and located adjacent to tRNA(leuX). We find that across the Salmonella genus the tRNA(leuX) region is a hypervariable hot spot for horizontal gene transfer; different isolates from the same S. enterica serovar can exhibit significant variation in this region. Many P4 phage, plasmid, and transposable element-associated genes are found adjacent to tRNA(leuX) in both Salmonella and E. coli, suggesting that these mobile genetic elements have played a major role in driving the variability of this region. Hide abstract

Dunstan SJ, Hawn TR, Hue NT, Parry CP, Ho VA, Vinh H, Diep TS, House D et al. 2005. Host susceptibility and clinical outcomes in toll-like receptor 5-deficient patients with typhoid fever in Vietnam. J Infect Dis, 191 (7), pp. 1068-1071. Read abstract | Read more

Toll-like receptor 5 (TLR5) mediates innate immune responses to bacterial pathogens by binding to flagellin. A polymorphism in the TLR5 gene introduces a premature stop codon (TLR5(392STOP)) that is associated with susceptibility to legionnaires disease. Here we investigated whether TLR5(392STOP) was associated with typhoid fever. The frequency of TLR5(392STOP) was not significantly different in 565 patients with typhoid fever and 281 ethnically matched control subjects. Furthermore, TLR5 deficiency had no measurable effect on a number of clinical parameters associated with typhoid fever, including fever clearance time, pathogen burden, disease severity, or age at acquisition of disease. TLR5 may not play an important role in TLR-stimulated innate immune responses to human infection with Salmonella enterica serovar Typhi. Initiation of these responses may rely on other TLRs that recognize different bacterial ligands. Hide abstract

Torok ME, Day JN, Hien TT, Farrar JJ. 2005. Immediate or deferred antiretroviral therapy for central nervous system opportunistic infections? AIDS, 19 (5), pp. 535-536. | Read more

de Jong MD, Van Cam B, Qui PT, Hien VM, Thanh TT, Hue NB, Beld M, Phuong LT et al. 2005. Brief report: Fatal avian influenza A (H5N1) in a child presenting with diarrhea followed by coma NEW ENGLAND JOURNAL OF MEDICINE, 352 (7), pp. 686-691. | Read more

de Jong MD, Bach VC, Phan TQ, Vo MH, Tran TT, Nguyen BH, Beld M, Le TP et al. 2005. Fatal avian influenza A (H5N1) in a child presenting with diarrhea followed by coma. N Engl J Med, 352 (7), pp. 686-691. Read abstract | Read more

In southern Vietnam, a four-year-old boy presented with severe diarrhea, followed by seizures, coma, and death. The cerebrospinal fluid contained 1 white cell per cubic millimeter, normal glucose levels, and increased levels of protein (0.81 g per liter). The diagnosis of avian influenza A (H5N1) was established by isolation of the virus from cerebrospinal fluid, fecal, throat, and serum specimens. The patient's nine-year-old sister had died from a similar syndrome two weeks earlier. In both siblings, the clinical diagnosis was acute encephalitis. Neither patient had respiratory symptoms at presentation. These cases suggest that the spectrum of influenza H5N1 is wider than previously thought. Hide abstract

Thwaites GE, Quy HT, Farrar JJ. 2005. Dexamethasone for tuberculous meningitis - Reply NEW ENGLAND JOURNAL OF MEDICINE, 352 (6), pp. 629-630.

Hien TT, Davis TME, Chuong LV, Ilett KF, Sinh DXT, Phu NH, Agus C, Chiswell GM, White NJ, Farrar J. 2005. Comparative pharmacokinetics of intramuscular artesunate and artemether in patients with severe Falciparum malaria (vol 11, pg 4234, 2004) ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 49 (2), pp. 871-871. | Read more

Beigel JH, Farrar J, Han AM, Hayden FG, Hyer R, de Jong MD, Lochindarat S, Nguyen TK et al. 2005. Avian influenza A (H5N1) infection in humans. N Engl J Med, 353 (13), pp. 1374-1385. | Read more

Zinderman CE, Wise R, Landow L. 2005. Fluid solutions in dengue shock syndrome. N Engl J Med, 353 (23), pp. 2510-2511. | Read more

Hien TT, de Jong M, Farrar J. 2004. Avian influenza--a challenge to global health care structures. N Engl J Med, 351 (23), pp. 2363-2365. | Read more

Dondorp AM, Newton PN, Mayxay M, Van Damme W, Smithuis FM, Yeung S, Petit A, Lynam AJ et al. 2004. Fake antimalarials in Southeast Asia are a major impediment to malaria control: multinational cross-sectional survey on the prevalence of fake antimalarials. Trop Med Int Health, 9 (12), pp. 1241-1246. Read abstract | Read more

To assess the prevalence of counterfeit antimalarial drugs in Southeast (SE) Asia. Hide abstract

Hien TT, Davis TM, Chuong LV, Ilett KF, Sinh DX, Phu NH, Agus C, Chiswell GM, White NJ, Farrar J. 2004. Comparative pharmacokinetics of intramuscular artesunate and artemether in patients with severe falciparum malaria. Antimicrob Agents Chemother, 48 (11), pp. 4234-4239. Read abstract | Read more

The first-dose pharmacokinetic properties of intramuscular (i.m.) artesunate (ARTS; 2.4 mg/kg immediately [stat], followed by 1.2 mg/kg i.m. daily) and artemether (ARM; 3.2 mg/kg i.m. stat, followed by 1.6 mg/kg i.m. daily) were compared in Vietnamese adults with severe falciparum malaria. A total of 19 patients were studied; 9 received ARTS, and 10 received ARM. ARTS was absorbed very rapidly; concentrations in plasma peaked between 1,362 and 8,388 nmol/liter (median, 5,710 nmol/liter) within 20 min of injection and then declined with a median (range) half-life (t(1/2)) of 30 (3 to 67) min. ARTS was hydrolyzed rapidly and completely to the biologically active metabolite dihydroartemisinin (DHA). Peak DHA concentrations in plasma ranged between 1,718 and 7,080 nmol/liter (median, 3,060 nmol/liter) and declined with a t(1/2) of 52 (26 to 69) min. In contrast, ARM was slowly and erratically absorbed. The absorption profile appeared biphasic. Maximum ARM concentrations in plasma ranged between 67 nmol/liter (a value close to the 50% inhibitory concentration for some Plasmodium falciparum isolates) and 1,631 nmol/liter (median, 574 nmol/liter) and occurred at a median (range) of 10 (1.5 to 24) h. There was relatively little conversion to DHA. After i.m. injection in cases of severe malaria, absorption of the water-soluble ARTS is rapid and extensive, whereas the oil-based ARM is slowly and erratically absorbed, with relatively little conversion to the more active DHA. On the basis of this pharmacological study, parenteral ARTS is preferable to ARM as an initial antimalarial therapy, particularly in the most seriously ill patients. These findings should be formally assessed by a randomized clinical trial. Hide abstract

Thwaites CL, Yen LM, Nga NT, Parry J, Binh NT, Loan HT, Thuy TT, Bethell D et al. 2004. Impact of improved vaccination programme and intensive care facilities on incidence and outcome of tetanus in southern Vietnam, 1993-2002. Trans R Soc Trop Med Hyg, 98 (11), pp. 671-677. Read abstract | Read more

Unvaccinated individuals throughout the world are vulnerable to tetanus, but there are few data regarding the impact of focused vaccination programmes and modern intensive care facilities on the disease, particularly in the developing world. The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam admitted 2422 patients with tetanus aged > or =1 year between April 1993 and December 2002, during which time vaccine coverage and treatment facilities improved. The proportion of children < or =10 years old admitted with tetanus fell from 11.1 to 5.6% over the 10 year period (P = 0.002). The proportion of women aged 20-40 years fell from 10.1 to 1.2% (P < 0.001). Mortality rates fell from a maximum of 27.81% in 1994 to 10.04% in 2002 (P < 0.001). Thus, a marked reduction in tetanus incidence has occurred in age groups specifically targeted by the national vaccination programme. However, tetanus continues to be a major cause of morbidity and mortality in individuals outside the target population. Improved intensive care facilities, such as mechanical ventilation and low-cost infection control procedures are associated with a significant reduction in mortality. Hide abstract

Stepniewska K, Taylor WR, Mayxay M, Price R, Smithuis F, Guthmann JP, Barnes K, Myint HY et al. 2004. In vivo assessment of drug efficacy against Plasmodium falciparum malaria: duration of follow-up. Antimicrob Agents Chemother, 48 (11), pp. 4271-4280. Read abstract | Read more

To determine the optimum duration of follow-up for the assessment of drug efficacy against Plasmodium falciparum malaria, 96 trial arms from randomized controlled trials (RCTs) with follow-up of 28 days or longer that were conducted between 1990 and 2003 were analyzed. These trials enrolled 13,772 patients, and participating patients comprised 23% of all patients enrolled in RCTs over the past 40 years; 61 (64%) trial arms were conducted in areas where the rate of malaria transmission was low, and 58 (50%) trial arms were supported by parasite genotyping to distinguish true recrudescences from reinfections. The median overall failure rate reported was 10% (range, 0 to 47%). The widely used day 14 assessment had a sensitivity of between 0 and 37% in identifying treatment failures and had no predictive value. Assessment at day 28 had a sensitivity of 66% overall (28 to 100% in individual trials) but could be used to predict the true failure rate if either parasite genotyping was performed (r(2) = 0.94) or if the entomological inoculation rate was known. In the assessment of drug efficacy against falciparum malaria, 28 days should be the minimum period of follow-up. Hide abstract

Louie JK, Chi NH, Thao LETT, Quang VM, Campbell J, Chau NV, Rutherford GW, Farrar JJ, Parry CM. 2004. Opportunistic infections in hospitalized HIV-infected adults in Ho Chi Minh City, Vietnam: a cross-sectional study. Int J STD AIDS, 15 (11), pp. 758-761. Read abstract | Read more

The HIV epidemic is emerging rapidly in Vietnam. We studied the prevalence of opportunistic infections by performing clinical and microbiological investigations in 100 hospitalized HIV-infected adults in Ho Cho Minh City, Vietnam. The median CD4 count was 20 cells/mm(3) and in-hospital mortality was 28%. The most frequent diagnoses were oral candidiasis (54), tuberculosis (37), wasting syndrome (34), lower respiratory tract infection (13), cryptococcosis (9), and penicilliosis (7). Bacterial (other than tuberculosis) and parasitic infections were uncommon. Regional differences should be considered when deciding which diagnostic procedures and prophylactic measures to implement. In Vietnam, routine mycobacterial blood cultures do not provide greater yield than chest radiography and sputum and lymph node aspirate smears. Prophylactic trimethoprim/sulphamethoxazole against Pneumocystis jiroveci pneumonia may confer little benefit, and high rates of isoniazid resistance may affect the efficacy and feasibility of tuberculosis chemoprophylaxis. However, the usefulness of itraconazole prophylaxis for cryptococcosis and penicilliosis merits further consideration. Hide abstract

Winter PM, Dung NM, Loan HT, Kneen R, Wills B, Thu LET, House D, White NJ, Farrar JJ, Hart CA, Solomon T. 2004. Proinflammatory cytokines and chemokines in humans with Japanese encephalitis. J Infect Dis, 190 (9), pp. 1618-1626. Read abstract | Read more

Japanese encephalitis virus (JEV), the mosquito-borne flavivirus, annually causes an estimated 35,000-50,000 encephalitis cases and 10,000-15,000 deaths in Asia, and there is no antiviral treatment. The role played by the immune response in determining the outcome of human infection with JEV is poorly understood, although, in animal models of flavivirus encephalitis, unregulated proinflammatory cytokine responses can be detrimental. Hide abstract

Thwaites GE, Nguyen DB, Nguyen HD, Hoang TQ, Do TT, Nguyen TC, Nguyen QH, Nguyen TT et al. 2004. Dexamethasone for the treatment of tuberculous meningitis in adolescents and adults. N Engl J Med, 351 (17), pp. 1741-1751. Read abstract | Read more

Tuberculous meningitis kills or disables more than half of those affected with the disease. Previous studies have been too small to determine whether adjunctive treatment with corticosteroids can reduce the risk of disability or death among adults with tuberculous meningitis, and the effect of coinfection with the human immunodeficiency virus (HIV) is unclear. Hide abstract

Wills BA, Oragui EE, Dung NM, Loan HT, Chau NV, Farrar JJ, Levin M. 2004. Size and charge characteristics of the protein leak in dengue shock syndrome. J Infect Dis, 190 (4), pp. 810-818. Read abstract | Read more

he mechanism underlying the transient vascular leak syndrome of dengue hemorrhagic fever (DHF) is unknown. We aimed to determine whether molecular size and charge selectivity, which help restrict plasma proteins within the intravascular space, are altered in patients with DHF and whether a disturbance of the anionic glycosaminoglycan (GAG) layer on the luminal endothelial surface contributes to disease pathogenesis. Hide abstract

Nguyen QC, Everest P, Tran TK, House D, Murch S, Parry C, Connerton P, Phan VB et al. 2004. A clinical, microbiological, and pathological study of intestinal perforation associated with typhoid fever. Clin Infect Dis, 39 (1), pp. 61-67. Read abstract | Read more

One of the most serious complications of typhoid fever is intestinal perforation. Of 27 patients admitted to a provincial hospital in the Mekong Delta region of Vietnam who had gastrointestinal perforation secondary to suspected typhoid fever, 67% were male, with a median age of 23 years and a median duration of illness of 10 days. Salmonella enterica subspecies enterica serotype Typhi (S. Typhi) was isolated from 11 (41%) of 27 patients; of 27 patients, only 4 (15%) had positive cultures from gut biopsies. S. Typhi DNA was detected by polymerase chain reaction for all perforation biopsy samples. Detailed histological examination of the gastrointestinal mucosa at the site of perforation in all cases showed a combination of discrete acute and chronic inflammation. Acute inflammation at the serosal surface indicated additional tissue damage after perforation. Immunohistochemical results showed that the predominant infiltrating cell types at the site of perforation were CD68+ leukocytes (macrophages) or CD3+ leukocytes (T lymphocytes). Hide abstract

My NV, Phuong NTQ, Ha NTT, Mai TTT, Anh NTT, Luat TD, Endy T, Cardosa MJ et al. 2004. Clinical diagnosis and assessment of severity of confirmed dengue in Vietnamese children. Is the World Health Organisation classification system helpful? (vol 70, pg 172, 2004) AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 70 (4), pp. 459-459.

Tran TH, Nguyen TL, Nguyen TD, Luong TS, Pham PM, Nguyen VV, Pham TS, Vo CD et al. 2004. Avian influenza A (H5N1) in 10 patients in Vietnam. N Engl J Med, 350 (12), pp. 1179-1188. Read abstract | Read more

Recent outbreaks of avian influenza A (H5N1) in poultry throughout Asia have had major economic and health repercussions. Human infections with this virus were identified in Vietnam in January 2004. Hide abstract

Thwaites GE, Caws M, Chau TT, Dung NT, Campbell JI, Phu NH, Hien TT, White NJ, Farrar JJ. 2004. Comparison of conventional bacteriology with nucleic acid amplification (amplified mycobacterium direct test) for diagnosis of tuberculous meningitis before and after inception of antituberculosis chemotherapy. J Clin Microbiol, 42 (3), pp. 996-1002. Read abstract | Read more

The role of nucleic acid amplification techniques in the rapid diagnosis of tuberculous meningitis remains uncertain. We compared the performance of Ziehl-Neelsen (ZN) staining, the Gen-Probe amplified Mycobacterium tuberculosis direct test (MTD), and culture with 341 cerebrospinal fluid specimens from 152 adults (73 with and 79 without tuberculous meningitis) before and after inception of antituberculosis chemotherapy. The sensitivity, specificity, and positive and negative predictive values of ZN staining before treatment were 34/66 (52%), 79/79 (100%), 34/34 (100%), and 79/111 (71%), compared with 25/66 (38%), 78/79 (99%), 25/26 (96%), and 79/120 (66%) for MTD. The sensitivity of combined ZN staining and MTD (either positive) was 45/66 (68%). The sensitivity of staining and culture fell more rapidly than that of MTD after the start of treatment: after 5 to 15 days of treatment, MTD was more sensitive than ZN staining (12/43 [28%] versus 2/43 [2%]; P = 0.013). Slower bacterial clearance was observed if M. tuberculosis was resistant to isoniazid and/or streptomycin: resistant organisms were more likely to be cultured from cerebrospinal fluid after 2 to 5 days of treatment than fully sensitive organisms (P < 0.001). The sensitivities of ZN staining, MTD, and the two tests combined were improved by repeated sampling to 38/59 (64%), 35/59 (59%), and 49/59 (83%), respectively. In conclusion, ZN staining of the cerebrospinal fluid is at least as good as MTD for the rapid diagnosis of tuberculosis and is much faster and less expensive. However, the combination of these methods on serial samples detects more cases. Alternative tests are still urgently required. Hide abstract

Vinh H, Parry CM, Hanh VT, Chinh MT, House D, Tham CT, Thao NT, Diep TS et al. 2004. Double blind comparison of ibuprofen and paracetamol for adjunctive treatment of uncomplicated typhoid fever. Pediatr Infect Dis J, 23 (3), pp. 226-230. Read abstract | Read more

Antipyretics reduce the prolonged, high fever characteristic of typhoid fever. The benefits of nonsteroidal drugs in this role have not been quantified. There have been concerns about the safety of antipyretics in typhoid. Hide abstract

Solomon T, Dung NM, Wills B, Winter PM, Loan HT, Kneen R, Diet TV, Thuy TTN, Khanh VC, Farrar JJ, Hart CA. 2004. Interferon alpha in the pathogenesis and treatment Japanese encephalitis JOURNAL OF NEUROVIROLOGY, 10 pp. 28-28.

Day JN, Hien TT, Farrar J. 2004. Expiry-date tampering. Lancet, 363 (9403), pp. 172. | Read more

Tran TH, Dolecek C, Pham PM, Nguyen TD, Nguyen TT, Le HT, Dong TH, Tran TT, Stepniewska K, White NJ, Farrar J. 2004. Dihydroartemisinin-piperaquine against multidrug-resistant Plasmodium falciparum malaria in Vietnam: randomised clinical trial. Lancet, 363 (9402), pp. 18-22. Read abstract | Read more

Southeast Asia has the most resistant malaria parasites in the world, which severely limits treatment options. There is general acceptance that to combat resistance, combinations of antimalarial drugs that include an artemisinin derivative should be used, and, if possible, these should be formulated in a single tablet. Hide abstract

Phuong CXT, Nhan NT, Kneen R, Bethell D, Dep LT, Nga NTT, Thuy PTT, Luat TD, Solomon T, Wills B, Parry CM. 2004. Evaluation of an algorithm for integrated management of childhood illness in an area of Vietnam with dengue transmission Tropical Medicine and International Health, 9 (5), pp. 573-581. Read abstract | Read more

OBJECTIVES: To determine whether nurses, using the WHO/UNICEF algorithm for integrated management of childhood illness (IMCI), modified to include dengue infection, satisfactorily classified children in an area endemic for dengue haemorrhagic fever (DHF). METHODS: Nurses assessed and classified, using the modified IMCI algorithm, a systematic sample of 1250 children aged 2 months to 10 years (n = 1250) presenting to a paediatric hospital in Dong Nai Province, Vietnam. Their classification was compared with that of a paediatrician, blind to the result of the nurses' assessment, which could be modified in the light of simple investigations, e.g. dengue serology. RESULTS: In children aged 2-59 months (n = 859), the nurses were able to classify, using the modified chart, the presenting illness in >99% of children and found more than one classification in 70%. For the children with pneumonia, diarrhoea, dengue shock syndrome, severe DHF and severe disease requiring urgent admission, the nurse's classification was >60% sensitive and >85% specific compared with that of the paediatrician. For the nurse's classification of DHF the specificity was 50-55% for the children <5 years and in children with definitive dengue serology. Alterations in the DHF algorithm improved specificity at the expense of sensitivity. CONCLUSION: Using the IMCI chart, nurses classified appropriately many of the major clinical problems in sick children <5 years in southern Vietnam. However, further modifications will be required in the fever section, particularly for dengue. The impact of using the IMCI chart in peripheral health stations remains to be evaluated. Hide abstract

Thwaites GE, Chau TT, Farrar JJ. 2004. Improving the bacteriological diagnosis of tuberculous meningitis. J Clin Microbiol, 42 (1), pp. 378-379. Read abstract | Read more

We made a bacteriological diagnosis of tuberculous meningitis in 107 of 132 (81%) adults with clinical tuberculous meningitis: acid-fast bacilli were seen in 77 of 132 (58%) and cultured from 94 of 132 (71%). Volume of cerebrospinal fluid, duration of symptoms, cerebrospinal fluid neutrophils, lactate, and glucose were all independently associated with bacteriological confirmation. Hide abstract

Freeman HR, Mai NT, Diep TS, Parry C, Hien TT, Farrar JJ. 2004. The role of the polymerase chain reaction in the diagnosis of bacterial meningitis in Vietnam. Ann Trop Med Parasitol, 98 (1), pp. 65-70. Read abstract | Read more

Bacterial meningitis remains an important cause of morbidity and mortality in Vietnam. Diagnosis is hampered by the ready availability of antibiotics in the community, leading to late presentation, masked clinical signs, and poor organism detection during the microscopical examination and culture of cerebrospinal fluid (CSF). In order to improve organism detection at the Hospital for Tropical Diseases in Ho Chi Minh City, a diagnostic PCR-based protocol was developed. This protocol was followed in the investigation of CSF samples from 36 patients with clinical signs of bacterial meningitis. Each sample was first tested in a semi-nested PCR using primers for the 16sRNA gene common to all bacteria. The products of this reaction were then amplified using a 16sru8 primer and primers specific for Neisseria meningitidis, Haemophilus influenzae or Streptococcus spp. The samples found positive for Streptococcus were further investigated in a nested PCR using primers specific for the pneumolysin gene of S. pneumoniae. The sensitivity of detection was increased from 36% with culture to 44% with PCR. Although the sample size was small, the results indicate that PCR would be a feasible and useful adjunct in the diagnosis of bacterial meningitis, particularly in areas where community antibiotic use is common. Hide abstract

Wain J, Diem Nga LT, Kidgell C, James K, Fortune S, Song Diep T, Ali T, O Gaora P et al. 2003. Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever. Antimicrob Agents Chemother, 47 (9), pp. 2732-2739. Read abstract | Read more

The first outbreak of multidrug-resistant (MDR) typhoid fever in Vietnam was in 1993, and by 1995 nearly 90% of cases were MDR. Plasmid HCM1, sequenced in full, is an incHI1 plasmid from Salmonella enterica serovar Typhi strain CT18, isolated in Vietnam in 1993. Restriction analysis shows that pHCM1 shares a restriction fragment length polymorphism (RFLP) pattern with plasmids isolated from the first outbreak and 10 of 17 MDR plasmids isolated from sporadic cases occurring at the same time in Vietnam. A core region of pHCM1 has significant DNA sequence similarity to plasmid R27, isolated in 1961 from S. enterica in the United Kingdom. There are five regions of DNA in pHCM1 which are not present in R27. Two of these are putative acquisition regions; the largest is 34.955 kbp in length and includes sequences of several antibiotic resistance genes and several insertion sequences. The borders of this region are defined by two identical IS10 left elements, associated with an inversion of DNA or with a truncated Tn10 element. The second, smaller region is 14.751 kbp and carries a trimethoprim resistance gene dfr14A cassette associated with a class 1 integrase. In 1993 to 1994, restriction analysis revealed some variations in the structures of Salmonella serovar Typhi MDR plasmids which were mapped to the two putative acquisition regions and three smaller variable regions. In 1996 a single RFLP type, RFLP7, was found to carry the dfrA7 and sul-1 genes, which were not present on R27 or pHCM1. This plasmid type appears to have a selective advantage over other plasmids with the same resistance phenotype. Hide abstract

Thwaites G, Thwaites L, Hien TT, Farrar J. 2003. Ethics of large clinical trials in rapidly lethal diseases. Lancet, 361 (9365), pp. 1296. | Read more

Parry CM, Hien TT, White NJ, Farrar JJ. 2003. Typhoid fever - Reply NEW ENGLAND JOURNAL OF MEDICINE, 348 (12), pp. 1184-1184.

Solomon T, Dung NM, Wills B, Kneen R, Gainsborough M, Diet TV, Thuy TT, Loan HT et al. 2003. Interferon alfa-2a in Japanese encephalitis: a randomised double-blind placebo-controlled trial. Lancet, 361 (9360), pp. 821-826. Read abstract | Read more

Japanese encephalitis virus (JEV), although confined to Asia, causes about 35000-50000 cases and 10000 deaths every year, and is the most important cause of encephalitis worldwide. There is no known antiviral treatment for any flavivirus. Results from in-vitro studies and work in animals have shown inteferon alfa has antiviral activity on Japanese encephalitis and other flaviviruses; therefore, we aimed to assess the efficacy of inteferon alfa-2a in Japanese encephalitis. Hide abstract

Thwaites CL, Farrar JJ. 2003. Magnesium sulphate as a first line therapy in the management of tetanus. Anaesthesia, 58 (3), pp. 286. | Read more

Thwaites CL, Farrar JJ. 2003. Preventing and treating tetanus. BMJ, 326 (7381), pp. 117-118. | Read more

Landaeta ME, Dove W, Vinh H, Cunliffe NA, Campbell J, Parry CM, Farrar JJ, Hart CA. 2003. Characterization of rotaviruses causing diarrhoea in Vietnamese children. Ann Trop Med Parasitol, 97 (1), pp. 53-59. Read abstract | Read more

Faecal samples from 123 children admitted to the Centre for Tropical Diseases in Ho Chi Minh city, Vietnam, with acute watery diarrhoea were screened by negative-stain electron microscopy for viral enteropathogens. In addition to the 48 children who were found to be infected with rotavirus only, one had both rotavirus and astrovirus, two had adenovirus 40/41, and one had astrovirus only. The rotaviruses were subjected to molecular analysis by electropherotyping, G- and P-genotyping (by reverse-transcriptase PCR), and amplicon sequencing. By use of newly designed PCR primers, all 49 isolates could be G-genotyped and all but one P-genotyped. Novel variants of G1-G1*--were the most commonly detected G-genotype and such variants of P[8]-P[8*]--were the second commonest P-genotype. The P[8*] and G1* amplicons were, respectively, only 92%-93.4% and 88.1%-89% similar to the corresponding sequences from the prototype P[8] G1 rotavirus, Wa. Several unusual P- and G-genotype combinations were detected. Four (8%) of the children investigated were each found to be co-infected with two different rotaviruses. These data add to our knowledge of the continuing evolution and diversity of human rotaviruses, and should help in the rational design of vaccines. Hide abstract

Quagliarello AB, Parry CM, Hien TT, Farrar JJ. 2003. Factors associated with carriage of penicillin-resistant Streptococcus pneumoniae among Vietnamese children: a rural-urban divide. J Health Popul Nutr, 21 (4), pp. 316-324. Read abstract

This study examined the relationship between antimicrobial resistance in Streptococcus pneumoniae and patterns of antimicrobial usage and over-the-counter dispensing by pharmacies in urban and rural districts of Vietnam. The antimicrobial susceptibility of S. pneumoniae carried by healthy urban and rural school children was determined. Questionnaires were distributed to parents to describe their healthcare-seeking behaviour. Mock parents presented standardized cases of mild respiratory infection and acute watery diarrhoea to pharmacies in the district surrounding each school. Penicillin resistance was significantly more common in S. pneumoniae carried by urban children compared to rural children as was recent antibiotic usage. Both urban and rural pharmacies showed high rates of dispensing inadequate antimicrobial regimens. The high level of antimicrobial resistance in S. pneumoniae may be related to greater antimicrobial usage. This may result from the much easier access to healthcare providers in urban areas and may suggest that relying solely on education without limiting access to outlets may have only limited impact. The results suggest a greater understanding of the subtleties of healthcare-seeking behaviour, and access to healthcare is needed to help refine and guide rationale suggestions to reduce the continued spread of drug resistance. Hide abstract

Chau TT, Thwaites GE, Chuong LV, Sinh DX, Farrar JJ. 2003. Headache and confusion: the dangers of a raw snail supper. Lancet, 361 (9372), pp. 1866. | Read more

Thwaites GE, Simmons CP, Than Ha Quyen N, Thi Hong Chau T, Phuong Mai P, Thi Dung N, Hoan Phu N, White NP, Tinh Hien T, Farrar JJ. 2003. Pathophysiology and prognosis in vietnamese adults with tuberculous meningitis. J Infect Dis, 188 (8), pp. 1105-1115. Read abstract | Read more

The pathogenesis of tuberculous meningitis remains unclear, and there are few data describing the kinetics of the immune response during the course of its treatment. We measured concentrations of pro- and anti-inflammatory cytokines in serial blood and cerebrospinal fluid (CSF) samples from 21 adults who were being treated for tuberculous meningitis. CSF concentrations of soluble tumor necrosis factor-alpha receptors and of matrix metalloprotein-9 and its tissue inhibitor were also measured, and blood-brain barrier permeability was assessed by the albumin and IgG partition indices. CSF concentrations of lactate, interleukin-8, and interferon-gamma were high before treatment and then decreased rapidly with antituberculosis chemotherapy. However, significant immune activation and blood-brain barrier dysfunction were still apparent after 60 days of treatment. Death was associated with high initial CSF concentrations of lactate, low numbers of white blood cells, in particular neutrophils, and low CSF glucose levels. Hide abstract

Van Doorn KJ, Pierard D, Verbeelen D, Basnyat B, Zaidi AKM, Hasan R, Bhutta ZA, Parry CM, Hien TT, White NJ, Farrar JJ. 2003. Typhoid fever [5] (multiple letters) New England Journal of Medicine, 348 (12), pp. 1182-1184. | Read more

Parry CM, Hien TT, Dougan G, White NJ, Farrar JJ. 2002. Typhoid fever. N Engl J Med, 347 (22), pp. 1770-1782. | Read more

Parry CM, Duong NM, Zhou J, Mai NT, Diep TS, Thinh LEQ, Wain J, Van Vinh Chau N et al. 2002. Emergence in Vietnam of Streptococcus pneumoniae resistant to multiple antimicrobial agents as a result of dissemination of the multiresistant Spain(23F)-1 clone. Antimicrob Agents Chemother, 46 (11), pp. 3512-3517. Read abstract | Read more

Surveillance for Streptococcus pneumoniae resistant to penicillin and other antimicrobial agents is necessary to define the optimal empirical antibiotic therapy for meningitis in resource-poor countries such as Vietnam. The clinical and microbiological features of 100 patients admitted to the Centre for Tropical Diseases in Ho Chi Minh City, Vietnam, between 1993 and 2002 with invasive pneumococcal disease were studied. A penicillin-nonsusceptible pneumococcus (MIC, > or =0.1 micro g/ml) was isolated from the blood or cerebrospinal fluid of 8% of patients (2 of 24) between 1993 and 1995 but 56% (20 of 36) during 1999 to 2002 (P < 0.0001). Pneumococcal isolates resistant to penicillin (MIC, > or =2.0 micro g/ml) increased from 0% (0 of 24) to 28% (10 of 36) (P = 0.002). Only one isolate was ceftriaxone resistant (MIC, 2.0 micro g/ml). Penicillin-nonsusceptible pneumococci were isolated from 78% of children younger than 15 years (28 of 36) compared with 25% of adults (16 of 64) (P = 0.0001). Isolation of a penicillin-nonsusceptible pneumococcus in adults with meningitis was independently associated with referral from another hospital (P = 0.005) and previous antibiotic therapy (P = 0.025). Multilocus sequence typing showed that 86% of the invasive penicillin-resistant pneumococcus isolates tested (12 of 14) were of the Spain(23F)-1 clone. The serotypes of >95% of the penicillin-nonsusceptible pneumococci were included in the currently available pneumococcal vaccines. Our findings point to the recent introduction and spread of the Spain(23F)-1 clone of penicillin-resistant pneumococci in Vietnam. Simple clinical predictors can be used to guide empirical antibiotic therapy of meningitis. Pneumococcal vaccination may help to control this problem. Hide abstract

Thwaites GE, Chau TT, Stepniewska K, Phu NH, Chuong LV, Sinh DX, White NJ, Parry CM, Farrar JJ. 2002. Diagnosis of adult tuberculous meningitis by use of clinical and laboratory features. Lancet, 360 (9342), pp. 1287-1292. Read abstract | Read more

The diagnosis of tuberculous meningitis is difficult. Discrimination of cases from those of bacterial meningitis by clinical features alone is often impossible, and current laboratory methods remain inadequate or inaccessible in developing countries. We aimed to create a simple diagnostic aid for tuberculous meningitis in adults on the basis of clinical and basic laboratory features. Hide abstract

Thwaites GE, Chau TT, Caws M, Phu NH, Chuong LV, Sinh DX, Drobniewski F, White NJ, Parry CM, Farrar JJ. 2002. Isoniazid resistance, mycobacterial genotype and outcome in Vietnamese adults with tuberculous meningitis. Int J Tuberc Lung Dis, 6 (10), pp. 865-871. Read abstract

Centre for Tropical Diseases, a 500-bed hospital for infectious diseases in Ho Chi Minh City, Vietnam. Hide abstract

Phu NH, Hien TT, Mai NT, Chau TT, Chuong LV, Loc PP, Winearls C, Farrar J, White N, Day N. 2002. Hemofiltration and peritoneal dialysis in infection-associated acute renal failure in Vietnam. N Engl J Med, 347 (12), pp. 895-902. Read abstract | Read more

In some parts of the world, peritoneal dialysis is widely used for renal replacement in acute renal failure. In resource-rich countries, it has been supplanted in recent years by hemodialysis and, most recently, by hemofiltration and associated techniques. The relative efficacy of peritoneal dialysis and hemofiltration is not known. Hide abstract

Wills BA, Oragui EE, Stephens AC, Daramola OA, Dung NM, Loan HT, Chau NV, Chambers M, Stepniewska K, Farrar JJ, Levin M. 2002. Coagulation abnormalities in dengue hemorrhagic Fever: serial investigations in 167 Vietnamese children with Dengue shock syndrome. Clin Infect Dis, 35 (3), pp. 277-285. Read abstract | Read more

The pathophysiological basis of hemorrhage in dengue infections remains poorly understood, despite the increasing global importance of these infections. A large prospective study of 167 Vietnamese children with dengue shock syndrome documented only minor prolongations of prothrombin and partial thromboplastin times but moderate to severe depression of plasma fibrinogen concentrations. A detailed study of 48 children revealed low plasma concentrations of the anticoagulant proteins C, S, and antithrombin III, which decreased with increasing severity of shock, probably because of capillary leakage. Concurrent increases in the levels of thrombomodulin, tissue factor, and plasminogen activator inhibitor type 1 (PAI-1) indicated increased production of these proteins. Thrombomodulin levels suggestive of endothelial activation correlated with increasing shock severity, whereas PAI-1 levels correlated with bleeding severity. Dengue virus can directly activate plasminogen in vitro. Rather than causing true disseminated intravascular coagulation, dengue infection may activate fibrinolysis primarily, degrading fibrinogen directly and prompting secondary activation of procoagulant homeostatic mechanisms. Hide abstract

House D, Chinh NT, Hien TT, Parry CP, Ly NT, Diep TS, Wain J, Dunstan S, White NJ, Dougan G, Farrar JJ. 2002. Cytokine release by lipopolysaccharide-stimulated whole blood from patients with typhoid fever. J Infect Dis, 186 (2), pp. 240-245. Read abstract | Read more

The ex vivo cytokine response to lipopolysaccharide (LPS) of whole blood from patients with typhoid fever was investigated. Tumor necrosis factor (TNF)-alpha release by LPS-stimulated blood was found to be lower during acute typhoid fever than after a course of antimicrobial therapy (P<or=.001). Ex vivo interleukin (IL)-1beta, but not IL-1 receptor antagonist, release was also depressed during the acute stage of typhoid fever. Low ex vivo production of TNF-alpha was associated with delayed recovery. No association was found between the TNFA-308 promoter polymorphism and LPS-induced TNF-alpha release, either during an active infection or after treatment. In acute typhoid fever, the ability of peripheral blood leukocytes to release proinflammatory cytokines in response to an inflammatory stimulus is depressed, and this may contribute to delayed recovery following antibiotic treatment. Hide abstract

Loke H, Bethell D, Phuong CX, Day N, White N, Farrar J, Hill A. 2002. Susceptibility to dengue hemorrhagic fever in vietnam: evidence of an association with variation in the vitamin d receptor and Fc gamma receptor IIa genes. Am J Trop Med Hyg, 67 (1), pp. 102-106. Read abstract

Dengue is an increasingly important cause of morbidity and mortality in the tropics, with more than a billion people at risk each year. Immunologic enhancement is thought to contribute to disease pathogenesis. Only a very small proportion of infected individuals develop life-threatening dengue hemorrhagic fever (DHF). In a large case-control study with 400 DHF patients and 300 matched controls, we have assessed five polymorphic non-HLA host genetic factors that might influence susceptibility to DHF. The less frequent t allele of a variant at position 352 of the vitamin D receptor (VDR) gene was associated with resistance to severe dengue (P = 0.03). Homozygotes for the arginine variant at position 131 of the Fc gammaRIIA gene, who have less capacity to opsonize IgG2 antibodies, may also be protected from DHF (one-tailed P = 0.03). No associations were found with polymorphisms in the mannose binding lectin, interleukin-1 (IL-4), and IL-1 receptor antagonist genes. Further studies to confirm these associations are warranted. Hide abstract

Twiddy SS, Farrar JJ, Vinh Chau N, Wills B, Gould EA, Gritsun T, Lloyd G, Holmes EC. 2002. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Virology, 298 (1), pp. 63-72. Read abstract | Read more

To elucidate the processes controlling the emergence and spread of dengue-2 virus (DEN-2) we examined the evolution of viral isolates sampled from both local (Viet Nam) and global populations. Our phylogenetic analysis, incorporating envelope (E) glycoprotein sequences from 147 isolates of DEN-2, provided a more complete picture of viral diversity, with a newly defined "Cosmopolitan" genotype having a near global distribution and two other genotypes restricted to Asia. By analyzing rates of synonymous and nonsynonymous substitution we determined that genotypes have experienced different selection pressures, with some evidence of positive selection in the Cosmopolitan genotype and one of the two Asian genotypes, but that the transition from sylvatic to human transmission was not accompanied by adaptive evolution of the E gene. Although there was no association between selection pressures acting on the E gene and proposed virulence differences among genotypes, some putatively selected amino acid sites have previously been implicated in changing viral pathogenicity, most notably E-390, and may also affect transmittability. These findings have implications for the future spread of DEN-2. Hide abstract

Kidgell C, Pickard D, Wain J, James K, Diem Nga LT, Diep TS, Levine MM, O'Gaora P et al. 2002. Characterisation and distribution of a cryptic Salmonella typhi plasmid pHCM2. Plasmid, 47 (3), pp. 159-171. Read abstract | Read more

pHCM2 is a 106 kbp cryptic plasmid harboured by Salmonella typhi CT18, originally isolated from a typhoid patient in Vietnam. The genome of S. typhi CT18, including pHCM2, has recently been completely sequenced and annotated. Bioinformatic analysis revealed that 57% of the coding sequences (CDSs) encoded on pHCM2 display over 97% DNA sequence identity to the virulence-associated plasmid of Yersinia pestis, pFra. pHCM2 encodes no obvious virulence-associated determinants or antibiotic resistance genes but does encode a wide array of putative genes directly related to DNA metabolism and replication. PCR analysis of a series of S. typhi isolates from Vietnam detected pHCM2-related DNA sequences in some S. typhi isolated before, but not after, 1994. Similar pHCM2-related sequences were also detected in S. typhi isolated from other regions of South East Asia and Pakistan but not elsewhere in the world. Hide abstract

Bartley LM, Carabin H, Vinh Chau N, Ho V, Luxemburger C, Hien TT, Garnett GP, Farrar J. 2002. Assessment of the factors associated with flavivirus seroprevalence in a population in Southern Vietnam. Epidemiol Infect, 128 (2), pp. 213-220. Read abstract | Read more

Dengue and Japanese encephalitis flaviviruses cause severe disease and are hyperendemic in southern Vietnam. This study assesses associations between sociodemographic factors and flavivirus seroprevalence in this region. Sera were collected from 308 community and hospital-based subjects between April 1996 and August 1997 and tested with an indirect ELISA. The factors associated with seroprevalence were assessed using multivariate logistic regression. In this first report of adjusted prevalence odds ratios (POR) for flavivirus infection in Vietnam, seropositivity was associated with increasing age in children (multiple regression coefficients for a child compared to an adult = -4.975 and for age in children = 0.354) and residence in the city compared to surrounding rural districts. The association with age indicates that subjects were most likely to have acquired infection in early childhood. This is key to the design of Vietnamese health education and immunization programmes. Hide abstract

Medana IM, Hien TT, Day NP, Phu NH, Mai NT, Chu'ong LV, Chau TT, Taylor A et al. 2002. The clinical significance of cerebrospinal fluid levels of kynurenine pathway metabolites and lactate in severe malaria. J Infect Dis, 185 (5), pp. 650-656. Read abstract | Read more

A retrospective study of 261 Vietnamese adults with severe malaria was conducted to determine the relationship between cerebrospinal fluid (CSF) levels of metabolites of the kynurenine pathway, the incidence of neurologic complications, and the disease outcome. Three metabolites were measured: the excitotoxin quinolinic acid (QA); the protective receptor antagonist kynurenic acid (KA); and the proinflammatory mediator picolinic acid (PA). These measurements were related prospectively to CSF lactate levels. QA and PA levels were elevated, compared with those of controls. There was no difference in the levels of KA between these groups. Although >40% of malaria patients had QA CSF concentrations in the micromolar range, there was no association with convulsions or depth of coma. Levels of QA and PA were associated significantly with death, but a multivariate analysis suggested that these elevations were a consequence of impaired renal function. CSF lactate remained an independent and significant predictor of poor outcome. Hide abstract

Medana IM, Day NP, Hien TT, Mai NT, Bethell D, Phu NH, Farrar J, Esiri MM, White NJ, Turner GD. 2002. Axonal injury in cerebral malaria. Am J Pathol, 160 (2), pp. 655-666. Read abstract | Read more

Impairment of consciousness and other signs of cerebral dysfunction are common complications of severe Plasmodium falciparum malaria. Although the majority of patients make a complete recovery a significant minority, particularly children, have sequelae. The pathological process by which P. falciparum malaria induces severe but usually reversible neurological complications has not been elucidated. Impairment of transport within nerve fibers could induce neurological dysfunction and may have the potential either to resolve or to progress to irreversible damage. Beta-amyloid precursor protein (beta-APP) immunocytochemistry, quantified using digital image analysis, was used to detect defects in axonal transport in brain sections from 54 Vietnamese cases with P. falciparum malaria. The frequency and extent of beta-APP staining were more severe in patients with cerebral malaria than in those with no clinical cerebral involvement. Beta-APP staining was often associated with hemorrhages and areas of demyelination, suggesting that multiple processes may be involved in neuronal injury. The age of focal axonal damage, as determined by the extent of the associated microglial response, varied considerably within tissue sections from individual patients. These findings suggest that axons are vulnerable to a broad range of cerebral insults that occur during P. falciparum malaria infection. Disruption in axonal transport may represent a final common pathway leading to neurological dysfunction in cerebral malaria. Hide abstract

Cao XT, Ngo TN, Wills B, Kneen R, Nguyen TT, Ta TT, Tran TT, Doan TK et al. 2002. Evaluation of the World Health Organization standard tourniquet test and a modified tourniquet test in the diagnosis of dengue infection in Viet Nam. Trop Med Int Health, 7 (2), pp. 125-132. Read abstract | Read more

A positive tourniquet test is one of several clinical parameters considered by the World Health Organization to be important in the diagnosis of dengue haemorrhagic fever, but no formal evaluation of the test has been undertaken. As many doctors remain unconvinced of its usefulness, this study was designed to assess the diagnostic utility of both the standard test and a commonly employed modified test. Hide abstract

Barcus MJ, Hien TT, White NJ, Laras K, Farrar J, Schwartz IK, Corwin A, Baird JK. 2002. Short report: hepatitis b infection and severe Plasmodium falciparum malaria in Vietnamese adults. Am J Trop Med Hyg, 66 (2), pp. 140-142. Read abstract

We investigated the prevalence of infection with hepatitis B virus among adult Vietnamese patients hospitalized for severe Plasmodiumfalciparum malaria. Sera from patients admitted with severe malaria in Ho Chi Minh City, Vietnam, between May 1991 and January 1996 were assayed for hepatitis B surface antigen (HB(s)Ag) by a commercial enzyme-linked immunosorbent assay kit. The overall prevalence of HB(s)Ag was 23.77% (77 of 324). This was higher than reported estimates of prevalence in the general catchment population for the study hospital (mean, 9.8%; range, 9-16%). No association was found between risk of death caused by severe malaria and HB(s)Ag. Patients admitted with cerebral malaria had a slightly greater risk of registering positive for HB(s)Ag (relative risk, 1.28; 95% confidence interval, 1.04-1.58) relative to other manifestations of severe malaria. Chronic infection with hepatitis B virus may be a risk factor for severe malaria. Hide abstract

Farrar J. 2002. Half a century on from the Coronation of Queen Elizabeth II: but more neurology needs to be done in the developing world Practical Neurology, 2 (4), pp. 188-191. | Read more

Thwaites GE, Farrar JJ. 2002. Miliary tuberculosis with meningitis Practical Neurology, 2 (4), pp. 230-231. | Read more

Twiddy SS, Farrar JJ, Chau NV, Wills B, Gould EA, Gritsun T, Lloyd G, Holmes EC. 2002. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus Virology, 298 (1), pp. 63-72. Read abstract | Read more

To elucidate the processes controlling the emergence and spread of dengue-2 virus (DEN-2) we examined the evolution of viral isolates sampled from both local (Viet Nam) and global populations. Our phylogenetic analysis, incorporating envelope (E) glycoprotein sequences from 147 isolates of DEN-2, provided a more complete picture of viral diversity, with a newly defined "Cosmopolitan" genotype having a near global distribution and two other genotypes restricted to Asia. By analyzing rates of synonymous and nonsynonymous substitution we determined that genotypes have experienced different selection pressures, with some evidence of positive selection in the Cosmopolitan genotype and one of the two Asian genotypes, but that the transition from sylvatic to human transmission was not accompanied by adaptive evolution of the E gene. Although there was no association between selection pressures acting on the E gene and proposed virulence differences among genotypes, some putatively selected amino acid sites have previously been implicated in changing viral pathogenicity, most notably E-390, and may also affect transmittability. These findings have implications for the future spread of DEN-2. © 2002 Elsevier Science (USA). Hide abstract

Medana IM, Mai NT, Day NP, Hien TT, Bethell D, Phu NH, Farrar J, White NJ, Turner GD. 2001. Cellular stress and injury responses in the brains of adult Vietnamese patients with fatal Plasmodium falciparum malaria. Neuropathol Appl Neurobiol, 27 (6), pp. 421-433. Read abstract | Read more

Immunohistochemical techniques have been used to investigate specific patterns of potentially reversible cellular injury, DNA damage, and apoptosis in the brainstems of Vietnamese patients who died of severe Plasmodium falciparum malaria. The degree and pattern of neuronal and glial stress responses were compared between patients with cerebral and non-cerebral malaria (CM), and appropriate non-malaria infected controls. The following markers were examined: (i) heat shock protein 70 (HSP70), for reversible injury; (ii) heme oxygenase-1, for oxidative stress; (iii & iv) two DNA-repair proteins, poly(ADP) ribose polymerase (PARP) and DNA-dependent protein kinase catalytic subunit; (v) poly(ADP) ribose, an end-product of PARP activity; and (vi) caspase-3-active, for apoptosis. Stress responses were found in a range of cell types as reflected by the widespread expression of HSP70. Oxidative stress predominated in the vicinity of vessels and haemorrhages. Some degree of DNA damage was found in the majority of malaria patients, but the distribution and frequency of the damage was much less than that observed in controls with irreversible neuronal injury. Similarly, caspase-3-active expression, as a measure of apoptosis, was no higher in the majority of malaria patients than the negative control cases, although 40% of CM cases expressed caspase-3-active in a small number of neurones of the pontine nuclei or within swollen axons of the pontocerebellar and corticospinal tracts. In conclusion, cells within the brainstem of all patients who died from severe malaria showed staining patterns indicative of considerable stress response and reversible neuronal injury. There was no evidence for a specific pattern of widespread irreversible cell damage in those patients with cerebral malaria. Hide abstract

Loke H, Bethell DB, Phuong CX, Dung M, Schneider J, White NJ, Day NP, Farrar J, Hill AV. 2001. Strong HLA class I--restricted T cell responses in dengue hemorrhagic fever: a double-edged sword? J Infect Dis, 184 (11), pp. 1369-1373. Read abstract | Read more

Dengue is an increasingly important cause of morbidity and mortality in the tropics, but vaccine development has been impeded by a poor understanding of disease pathogenesis and, in particular, of immunologic enhancement. In a large case-control study of Vietnamese patients with dengue hemorrhagic fever (DHF), variation at the HLA-A locus was significantly associated with susceptibility to DHF (P=.02), and specific HLA-A susceptibility and resistance alleles were identified. HLA-A-specific epitopes were predicted from binding motifs, and ELISPOT analyses of patients with DHF revealed high frequencies of circulating CD8 T lymphocytes that recognized both serotype-specific and -cross-reactive dengue virus epitopes. Thus, strong CD8 T cell responses are induced by natural dengue virus infection, and HLA class I genetic variation is a risk factor for DHF. These genetic and immunologic data support both protective and pathogenic roles for dengue virus-specific CD8 T cell responses in severe disease. The potentially pathogenic role of serotype-cross-reactive CD8 T cells poses yet another obstacle to successful dengue vaccine development. Hide abstract

Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL et al. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature, 413 (6858), pp. 848-852. Read abstract | Read more

Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis. Hide abstract

Newton P, Proux S, Green M, Smithuis F, Rozendaal J, Prakongpan S, Chotivanich K, Mayxay M et al. 2001. Fake artesunate in southeast Asia. Lancet, 357 (9272), pp. 1948-1950. Read abstract | Read more

Artesunate is a key antimalarial drug in the treatment of multidrug-resistant Plasmodium falciparum malaria in southeast Asia. We investigated the distribution of counterfeit artesunate tablets by use of the validated, simple, and inexpensive Fast Red TR dye technique. We also aimed to identify distinguishing characteristics of the fake drugs. Of 104 shop-bought "artesunate" samples from Cambodia, Laos, Myanmar (Burma), Thailand, and Vietnam, 38% did not contain artesunate. Characteristics such as cost and physical appearance of the tablets and packaging reliably predicted authenticity. The illicit trade in counterfeit antimalarials is a great threat to the lives of patients with malaria. The dye test will assist national malaria control authorities in urgently needed campaigns to stop this murderous trade. Hide abstract

Wain J, Pham VB, Ha V, Nguyen NM, To SD, Walsh AL, Parry CM, Hasserjian RP et al. 2001. Quantitation of bacteria in bone marrow from patients with typhoid fever: relationship between counts and clinical features. J Clin Microbiol, 39 (4), pp. 1571-1576. Read abstract | Read more

Enteric fever is the only bacterial infection of humans for which bone marrow examination is routinely recommended. A prospective study of the concentrations of bacteria in the bone marrow and their relationship to clinical features was conducted with 120 Vietnamese patients with suspected enteric fever, of whom 89 had confirmed typhoid fever. Ninety-three percent of the Salmonella enterica serovar Typhi samples isolated were resistant to ampicillin, chloramphenicol, and co-trimoxazole. For 81 patients with uncomplicated typhoid and satisfactory bone marrow aspirates, the number of serovar Typhi CFU in bone marrow aspirates was a median value of 9 (interquartile range [IQR], 1 to 85; range, 0.1 to 1,580) compared to 0.3 (IQR, 0.1 to 10; range, 0.1 to 399) CFU/ml in simultaneously sampled blood. The ratio of individual blood counts to bone marrow counts was 10 (IQR, 2.3 to 97.5). The number of bacteria in blood but not bone marrow was correlated inversely with the duration of preceding fever. Thus, with increasing duration of illness the ratio of bone marrow-to-blood bacterial concentrations increased; the median ratio was 4.8 (IQR, 1 to 27.5) during the first week compared with 158 (IQR, 60 to 397) during the third week. After lysing the host cells, the median ratio of viable bone marrow to blood increased, reflecting the higher concentration of intracellular serovar Typhi in the bone marrow. Effective antibiotic pretreatment had a significantly greater effect in reducing blood counts compared to bone marrow counts (P < 0.001). Thus, bacteria in the bone marrow of typhoid patients are less affected by antibiotic treatment than bacteria in the blood. The numbers of bacteria in bone marrow correlated negatively with the white blood cell (R = -0.3, P = 0.006) and platelet counts (R = -0.32, P = 0.01) and positively with fever clearance time after treatment (R = 0.4, P < 0.001). The bacterial load in bone marrow therefore may reflect the clinical course of the infection, and high levels may suppress neutrophil proliferation. Hide abstract

Dunstan SJ, Ho VA, Duc CM, Lanh MN, Phuong CX, Luxemburger C, Wain J, Dudbridge F et al. 2001. Typhoid fever and genetic polymorphisms at the natural resistance-associated macrophage protein 1. J Infect Dis, 183 (7), pp. 1156-1160. Read abstract | Read more

Control of Salmonella enterica serovar Typhimurium (S. typhimurium) infection in the mouse model of typhoid fever is critically dependent on the natural resistance-associated macrophage protein 1 (Nramp1). In this study, we examined the role of genetic polymorphisms in the human homologue, NRAMP1, in resistance to typhoid fever in southern Vietnam. Patients with blood-culture-confirmed typhoid fever and healthy control subjects were genotyped for 6 polymorphic markers within and near NRAMP1 on chromosome 2q35. Four single base-pair polymorphisms (274 C/T, 469+14 G/C, 1465-85 G/A, and D543N), a (GT)(n) repeat in the promoter region of NRAMP1 and D2S1471, and a microsatellite marker approximately 130-kb downstream of NRAMP1 were examined. The allelic and genotypic frequencies for each polymorphism were compared in case patients and control subjects. No allelic association was identified between the NRAMP1 alleles and typhoid fever susceptibility. In addition, neither homozygotes nor heterozygotes for any NRAMP1 variants were at increased risk of typhoid fever. Hide abstract

Prentice MB, James KD, Parkhill J, Baker SG, Stevens K, Simmonds MN, Mungall KL, Churcher C et al. 2001. Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid. J Bacteriol, 183 (8), pp. 2586-2594. Read abstract | Read more

Population genetic studies suggest that Yersinia pestis, the cause of plague, is a clonal pathogen that has recently emerged from Yersinia pseudotuberculosis. Plasmid acquisition is likely to have been a key element in this evolutionary leap from an enteric to a flea-transmitted systemic pathogen. However, the origin of Y. pestis-specific plasmids remains obscure. We demonstrate specific plasmid rearrangements in different Y. pestis strains which distinguish Y. pestis bv. Orientalis strains from other biovars. We also present evidence for plasmid-associated DNA exchange between Y. pestis and the exclusively human pathogen Salmonella enterica serovar Typhi. Hide abstract

Price NM, Farrar J, Tran TT, Nguyen TH, Tran TH, Friedland JS. 2001. Identification of a matrix-degrading phenotype in human tuberculosis in vitro and in vivo. J Immunol, 166 (6), pp. 4223-4230. Read abstract

Tuberculous meningitis is characterized by cerebral tissue destruction. Monocytes, pivotal in immune responses to Mycobacterium tuberculosis, secrete matrix metalloproteinase-9 (MMP-9), which facilitates leukocyte migration across the blood-brain barrier, but may cause cerebral injury. In vitro, human monocytic (THP-1) cells infected by live, virulent M. tuberculosis secreted MMP-9 in a dose-dependent manner. At 24 h, MMP-9 concentrations increased 10-fold to 239 +/- 75 ng/ml (p = 0.001 vs controls). MMP-9 mRNA became detectable at 24--48 h. In contrast, tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) gene expression and secretion were similar to constitutive levels from controls at 24 h and increased just 5-fold by 48 h. In vivo investigation revealed MMP-9 concentration per leukocyte in cerebrospinal fluid (CSF) from tuberculous meningitis patients (n = 23; median (range), 3.19 (0.19--31.00) ng/ml/cell) to be higher than that in bacterial (n = 12; 0.23 (0.01--18.37) ng/ml/cell) or viral meningitis (n = 20; 0.20 (0.04--31.00) ng/ml/cell; p < 0.01). TIMP-1, which was constitutively secreted into CSF, was not elevated in tuberculous compared with bacterial meningitis or controls. Thus, a phenotype in which MMP-9 activity is relatively unrestricted by TIMP-1 developed both in vitro and in vivo. This is functionally significant, since MMP-9 concentrations per CSF leukocyte (but not TIMP-1 concentrations) were elevated in fatal tuberculous meningitis and in patients with signs of cerebral tissue damage (unconsciousness, confusion, or neurological deficit; p < 0.05). However, MMP-9 activity was unrelated to the severity of systemic illness. In summary, M. tuberculosis-infected monocytic cells develop a matrix-degrading phenotype, which was observed in vivo and relates to clinical signs reflecting cerebral injury in tuberculous meningitis. Hide abstract

House D, Wain J, Ho VA, Diep TS, Chinh NT, Bay PV, Vinh H, Duc M et al. 2001. Serology of typhoid fever in an area of endemicity and its relevance to diagnosis. J Clin Microbiol, 39 (3), pp. 1002-1007. Read abstract | Read more

Currently, the laboratory diagnosis of typhoid fever is dependent upon either the isolation of Salmonella enterica subsp. enterica serotype Typhi from a clinical sample or the detection of raised titers of agglutinating serum antibodies against the lipopolysaccharide (LPS) (O) or flagellum (H) antigens of serotype Typhi (the Widal test). In this study, the serum antibody responses to the LPS and flagellum antigens of serotype Typhi were investigated with individuals from a region of Vietnam in which typhoid is endemic, and their usefulness for the diagnosis of typhoid fever was evaluated. The antibody responses to both antigens were highly variable among individuals infected with serotype Typhi, and elevated antibody titers were also detected in a high proportion of serum samples from healthy subjects from the community. In-house enzyme-linked immunosorbent assays (ELISAs) for the detection of specific classes of anti-LPS and antiflagellum antibodies were compared with other serologically based tests for the diagnosis of typhoid fever (Widal TO and TH, anti-serotype Typhi immunoglobulin M [IgM] dipstick, and IDeaL TUBEX). At a specificity of > or =0.93, the sensitivities of the different tests were 0.75, 0.55, and 0.52 for the anti-LPS IgM, IgG, and IgA ELISAs, respectively; 0.28 for the antiflagellum IgG ELISA; 0.47 and 0.32 for the Widal TO and TH tests, respectively; and 0.77 for the anti-serotype Typhi IgM dipstick assay. The specificity of the IDeaL TUBEX was below 0.90 (sensitivity, 0.87; specificity, 0.76). The serological assays based on the detection of IgM antibodies against either serotype Typhi LPS (ELISA) or whole bacteria (dipstick) had a significantly higher sensitivity than the Widal TO test when used with a single acute-phase serum sample (P < or = 0.007). These tests could be of use for the diagnosis of typhoid fever in patients who have clinical typhoid fever but are culture negative or in regions where bacterial culturing facilities are not available. Hide abstract

Ngo NT, Cao XT, Kneen R, Wills B, Nguyen VM, Nguyen TQ, Chu VT, Nguyen TT et al. 2001. Acute management of dengue shock syndrome: a randomized double-blind comparison of 4 intravenous fluid regimens in the first hour. Clin Infect Dis, 32 (2), pp. 204-213. Read abstract | Read more

Dengue hemorrhagic fever is an important cause of morbidity among Asian children, and the more severe dengue shock syndrome (DSS) causes a significant number of childhood deaths. DSS is characterized by a massive increase in systemic capillary permeability with consequent hypovolemia. Fluid resuscitation is critical, but as yet there have been no large trials to determine the optimal fluid regimen. We undertook a randomized blinded comparison of 4 fluids (dextran, gelatin, lactated Ringer's, and "normal" saline) for initial resuscitation of 230 Vietnamese children with DSS. All the children survived, and there was no clear advantage to using any of the 4 fluids, but the longest recovery times occurred in the lactated Ringer's group. The most significant factor determining clinical response was the pulse pressure at presentation. A comparison of the colloid and crystalloid groups suggested benefits in children presenting with lower pulse pressures who received one of the colloids. Further large-scale studies, stratified for admission pulse pressure, are indicated. Hide abstract

Dunstan SJ, Stephens HA, Blackwell JM, Duc CM, Lanh MN, Dudbridge F, Phuong CX, Luxemburger C et al. 2001. Genes of the class II and class III major histocompatibility complex are associated with typhoid fever in Vietnam. J Infect Dis, 183 (2), pp. 261-268. Read abstract | Read more

The influence of genes of the major histocompatibility complex (MHC) class II and class III loci on typhoid fever susceptibility was investigated. Individuals with blood culture-confirmed typhoid fever and control subjects from 2 distinct geographic locations in southern Vietnam were genotyped for HLA-DRB1 and HLA-DQB1 alleles, the gene that encodes tumor necrosis factor (TNF)-alpha (TNFA [-238] and TNFA [-308]), the gene that encodes lymphotoxin-alpha, and alleles of the TNF-alpha microsatellite. HLA-DRB1*0301/6/8, HLA-DQB1*0201-3, and TNFA*2 (-308) were associated with susceptibility to typhoid fever, whereas HLA-DRB1*04, HLA-DQB1*0401/2, and TNFA*1 (-308) were associated with disease resistance. The frequency of all possible haplotypes of the 3 individually associated loci were estimated and were found to be significantly different in typhoid case patients and control subjects (chi2=55.56, 32 df; P=.006). Haplotypes that were either protective (TNFA*1 [-308].DRB1*04) or predisposed individuals to typhoid fever (TNFA*2 [-308].DRB1*0301) were determined. This report identifies a genetic association in humans between typhoid fever and MHC class II and III genes. Hide abstract

Luxemburger C, Chau MC, Mai NL, Wain J, Tran TH, Simpson JA, Le HK, Nguyen TT, White NJ, Farrar JJ. 2001. Risk factors for typhoid fever in the Mekong delta, southern Viet Nam: a case-control study. Trans R Soc Trop Med Hyg, 95 (1), pp. 19-23. Read abstract | Read more

In order to identify risk factors for typhoid fever in a highly endemic area, we undertook a case-control study in the Mekong delta, Viet Nam. Cases were 144 consecutive patients admitted to hospital with blood culture-confirmed typhoid fever. Two controls (1 in the hospital and 1 in the community) were chosen for each case. Standardized interviews were conducted with questions regarding recent contact with a typhoid fever patient, eating habits, hygiene and socio-economic level. Cases were more likely to have been in contact with a patient with typhoid fever than hospital controls (adjusted odds ratio (OR) = 5.2, 95% confidence interval (95% CI) 1.7-15.9) or community controls (adjusted OR = 11.9, 95% CI 2.3-60.7); 11% and 14% of typhoid fever cases (compared to hospital or community controls, respectively) were attributable to recent contact with a patient with this disease. These findings suggest that strategies directed towards the persons in contact with a patient might reduce the incidence of secondary cases of typhoid fever. Hide abstract

Farrar JJ, Yen LM, Cook T, Fairweather N, Binh N, Parry J, Parry CM. 2000. Tetanus. J Neurol Neurosurg Psychiatry, 69 (3), pp. 292-301. | Read more

Brown HC, Chau TT, Mai NT, Day NP, Sinh DX, White NJ, Hien TT, Farrar J, Turner GD. 2000. Blood-brain barrier function in cerebral malaria and CNS infections in Vietnam. Neurology, 55 (1), pp. 104-111. Read abstract | Read more

The intraerythrocytic parasite Plasmodium falciparum induces the life-threatening neurologic syndrome of cerebral malaria (CM) from within cerebral blood vessels, without entering the brain parenchyma. Hide abstract

Chinh NT, Parry CM, Ly NT, Ha HD, Thong MX, Diep TS, Wain J, White NJ, Farrar JJ. 2000. A randomized controlled comparison of azithromycin and ofloxacin for treatment of multidrug-resistant or nalidixic acid-resistant enteric fever. Antimicrob Agents Chemother, 44 (7), pp. 1855-1859. Read abstract | Read more

To examine the efficacy and safety of short courses of azithromycin and ofloxacin for treating multidrug-resistant (MDR, i.e., resistant to chloramphenicol, ampicillin, and cotrimoxazole) and nalidixic acid-resistant enteric fever, azithromycin (1 g once daily for 5 days at 20 mg/kg/day) and ofloxacin (200 mg orally twice a day for 5 days at 8 mg/kg/day) were compared in an open randomized study in adults admitted to a hospital with uncomplicated enteric fever. A total of 88 blood culture-confirmed patients were enrolled in the study (86 with Salmonella enterica serovar Typhi and 2 with S. enterica serovar Paratyphi A). Of these, 44 received azithromycin and 44 ofloxacin. A total of 68 of 87 (78%) isolates were MDR serovar Typhi, and 46 of 87 (53%) were nalidixic acid resistant. The MIC(90) (range) of azithromycin was 8 (4 to 16) microgram/ml for the isolates. The MIC(90) (range) of ofloxacin for the nalidixic acid-sensitive isolates was 0.03 (0.015 to 0.06) microgram/ml and for the nalidixic acid-resistant isolates it was 0.5 (0.25 to 1.0) microgram/ml. There was no significant difference in the overall clinical cure rate with ofloxacin and azithromycin (38 of 44 [86.4%] versus 42 of 44 [95.5%]; P = 0.27) or in the patients infected with nalidixic acid-resistant typhoid (17 of 21 [81.0%] versus 24 of 25 [96.0%]; P = 0.16). However, patients with nalidixic acid-resistant typhoid treated with ofloxacin had a longer fever clearance time compared with those treated with azithromycin (174 [60 to 264] versus 135 [72 to 186] h; P = 0.004) and had positive fecal cultures after the end of treatment (7 of 17 [41%] versus 0 of 19 [0%]; P = 0.002). Both antibiotics were well tolerated. A 5-day course of azithromycin was effective for the treatment of enteric fever due to MDR and nalidixic-acid-resistant serovar Typhi, whereas the ofloxacin regimen chosen was less satisfactory for these strains. Hide abstract

Kissinger E, Hien TT, Hung NT, Nam ND, Tuyen NL, Dinh BV, Mann C, Phu NH et al. 2000. Clinical and neurophysiological study of the effects of multiple doses of artemisinin on brain-stem function in Vietnamese patients. Am J Trop Med Hyg, 63 (1-2), pp. 48-55. Read abstract

The qinghaosu (artemisinin) group of drugs is the most important new class of antimalarials developed in the last fifty years. Although there has been no clinical evidence of neurotoxicity, an unusual pattern of damage to specific brain-stem nuclei has been reported in experimental animals receiving high doses of arteether or artemether. Detailed clinical examinations, audiometry, and brain stem auditory evoked potentials (BSAEPs) were assessed in 242 Vietnamese subjects who had previously received up to 21 antimalarial treatment courses of artemisinin or artesunate alone and 108 controls from the same location who had not received these drugs. There was no evidence of a drug effect on the clinical or neurophysiological parameters assessed. In this population there was no clinical or neurophysiological evidence of brain-stem toxicity that could be attributed to exposure to artemisinin or artesunate. Hide abstract

Wills B, Farrar J. 2000. Central nervous system infections in the tropics: diagnosis, treatment and prevention. Curr Opin Infect Dis, 13 (3), pp. 259-264. Read abstract | Read more

The present review is a brief discussion of some of the important new developments that have been reported relating to bacterial and viral infections of the central nervous system. For many of these conditions, certain issues remain unresolved, including what is the best diagnostic approach, what is the optimum treatment and how best to prevent such conditions. The development of improved surveillance, more effective vaccines and a greater understanding of the pathophysiology of these diseases all offer great potential benefits. The hope is that these advances, when they come, will be affordable to those who need them most. Hide abstract

Solomon T, Dung NM, Vaughn DW, Kneen R, Thao LT, Raengsakulrach B, Loan HT, Day NP et al. 2000. Neurological manifestations of dengue infection. Lancet, 355 (9209), pp. 1053-1059. Read abstract | Read more

Severe forms of dengue, the most important arboviral infection of man, are associated with haemorrhagic disease and a generalised vascular leak syndrome. The importance of dengue as a cause of neurological disease is uncertain. Hide abstract

Parry CM, Diep TS, Wain J, Hoa NT, Gainsborough M, Nga D, Davies C, Phu NH, Hien TT, White NJ, Farrar JJ. 2000. Nasal carriage in Vietnamese children of Streptococcus pneumoniae resistant to multiple antimicrobial agents. Antimicrob Agents Chemother, 44 (3), pp. 484-488. Read abstract | Read more

Resistance to antimicrobial agents in Streptococcus pneumoniae is increasing rapidly in many Asian countries. There is little recent information concerning resistance levels in Vietnam. A prospective study of pneumococcal carriage in 911 urban and rural Vietnamese children, of whom 44% were nasal carriers, was performed. Carriage was more common in children <5 years old than in those >/=5 years old (192 of 389 [49.4%] versus 212 of 522 [40.6%]; P, 0.01). A total of 136 of 399 isolates (34%) had intermediate susceptibility to penicillin (MIC, 0.1 to 1 mg/liter), and 76 of 399 isolates (19%) showed resistance (MIC, >1.0 mg/liter). A total of 54 of 399 isolates (13%) had intermediate susceptibility to ceftriaxone, and 3 of 399 isolates (1%) were resistant. Penicillin resistance was 21.7 (95% confidence interval, 7.0 to 67.6) times more common in urban than in rural children (35 versus 2%; P, <0.001). More than 40% of isolates from urban children were also resistant to erythromycin, trimethoprim-sulfamethoxazole, chloramphenicol, and tetracycline. Penicillin resistance was independently associated with an urban location when the age of the child was controlled for. Multidrug resistance (resistance to three or more antimicrobial agent groups) was present in 32% of isolates overall but in 39% of isolates with intermediate susceptibility to penicillin and 86% of isolates with penicillin resistance. The predominant serotypes of the S. pneumoniae isolates were 19, 23, 14, 6, and 18. Almost half of the penicillin-resistant isolates serotyped were serotype 23, and these isolates were often multidrug resistant. This study suggests that resistance to penicillin and other antimicrobial agents is common in carriage isolates of S. pneumoniae from children in Vietnam. Hide abstract

Thwaites G, Chau TT, Mai NT, Drobniewski F, McAdam K, Farrar J. 2000. Tuberculous meningitis. J Neurol Neurosurg Psychiatry, 68 (3), pp. 289-299. Read abstract | Read more

Uncertainty and doubt dominate all aspects of tuberculous meningitis (TBM). The variable natural history and accompanying clinical features of TBM hinders the diagnosis. Ziehl-Neelsen staining lacks sensitivity and culture results are often insufficiently timely to aid clinical judgement. New rapid diagnostic methods are incompletely evaluated, and many are not suitable for laboratories in low income countries. The duration of chemotherapy for TBM is unclear and the benefits of adjuvant corticosteroids remain in doubt. The only uncomfortable certainties lie in the fatal consequences of missed diagnoses and delayed treatment. This review will discuss the current uncertainties surrounding TBM. More attention will be given to diagnosis and management, as these areas have a direct bearing on patient outcome. Hide abstract

Gamble J, Bethell D, Day NP, Loc PP, Phu NH, Gartside IB, Farrar JF, White NJ. 2000. Age-related changes in microvascular permeability: a significant factor in the susceptibility of children to shock? Clin Sci (Lond), 98 (2), pp. 211-216. Read abstract | Read more

During studies of the pathogenesis of dengue shock syndrome, a condition largely confined to childhood and characterized by a systemic increase in vascular permeability, we observed that healthy controls, age-matched to children with dengue shock syndrome, gave high values of filtration capacity (K(f)), a factor describing vascular permeability. We hypothesized that K(f) might be age dependent. Calf K(f) was studied in 89 healthy Vietnamese subjects aged 5 to 77 years. The K(f) was highest in the youngest children [7. 53 (1.96-15.46) K(f)U; median (range); where the units of K(f), K(f)U=ml.min(-1).100 ml(-1).mmHg(-1)]. Values were 3- to 4-fold lower towards the end of the second decade [4.69 (1.91-7.06) K(f)U]. Young mammals are known to have a larger microvascular surface area per unit volume of skeletal muscle than adults. During development the proportion of developing vessels is greater. Moreover, the novel microvessels are known to be more permeable to water and plasma proteins than when mature. These factors may explain why children more readily develop hypovolaemic shock than adults in dengue haemorrhagic fever and other conditions characterized by increased microvascular permeability. Hide abstract

Connerton P, Wain J, Hien TT, Ali T, Parry C, Chinh NT, Vinh H, Ho VA et al. 2000. Epidemic typhoid in vietnam: molecular typing of multiple-antibiotic-resistant Salmonella enterica serotype typhi from four outbreaks. J Clin Microbiol, 38 (2), pp. 895-897. Read abstract

Multidrug-resistant Salmonella enterica serotype Typhi isolates from four outbreaks of typhoid fever in southern Vietnam between 1993 and 1997 were compared. Pulsed-field gel electrophoresis, bacteriophage and plasmid typing, and antibiotic susceptibilities showed that independent outbreaks of multidrug-resistant typhoid fever in southern Vietnam are caused by single bacterial strains. However, different outbreaks do not derive from the clonal expansion of a single multidrug-resistant serotype Typhi strain. Hide abstract

Farrar J, Newton C. 2000. Neurological aspects of tropical disease J Neurol Neurosurg Psychiatry, 68 (2), pp. 135-136. | Read more

Parry CM, Wuthiekanun V, Hoa NT, Diep TS, Thao LT, Loc PV, Wills BA, Wain J, Hien TT, White NJ, Farrar JJ. 1999. Melioidosis in Southern Vietnam: clinical surveillance and environmental sampling. Clin Infect Dis, 29 (5), pp. 1323-1326. Read abstract | Read more

From 1992-1998, Burkholderia pseudomallei was isolated from only 9 (0.25%) of 3653 cultures of blood from febrile patients admitted to the Centre for Tropical Diseases in Ho Chi Minh City, an infectious disease referral center for southern Vietnam. Soil was sampled from 407 sites in 147 rice fields along the 5 major roads radiating from Ho Chi Minh City. B. pseudomallei was isolated from 73 sites (18%) in 39 rice fields (27%), but only 15 (21%) of the 71 isolates from 9 (6%) of 147 fields were the virulent l-arabinose (ara)-negative biotype. All except 1 of the fields with the ara-negative biotype were close to the homes of the patients with melioidosis. The low incidence of melioidosis in the provinces around Ho Chi Minh City may be explained by the restricted distribution of ara-negative B. pseudomallei in the soil in this area. Hide abstract

Farrar JJ. 1999. Nipah-virus encephalitis--investigation of a new infection. Lancet, 354 (9186), pp. 1222-1223. | Read more

Chau NV, Hien TT, Sellar R, Kneen R, Farrar JJ. 1999. "Can't you use another vaccine?" Postrabies vaccination encephalitis. J Neurol Neurosurg Psychiatry, 67 (4), pp. 555-556. | Read more

Dung NM, Day NP, Tam DT, Loan HT, Chau HT, Minh LN, Diet TV, Bethell DB et al. 1999. Fluid replacement in dengue shock syndrome: a randomized, double-blind comparison of four intravenous-fluid regimens. Clin Infect Dis, 29 (4), pp. 787-794. Read abstract | Read more

Dengue hemorrhagic fever and dengue shock syndrome (DSS) are major causes of childhood morbidity and mortality in many tropical countries. Increased intravascular permeability leading to shock is the cardinal feature of DSS. Fluid resuscitation to counteract massive plasma leakage is the mainstay of treatment. A double-blind, randomized trial comparing four intravenous-fluid regimens for acute resuscitation of 50 children with DSS was conducted. Colloids (dextran 70 or the protein digest gelafundin 35,000) restored cardiac index and blood pressure and normalized hematocrit more rapidly than crystalloids (Ringer's lactate or 0.9%-weight/volume saline). Dextran 70 provided the most rapid normalization of the hematocrit and restoration of the cardiac index, without adverse effects, and may be the preferred solution for acute resuscitation in DSS. Further large-scale double-blind trials are required to provide an evidence-based approach to the management of DSS. Hide abstract

Parry CM, Hoa NT, Diep TS, Wain J, Chinh NT, Vinh H, Hien TT, White NJ, Farrar JJ. 1999. Value of a single-tube widal test in diagnosis of typhoid fever in Vietnam. J Clin Microbiol, 37 (9), pp. 2882-2886. Read abstract

The diagnostic value of an acute-phase single-tube Widal test for suspected typhoid fever was evaluated with 2,000 Vietnamese patients admitted to an infectious disease referral hospital between 1993 and 1998. Test patients had suspected typhoid fever and a blood culture positive for Salmonella typhi (n= 1,400) or Salmonella paratyphi A (n = 45). Control patients had a febrile illness for which another cause was confirmed (malaria [n = 103], dengue [n = 76], or bacteremia due to another microorganism [n = 156] or tetanus (n = 265). An O-agglutinin titer of >/=100 was found in 18% of the febrile controls and 7% of the tetanus patients. Corresponding values for H agglutinins were 8 and 1%, respectively. The O-agglutinin titer was >/=100 in 83% of the blood culture-positive typhoid fever cases, and the H-agglutinin titer was >/=100 in 67%. The disease prevalence in investigated patients in this hospital was 30.8% (95% confidence interval, 26.8 to 35.1%); at this prevalence, an elevated level of H agglutinins gave better positive predictive values for typhoid fever than did O agglutinins. With a cutoff titer of >/=200 for O agglutinin or >/=100 for H agglutinin, the Widal test would diagnose correctly 74% of the blood culture-positive cases of typhoid fever. However, 14% of the positive results would be false-positive, and 10% of the negative results would be false-negative. The Widal test can be helpful in the laboratory diagnosis of typhoid fever in Vietnam if interpreted with care. Hide abstract

Brown H, Hien TT, Day N, Mai NT, Chuong LV, Chau TT, Loc PP, Phu NH et al. 1999. Evidence of blood-brain barrier dysfunction in human cerebral malaria. Neuropathol Appl Neurobiol, 25 (4), pp. 331-340. Read abstract | Read more

Patients infected with the malaria parasite Plasmodium falciparum may develop a diffuse reversible encephalopathy, termed cerebral malaria. It is unclear how the intraerythrocytic parasite, which sequesters in the cerebral microvasculature but does not enter the brain parenchyma, induces this neurological syndrome. Adhesion of parasitized red blood cells in the brain microvasculature is mediated by specific receptors on the host endothelium, including intercellular adhesion molecule (ICAM)-1, CD36 and CD31. Leucocyte binding to cerebral endothelial cells in culture induces intracellular signalling via ICAM-1. The hypothesis that parasitized red blood cells binding to receptors on cerebral endothelial cells causes changes in the integrity of the blood-brain barrier was tested. Immunohistochemistry was used to examine the blood-brain barrier in human cerebral malaria, with antibodies to macrophage and endothelial activation markers, intercellular junction proteins, and plasma proteins. The distribution of the cell junction proteins occludin, vinculin and ZO-1 were altered in cerebral malaria cases compared to controls. While fibrinogen was the only plasma protein detected in the perivascular space, there was widespread perivascular macrophage activation, suggesting that these cells had been exposed to plasma proteins. It was concluded that functional changes to the blood-brain barrier occur in cerebral malaria, possibly as a result of the binding of parasitized red blood cells to cerebral endothelial cells. These changes require further examination in vitro. Hide abstract

Wain J, Hien TT, Connerton P, Ali T, Parry CM, Chinh NT, Vinh H, Phuong CX et al. 1999. Molecular typing of multiple-antibiotic-resistant Salmonella enterica serovar Typhi from Vietnam: application to acute and relapse cases of typhoid fever. J Clin Microbiol, 37 (8), pp. 2466-2472. Read abstract

The rate of multiple-antibiotic resistance is increasing among Salmonella enterica serovar Typhi strains in Southeast Asia. Pulsed-field gel electrophoresis (PFGE) and other typing methods were used to analyze drug-resistant and -susceptible organisms isolated from patients with typhoid fever in several districts in southern Vietnam. Multiple PFGE and phage typing patterns were detected, although individual patients were infected with strains of a single type. The PFGE patterns were stable when the S. enterica serovar Typhi strains were passaged many times in vitro on laboratory medium. Paired S. enterica serovar Typhi isolates recovered from the blood and bone marrow of individual patients exhibited similar PFGE patterns. Typing of S. enterica serovar Typhi isolates from patients with relapses of typhoid indicated that the majority of relapses were caused by the same S. enterica serovar Typhi strain that was isolated during the initial infection. However, some individuals were infected with distinct and presumably newly acquired S. enterica serovar Typhi isolates. Hide abstract

Solomon T, Thao LT, Dung NM, Kneen R, Hung NT, Nisalak A, Vaughn DW, Farrar J, Hien TT, White NJ, Cardosa MJ. 1998. Rapid diagnosis of Japanese encephalitis by using an immunoglobulin M dot enzyme immunoassay. J Clin Microbiol, 36 (7), pp. 2030-2034. Read abstract

Japanese encephalitis (JE) occurs in rural settings in southern and eastern Asia, where diagnostic facilities are limited. For the diagnosis of JE virus (JEV) infection, we developed a nitrocellulose membrane-based immunoglobulin M (IgM) capture dot enzyme immunoassay (MAC DOT) that is rapid, simple to use, requires no specialized equipment, and can distinguish JEV from dengue infection. In a prospective field study in southern Vietnam, 155 cerebrospinal fluid (CSF) and 341 serum samples were collected from 111 children and 83 adults with suspected encephalitis. The JEV MAC DOT, performed on site, was scored visually from negative to strongly positive by two observers, and the results were compared subsequently with those of the standard IgM capture enzyme-linked immunosorbent assay. For the 179 patients with adequate specimens, the MAC DOT correctly identified 59 of 60 JEV-positive patients and 118 of 119 JEV-negative patients (sensitivity [95% confidence intervals], 98.3% [92.1 to 99.91%]; specificity, 99.2% [95.9 to 100.0%]; positive predictive value, 0.98; negative predictive value, 0.99). The MAC DOT also correctly identified three patients with dengue encephalopathy. Admission specimens were positive for 73% of JE patients. Interobserver agreement for MAC DOT diagnosis was excellent (kappa = 0.94). The JEV MAC DOT is a simple and reliable rapid diagnostic test for JE in rural hospitals. Hide abstract

Vincent A, Jacobson L, Plested P, Polizzi A, Tang T, Riemersma S, Newland C, Ghorazian S et al. 1998. Antibodies affecting ion channel function in acquired neuromyotonia, in seropositive and seronegative myasthenia gravis, and in antibody-mediated arthrogryposis multiplex congenita. Ann N Y Acad Sci, 841 (1 MYASTHENIA GR), pp. 482-496. Read abstract | Read more

A new autoimmune disease affecting the neuromuscular junction has been defined. Acquired neuromyotonia is associated with antibodies to voltage-gated potassium channels that act, at least in part, by reducing potassium channel function with resulting neuronal hyperactivity. This condition is quite frequently associated with thymoma and, in many cases, antibodies to acetylcholine receptors are present as well as antibodies to VGKC. Improvements in techniques and the availability of cloned DNA and recombinant forms of the AChR subunits have led to new observations concerning the specificity and roles of antibodies in myasthenia gravis. The transfection of a cell line with the epsilon subunit means that we can now accurately compare antibodies reactive with adult and fetal human AChR. This may help to determine the relationship between AChR subunit expression in different tissues and the induction of antibodies that bind specifically to the two forms, as well as to clarify the role of antibodies to fetal or adult AChR in causing ocular muscle symptoms. Serum antibodies from a few mothers with obstetric histories of recurrent arthrogryposis multiplex congenita in their babies specifically inhibit the function of fetal AChR. These observations not only explain the cause of some cases of arthrogryposis multiplex congenita, but also suggest that other fetal-specific antibodies might be responsible for other fetal or neonatal conditions. An animal model has been established to enable us to investigate the role of maternal serum factors in causing such disorders. Seronegative MG has been the subject of many studies from our laboratory over the last ten years. The transience of the effects of SNMG plasmas on AChR function strongly suggests that the plasma antibodies do not bind directly to the AChR, but inhibit function by some indirect mechanism. They do not appear to act via the cAMP-dependent protein kinase pathway, and studies are in progress to investigate the involvement of other second messenger systems. Hide abstract

Matthews I, Farrar J, McLachlan S, Rapoport B, Newsom-Davis J, Willcox N, Vincent A. 1998. Production of Fab fragments against the human acetylcholine receptor from myasthenia gravis thymus lambda and kappa phage libraries. Ann N Y Acad Sci, 841 (1 MYASTHENIA GR), pp. 418-421. | Read more

Parry C, Wain J, Chinh NT, Vinh H, Farrar JJ. 1998. Quinolone-resistant Salmonella typhi in Vietnam. Lancet, 351 (9111), pp. 1289. | Read more

Farrar J, Portolano S, Willcox N, Vincent A, Jacobson L, Newsom-Davis J, Rapoport B, McLachlan SM. 1997. Diverse Fab specific for acetylcholine receptor epitopes from a myasthenia gravis thymus combinatorial library. Int Immunol, 9 (9), pp. 1311-1318. Read abstract | Read more

The muscle weakness in myasthenia gravis (MG) is caused by heterogeneous high-affinity IgG autoantibodies to the nicotinic acetylcholine receptor (AChR), a complex ion channel glycoprotein. These antibodies are clearly responsible for reducing AChR numbers at the neuromuscular junction in myasthenia; however, the origins, diversity, specificity and pathogenicity of individual antibodies have not yet been established. We have cloned and characterized four different AChR-specific Fab from an MG patient's thymus by screening an IgG1/kappa gene combinatorial lambda phage library with soluble human AChR labeled with [125I] alpha-bungarotoxin. Unlike most previously cloned human antibodies, all four Fab immunoprecipitated soluble human muscle AChR. Two Fab strongly inhibited binding of mAb to the main immunogenic region on the alpha subunits and one Fab bound to an epitope on the fetal-specific gamma subunit. In sensitivity and fine specificity, these Fab resembled the anti-AChR antibodies found in many MG patients, including the donor. The closest germline counterparts for their heavy chains were in VH families 1, 3 and 4; however, there were many differences consistent with an antigen-driven response of diverse B cell clones. The combinatorial approach holds promise for further analysis of human autoantibodies. Hide abstract

Humphries J, Akintunde C, Richens J, Cann K, Farrar J, Woodrow D, Tong W, Keat A. 1996. Search for infective agents in undifferentiated oligoarthritis in Papua New Guinea. Br J Rheumatol, 35 (5), pp. 492-493.

Fitt GJ, Farrar J, Baird AE, Brooks M, Gilligan A, Donnan GA, Hennessy O. 1993. Intra-arterial streptokinase in acute ischaemic stroke. A pilot study. Med J Aust, 159 (5), pp. 331-334. Read abstract

To assess the safety and efficacy of the intra-arterial administration of streptokinase within 24 hours of acute ischaemic stroke. Hide abstract

Farrar J, Donnan GA. 1993. Capsular warning syndrome preceding pontine infarction. Stroke, 24 (5), pp. 762. | Read more

Rae P, Farrar J, Beckett G, Toft A. 1993. Assessment of thyroid status in elderly people. BMJ, 307 (6897), pp. 177-180.

FARRAR J, TOFT A. 1991. I-131 TREATMENT OF HYPERTHYROIDISM - CURRENT ISSUES CLINICAL ENDOCRINOLOGY, 35 (3), pp. 207-212. | Read more

Farrar JJ, Toft AD. 1991. Iodine-131 treatment of hyperthyroidism: current issues. Clin Endocrinol (Oxf), 35 (3), pp. 207-212. | Read more

Tickle C, Crawley A, Farrar J. 1989. Retinoic acid application to chick wing buds leads to a dose-dependent reorganization of the apical ectodermal ridge that is mediated by the mesenchyme. Development, 106 (4), pp. 691-705. Read abstract

Local application of retinoic acid to wing buds of chick embryos leads to dose- and position-dependent changes in the pattern of cellular differentiation. Early effects of retinoid treatment on the apical ectodermal ridge coordinate pattern changes and morphogenesis. The length of the apical ridge increases when additional digits will form but decreases when digits are lost. These changes in length can be understood in terms of a threshold response to the local retinoid concentration that results in either disappearance or maintenance of the ridge (Lee & Tickle, J. Embryol. exp. Morph. 90, 139-169 (1985)). Here, we have analysed the mechanisms involved in ridge disappearance by locally applying retinoic acid to the apex of stage 20 chick wing buds. With this treatment regime, low doses give duplicated digit patterns and higher doses truncations. The height of the apical ridge is progressively reduced with increasing doses of retinoid and the time course of ridge flattening indicates that the height of the ridge is correlated with bud outgrowth. With high doses of retinoic acid, the typical ridge, a pseudostratified epithelium in which the columnar cells are tightly packed, disappears and the epithelium at the tip of the bud consists of loosely packed cuboidal cells. Shortly after treatment, there is a decrease in the number of gap junctions between ridge cells. This early change in cell contacts suggests that gap junctions may be involved in maintaining epithelial morphology. When treated epithelium is recombined with untreated mesenchyme, an apical ridge is reestablished and distal structures can be generated. In contrast, when treated mesenchyme is recombined with the epithelium from normal buds, only proximal structures are formed. Therefore, retinoids can lead to a reorganization of the apical ectodermal ridge which is mediated and maintained by the mesenchyme. Hide abstract

Farrar J, Kapadia F. 1989. Cardiac complications of total parenteral nutrition: the role of two-dimensional echocardiography in diagnosis. Ann R Coll Surg Engl, 71 (4), pp. 274.

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