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HIV (human immunodeficiency virus) is a virus that weakens the immune system and hinders the body’s ability to fight disease.
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region.
BackgroundMultidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined.MethodsIn a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively.ResultsIn total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1-3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P ConclusionsOur data indicate a drastic increase of FQ resistance, as well as emerging bedaquiline resistance which endangers the success of newly endorsed MDR-TB treatment regimens. Rapid changes in treatment and control strategies are required to contain transmission of highly successful pre-XDR L2 strains in the Mumbai Metropolitan region but presumably also India-wide.
tstrait: a quantitative trait simulator for ancestral recombination graphs.
SummaryAncestral recombination graphs (ARGs) encode the ensemble of correlated genealogical trees arising from recombination in a compact and efficient structure, and are of fundamental importance in population and statistical genetics. Recent breakthroughs have made it possible to simulate and infer ARGs at biobank scale, and there is now intense interest in using ARG-based methods across a broad range of applications, particularly in genome-wide association studies (GWAS). Sophisticated methods exist to simulate ARGs using population genetics models, but there is currently no software to simulate quantitative traits directly from these ARGs. To apply existing quantitative trait simulators users must export genotype data, losing important information about ancestral processes and producing prohibitively large files when applied to the biobank-scale datasets currently of interest in GWAS. We present tstrait, an open-source Python library to simulate quantitative traits on ARGs, and show how this user-friendly software can quickly simulate phenotypes for biobank-scale datasets on a laptop computer.Availability and implementationtstrait is available for download on the Python Package Index. Full documentation with examples and workflow templates is available on https://tskit.dev/tstrait/docs/, and the development version is maintained on GitHub (https://github.com/tskit-dev/tstrait).
Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID‐19
AbstractObjectiveEndocrine systems are disrupted in acute illness, and symptoms reported following coronavirus disease 2019 (COVID‐19) are similar to those found with clinical hormone deficiencies. We hypothesised that people with severe acute COVID‐19 and with post‐COVID symptoms have glucocorticoid and sex hormone deficiencies.Design/PatientsSamples were obtained for analysis from two UK multicentre cohorts during hospitalisation with COVID‐19 (International Severe Acute Respiratory Infection Consortium/World Health Organisation [WHO] Clinical Characterization Protocol for Severe Emerging Infections in the UK study), and at follow‐up 5 months after hospitalisation (Post‐hospitalisation COVID‐19 study).MeasurementsPlasma steroids were quantified by liquid chromatography–mass spectrometry. Steroid concentrations were compared against disease severity (WHO ordinal scale) and validated symptom scores. Data are presented as geometric mean (SD).ResultsIn the acute cohort (n = 239, 66.5% male), plasma cortisol concentration increased with disease severity (cortisol 753.3 [1.6] vs. 429.2 [1.7] nmol/L in fatal vs. least severe, p < .001). In males, testosterone concentrations decreased with severity (testosterone 1.2 [2.2] vs. 6.9 [1.9] nmol/L in fatal vs. least severe, p < .001). In the follow‐up cohort (n = 198, 62.1% male, 68.9% ongoing symptoms, 165 [121–192] days postdischarge), plasma cortisol concentrations (275.6 [1.5] nmol/L) did not differ with in‐hospital severity, perception of recovery, or patient‐reported symptoms. Male testosterone concentrations (12.6 [1.5] nmol/L) were not related to in‐hospital severity, perception of recovery or symptom scores.ConclusionsCirculating glucocorticoids in patients hospitalised with COVID‐19 reflect acute illness, with a marked rise in cortisol and fall in male testosterone. These findings are not observed 5 months from discharge. The lack of association between hormone concentrations and common post‐COVID symptoms suggests steroid insufficiency does not play a causal role in this condition.
Artificial Intelligence-Based Quality Assessment of Histopathology Whole-Slide Images within a Clinical Workflow: Assessment of ‘PathProfiler’ in a Diagnostic Pathology Setting
Digital pathology continues to gain momentum, with the promise of artificial intelligence to aid diagnosis and for assessment of features which may impact prognosis and clinical management. Successful adoption of these technologies depends upon the quality of digitised whole-slide images (WSI); however, current quality control largely depends upon manual assessment, which is inefficient and subjective. We previously developed PathProfiler, an automated image quality assessment tool, and in this feasibility study we investigate its potential for incorporation into a diagnostic clinical pathology setting in real-time. A total of 1254 genitourinary WSI were analysed by PathProfiler. PathProfiler was developed and trained on prostate tissue and, of the prostate biopsy WSI, representing 46% of the WSI analysed, 4.5% were flagged as potentially being of suboptimal quality for diagnosis. All had concordant subjective issues, mainly focus-related, 54% severe enough to warrant remedial action which resulted in improved image quality. PathProfiler was less reliable in assessment of non-prostate surgical resection-type cases, on which it had not been trained. PathProfiler shows potential for incorporation into a digitised clinical pathology workflow, with opportunity for image quality improvement. Whilst its reliability in the current form appears greatest for assessment of prostate specimens, other specimen types, particularly biopsies, also showed benefit.
Clinical presentation and treatment of 2 patients with infection caused by Chromobacterium violaceum in Vietnam.
Chromobacterium violaceum is a rare but severe and often fatal cause of disease in humans. We present 2 clinical cases of sepsis and skin abscesses / cellulitis caused by C. violaceum seen in a referral hospital for infectious diseases in Vietnam. Both patients survived, but appropriate antibiotic treatment was only installed after culture of the organism. We reviewed and summarised the characteristics of C. violaceum infection and treatment.
Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
AbstractSARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited. Here we studied ~45,000 reinfections from the UK’s national COVID-19 Infection Survey and quantified the risk of reinfection in multiple waves, including those driven by BA.1, BA.2, BA.4/5, and BQ.1/CH.1.1/XBB.1.5 variants. Reinfections were associated with lower viral load and lower percentages of self-reporting symptoms compared with first infections. Across multiple Omicron waves, estimated protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Estimated protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year). Those 14–180 days after receiving their most recent vaccination had a lower risk of reinfection than those >180 days from their most recent vaccination. Reinfection risk was independently higher in those aged 30–45 years, and with either low or high viral load in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; both viral evolution and waning immunity are independently associated with reinfection.
Ecology of End-of-life Medical Care for Advanced Cancer Patients in China.
AimsCancer is a leading cause of death worldwide. Approximately 30% of global cancer-related deaths occur in mainland China. However, there is a paucity of information regarding the end-of-life care-seeking behavior of patients with advanced cancer in China. Our study was to investigate end-of-life care-seeking behavior and to quantify the association between sociodemographic characteristics and the location and pattern of end-of-life care.MethodsWe conducted a mortality follow-back survey using caregivers' interviews to estimate the number of individuals pre 1000 who died between 2013 and 2021 in the last 3 months of life. We collected data on hospitalization, outpatient visits, cardiopulmonary resuscitation, palliative care and hospice utilization, and place of death, stratified by age, gender, marital status, household income, residential zone, insurance type, and the primary end-of-life decision-maker of the decedents.ResultsWe analyzed data from 857 deceased cancer patients, representing an average of 1000 individuals. Among these patients, 861 experienced at least moderate or more severe pain, 774 were hospitalized at least once, 468 received intensive treatment, 389 had at least one outpatient visit, 270 died in the hospital, 236 received cardiopulmonary resuscitation and 99 received specialist hospice care.ConclusionsOur study provides insights into the end-of-life care-seeking behavior of advanced cancer patients in China and our findings serve as a useful benchmark for estimating the use of end-of-life medical care. It highlights the need for the establishment of an accessible and patient-centered palliative care and hospice system.
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci
AbstractStreptococcus pneumoniae (pneumococcus) is a nasopharyngeal commensal and respiratory pathogen. This study characterises the immunoglobulin G (IgG) repertoire recognising pneumococci from birth to 24 months old (mo) in a prospectively-sampled cohort of 63 children using a panproteome array. IgG levels are highest at birth, due to transplacental transmission of maternal antibodies. The subsequent emergence of responses to individual antigens exhibit distinct kinetics across the cohort. Stable differences in the strength of individuals’ responses, correlating with maternal IgG concentrations, are established by 6 mo. By 12 mo, children develop unique antibody profiles that are boosted by re-exposure. However, some proteins only stimulate substantial responses in adults. Integrating genomic data on nasopharyngeal colonisation demonstrates rare pneumococcal antigens can elicit strong IgG levels post-exposure. Quantifying such responses to the diverse core loci (DCL) proteins is complicated by cross-immunity between variants. In particular, the conserved N terminus of DCL protein zinc metalloprotease B provokes the strongest early IgG responses. DCL proteins’ ability to inhibit mucosal immunity likely explains continued pneumococcal carriage despite hosts’ polyvalent antibody repertoire. Yet higher IgG levels are associated with reduced incidence, and severity, of pneumonia, demonstrating the importance of the heterogeneity in response strength and kinetics across antigens and individuals.
Interpretations of Studies on SARS-CoV-2 Vaccination and Post-acute COVID-19 Sequelae.
This article discusses causal interpretations of epidemiologic studies of the effects of vaccination on sequelae after acute severe acute respiratory syndrome coronavirus 2 infection. To date, researchers have tried to answer several different research questions on this topic. While some studies assessed the impact of postinfection vaccination on the presence of or recovery from post-acute coronavirus disease 2019 syndrome, others quantified the association between preinfection vaccination and postacute sequelae conditional on becoming infected. However, the latter analysis does not have a causal interpretation, except under the principal stratification framework-that is, this comparison can only be interpreted as causal for a nondiscernible stratum of the population. As the epidemiology of coronavirus disease 2019 is now nearly entirely dominated by reinfections, including in vaccinated individuals, and possibly caused by different Omicron subvariants, it has become even more important to design studies on the effects of vaccination on postacute sequelae that address precise causal questions and quantify effects corresponding to implementable interventions.
Expanded Access Programme for the use of tecovirimat for the treatment of monkeypox infection: A study protocol for an Expanded Access Programme.
BackgroundMonkeypox is a viral zoonotic disease commonly reported in humans in parts of Central and West Africa. This protocol is for an Expanded Access Programme (EAP) to be implemented in the Central African Republic, where Clade I monkeypox virus diseases is primarily responsible for most monkeypox infections. The objective of the programme is to provide patients with confirmed monkeypox with access to tecovirimat, a novel antiviral targeting orthopoxviruses, and collect data on clinical and virological outcomes of patients to inform future research.MethodsThe study will be conducted at participating hospitals in the Central African Republic. All patients who provide informed consent to enrol in the programme will receive tecovirimat. Patients will remain in hospital for the duration of treatment. Data on clinical signs and symptoms will be collected every day while the patient is hospitalised. Blood, throat and lesion samples will be collected at baseline and then on days 4, 8, 14 and 28. Patient outcomes will be assessed on Day 14 -end of treatment-and at Day 28. Adverse event and serious adverse event data will be collected from the point of consent until Day 28.DiscussionThis EAP is the first protocolised treatment programme in Clade I MPXV. The data generated under this protocol aims to describe the use of tecovirimat for Clade I disease in a monkeypox endemic region of Central Africa. It is hoped that this data can inform the definition of outcome measures used in future research and contribute to the academic literature around the use of tecovirimat for the treatment of monkeypox. The EAP also aims to bolster research capacity in the region in order for robust randomised controlled trials to take place for monkeypox and other diseases.Trial registration{2a & 2b}: ISRCTN43307947.
Analysis of primary care electronic health record data of people living with hepatitis B virus: infection and hepatocellular carcinoma risk associated with socio-economic deprivation.
ObjectivesWe set out to characterise chronic hepatitis B (CHB) in the primary care population in England and investigate risk factors for progression to hepatocellular carcinoma (HCC).Study designRetrospective cohort study.MethodsWe identified 8039 individuals with CHB in individuals aged ≥18 years between 1999 and 2019 in the English primary care database QResearch. HCC risk factors were investigated using Cox proportional hazards modelling.ResultsMost of those with a record of CHB were males (60%) of non-White ethnicity (>70%), and a high proportion were in the most deprived Townsend deprivation quintile (44%). Among 7029 individuals with longitudinal data, 161 HCC cases occurred. Increased HCC hazards were significantly associated with male sex (adjusted hazards ratio [aHR] 3.17, 95% confidence interval [95% CI] 1.92-5.23), in the fifth deprivation quintile as compared to the third quintile (aHR 1.69, 95% CI 1.01-2.84), with older age (for age groups 56-65 and ≥66 years, compared to 26-35 years, aHRs 2.82 [95% CI 1.45-5.46] and 3.76 [95% CI 1.79-7.9], respectively), Caribbean ethnicity (aHR 3.32, 95% CI 1.43-7.71, compared to White ethnicity), ascites (aHR 3.15, 95% CI 1.30-7.67), cirrhosis (aHR 6.55, 95% CI 4.57-9.38) and peptic ulcer disease (aHR 2.26, 95% CI 1.45-3.51).ConclusionsTargeting interventions and HCC surveillance at vulnerable groups is essential to improve CHB outcomes and to support progress towards international goals for the elimination of hepatitis infection as a public health threat.
Eight years into the horizon of aspirational maternal and newborn health pledges: a nationwide cross-sectional exploration of the Burundian EmONC network capacity and budget deficits
Objective The Burundian emergency obstetric and neonatal care (EmONC) programme, which was initiated in 2017 and supported by a specific policy, does not appear to reverse maternal and newborn mortality trends. Our study examined the capacity challenges facing participating EmONC facilities and developed alternative investment proposals to improve their readiness paying particular attention to EmONC professionals, physical infrastructure, and capital equipment. Design Cross-sectional study. Setting Burundian EmONC facilities (n=112). Participants We examined EmONC policy documents, consulted 12 maternal and newborn health experts and 23 stakeholders and policymakers, surveyed all EmONC facilities (n=112), and collected cost data from the Ministry of Health and local suppliers in Burundi. We developed three context-specific EmONC resource benchmark standards by facility type; the Burundian policy norms and the expert minimum and maximum suggested thresholds; and used these alternatives to estimate EmONC resource gaps. We forecasted three corresponding budget estimates needed to address prevailing deficits taking a government perspective for a 5-year EmONC investment strategy. Additionally, we explored relationships between EmONC professionals and selected measures of service delivery using bivariate analyses and graphically. Results The lowest EmONC resource benchmark revealed that 95% of basic EmONC and all comprehensive EmONC facilities lack corresponding sets of human resources and 90% of all facilities need additional physical infrastructure and capital equipment. Assessed against the highest benchmark which proposes the most progressive set of standards for the prevailing workloads, Burundi would require 162 more medical doctors, 1005 midwives and nurses, 132 delivery rooms, 191 delivery tables, 678 and 156 maternity and newborn care beds, and 395 incubators amounting to US$32.9 million additional budget for 5 years. Conclusion We demonstrated that Burundian EmONC facilities face enormous capacity challenges equivalent to US$32.9 million funding gap for 5 years; averagely approximating to 5.96% total health budget increase annually.
Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine.
Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6-14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4+ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol.