Prof Derrick Crook
|Technology Exchange:||Bioinformatics, Computational biology, Mass spectrometry, Medical statistics, SNP typing and Statistical genetics|
|Scientific Themes:||Immunology & Infectious Disease|
The current programme of research carried out by Professor Derrick Crook's research consortium is largely focussed on translating new molecular technologies and advances in informatics into the investigation of microbial transmission, diagnosis of infectious disease and identifying novel outbreaks of communicable disease. This research is being undertaken through a joint programme of work funded by the Oxford BRC Infection Theme and the Modernising Medical Microbiology UK Clinical Research Consortium (UK-CRC), which consists of the Health Protection Agency (HPA), Wellcome Trust Sanger Institute and the University of Oxford combined with the ORH NHS Trust. In Oxford this involves joint working relationships with Professor Peter Donnelly, Department of Statistics and the Wellcome Trust Centre for Human Genetics (WTCHG), Professor Adrian Hill, Nuffield Department of Medicine, Professor Andrew Pollard, Department of Paediatrics and Professor David Mant and Professor Alastair Gray, Department of Public Health and Primary Care. The aims and objectives of this research is to translate deep sequencing of pathogens on an epidemiological scale for tracking hospital and locally acquired infections and it is focussed on four different major pathogens; Staphylococcus aureus (including MRSA), Clostridium difficile, Norovirus and Mycobacterium tuberculosis. A database linkage project that facilitates investigations of patterns of infectious disease among patients using the Oxford Hospitals and GPs, is also being carried out in tangent for the first three pathogens. Overall this joint programme of work is nationally leading the way in this area and is likely to radically transform the practice of microbiology and infectious disease as well as microbial research in the coming years.
Other research currently being carried out within Derrick Crook's group covers respiratory and gastrointestinal infections and diagnostics, Haemophilus genomics and capsular switch vaccine escape in Pneumococcus. Within the area of diagnostics a HTA funded project investigating the identification of C. difficile and other pathogens from patient stool samples with MassTag multiplex PCR and MLST is being carried out.
|Christine McCartney||Health Protection Agency (HPA) - London||United Kingdom|
|Prof Julian Parkhill||Wellcome Trust Sanger Institute (WTSI)||United Kingdom|
|Mark Wilcox||Health Protection Agency (HPA) - Leeds||United Kingdom|
|Grace Smith||Health Protection Agency (HPA) - Birmingham||United Kingdom|
|Martin Llewelyn||Health Protection Agency (HPA) - Brighton||United Kingdom|
|Dr Jenny Taylor||Wellcome Trust Centre for Human Genetics||University of Oxford||United Kingdom|
Circulation of methicillin-resistant Staphylococcus aureus (MRSA) outside hospitals could alter the impact of hospital-based control strategies. We investigated two groups of cases (each matched to controls with MRSA): 61 'community cases' not in acute hospital in the year before MRSA isolation; and 21 cases with ciprofloxacin-sensitive (CipS) MRSA. Multi-locus sequence typing, spa-typing and Panton-Valentine leukocidin gene testing were performed and demographics obtained. Additional questionnaires were completed by community case GPs. Community cases comprised 6% of Oxfordshire MRSA. Three community cases had received no regular healthcare or antibiotics: one was infected with CipS. Ninety-one percent of community cases had healthcare-associated sequence type (ST)22/36; CipS MRSA cases had heterogeneous STs but many had recent healthcare exposure. A substantial minority of UK MRSA transmission may occur outside hospitals. Hospital strains are becoming 'feral' or persisting in long-term carriers in the community with regular healthcare contacts; those with recent healthcare exposure may nevertheless acquire non-hospital epidemic MRSA strains in the community. Hide abstract
A robust high-throughput multilocus sequence typing (MLST) scheme for Clostridium difficile was developed and validated using a diverse collection of 50 reference isolates representing 45 different PCR ribotypes and 102 isolates from recent clinical samples. A total of 49 PCR ribotypes were represented overall. All isolates were typed by MLST and yielded 40 sequence types (STs). A web-accessible database was set up (http://pubmlst.org/cdifficile/) to facilitate the dissemination and comparison of C. difficile MLST genotyping data among laboratories. MLST and PCR ribotyping were similar in discriminatory abilities, having indices of discrimination of 0.90 and 0.92, respectively. Some STs corresponded to a single PCR ribotype (32/40), other STs corresponded to multiple PCR ribotypes (8/40), and, conversely, the PCR ribotype was not always predictive of the ST. The total number of variable nucleotide sites in the concatenated MLST sequences was 103/3,501 (2.9%). Concatenated MLST sequences were used to construct a neighbor-joining tree which identified four phylogenetic groups of STs and one outlier (ST-11; PCR ribotype 078). These groups apparently correlate with clades identified previously by comparative genomics. The MLST scheme was sufficiently robust to allow direct genotyping of C. difficile in total stool DNA extracts without isolate culture. The direct (nonculture) MLST approach may prove useful as a rapid genotyping method, potentially benefiting individual patients and informing hospital infection control. Hide abstract
Type IV secretion systems (T4SSs) are multisubunit cell-envelope-spanning structures, ancestrally related to bacterial conjugation machines, which transfer proteins and nucleoprotein complexes across membranes. T4SSs mediate horizontal gene transfer, thus contributing to genome plasticity and the evolution of pathogens through dissemination of antibiotic resistance and virulence genes. Moreover, T4SSs are also used for the delivery of bacterial effector proteins across the bacterial membrane and the plasmatic membrane of eukaryotic host cell, thus contributing directly to pathogenicity. T4SSs are usually encoded by multiple genes organized into a single functional unit. Based on a number of features, the organization of genetic determinants, shared homologies and evolutionary relationships, T4SSs have been divided into several groups. Type F and P (type IVA) T4SSs resembling the archetypal VirB/VirD4 system of Agrobacterium tumefaciens are considered to be the paradigm of type IV secretion, while type I (type IVB) T4SSs are found in intracellular bacterial pathogens, Legionella pneumophila and Coxiella burnetii. Several novel T4SSs have been identified recently and their functions await investigation. The most recently described GI type T4SSs play a key role in the horizontal transfer of a wide variety of genomic islands derived from a broad spectrum of bacterial strains. Hide abstract
PCR-based serotyping of Streptococcus pneumoniae has been proposed as a simpler approach than conventional methods, but has not been applied to strains in Asia where serotypes are diverse and different from other part of the world. Furthermore, PCR has not been used to determine serotype distribution in culture-negative meningitis cases. Hide abstract
A 10-year invasive pneumococcal disease (IPD) enhanced surveillance project in the Oxfordshire region of the UK between 1996 and 2005 identified a total of 2691 Streptococcus pneumoniae isolates from all ages that provided a comprehensive description of pneumococcal epidemiology. All isolates were serotyped and those from children under 5 years of age were genotyped and a matched case-control study using adults hospitalized between 1995 and 2000 was performed to estimate the effectiveness of the pneumococcal polysaccharide vaccine in the local population. Fifty-one serotypes were isolated, with different age distributions. The overall incidence of IPD was 9.2 cases per 100 000 population per annum [95 % confidence interval (CI), 8.6-9.9] and that of meningitis was 0.7 per 100 000 population per annum (95 % CI 0.5-0.9). After adjusting for age, serotype 1 was found to be less likely to be associated with meningitis versus other IPD, compared with the most common serotype 14, whereas serotype 12F was more likely to cause meningitis than other IPD. There were significant temporal changes in IPD incidence of four serotypes, with decreases in serotypes 1, 12F and 14 and increases in serotype 8. A possible novel variant (from serotype 6A to 6B) was found using multilocus sequence typing analysis. From the matched case-control study of adults, the pneumococcal polysaccharide vaccine effectiveness was estimated to be 43 % (2-68 %), which did not change significantly after adjustment for pre-existing co-morbidities. The data provide a baseline against which the impact of the pneumococcal conjugate vaccine introduced in the UK in 2006 could be measured. Hide abstract
To compare characteristics of methicillin resistant Staphylococcus aureus (MRSA) and methicillin susceptible S. aureus (MSSA) bacteraemia detected on admission to a UK hospital and to determine whether these organisms are community-acquired. Hide abstract
Despite a substantial burden of non-bacteraemic methicillin resistant Staphylococcus aureus (MRSA) disease, most MRSA surveillance schemes are based on bacteraemias. Using bacteraemia as an outcome, trends at hospital level are difficult to discern, due to random variation. We investigated rates of nosocomial bacteraemic and non-bacteraemic MRSA infection as surveillance outcomes. Hide abstract
BMJ, 337 (nov20 2), pp. a2097. | Read more2008. Fairness of financial penalties to improve control of Clostridium difficile.
Computational and statistical methods for analysis of pathogen genomic variation
Accurate determination of the genetic variants within parasites and bacteria causing infections is critical for the study of these pathogens, whether it be their epidemiology, evolution, surveillance or basic biology. High throughput sequencing, together with large collaborativeprojects collecting data from field-sites across the world and from hospitals, shows much promise as an enabling technology to this end. However pathogen genomes can exhibit extremely high levels of diversity, ...