Nicholas R Thomson

Wellcome Trust Sanger Institute, Cambridge, England, United Kingdom

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Publications (169)1546.29 Total impact

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    ABSTRACT: On 28 November 2011, as part of a local food survey, Public Health England (PHE; formerly the Health Protection Agency) Food Water and Environment (FWE) Laboratory in Preston, England, confirmed the presence of Salmonella in a ready to eat watermelon slice purchased from a major supermarket retailer. The isolate was sent to the Gastrointestinal Bacteria Reference Unit (GBRU) at Colindale, London who reported it as Salmonella enterica subspecies enterica serovar Newport on 6 December 2011. On 13 December 2011, the result was communicated through the Rapid Alert System for Food and Feed (RASFF) of the European Commission [1]. In late December 2011, Health Protection Scotland (HPS) reported four cases of S. Newport, all with the same pulsed-field gel electrophoresis (PFGE) profile which had not previously been seen. Concurrently in England, Wales and Northern Ireland, reporting of S. Newport infections exceeded expected levels. Molecular analysis of isolates from the human cases from all four countries indicated a PFGE profile indistinguishable from the sliced watermelon isolate. On 13 January 2012, Germany reported through the Epidemic Intelligence Information System (EPIS) at the European Centre of Disease Prevention and Control (ECDC) fourteen S. Newport isolates that were indistinguishable from the PFGE profile of the sliced watermelon isolate. Four cases with this profile were also reported in Ireland in January 2012. A multi-agency outbreak control team (OCT) was convened on 16 January 2012 comprising staff from PHE, Public Health Wales (PHW), HPS and the United Kingdom (UK) Food Standards Agency (FSA). There were separate communications with the Robert Koch Institute (RKI) regarding the German cases and with the Health Protection Surveillance Centre (HPSC) and the National Salmonella, Shigella and Listeria Reference Laboratory (NSSLRL) regarding cases from Ireland. German and Irish public health and food safety authorities subsequently joined the OCT. The aims of investigations were to gather and collate information on exposures, to identify the potential source(s), to institute immediate control measures and to determine if there were any lessons to be learnt regarding future prevention. We describe an outbreak of S. Newport across six countries linked to the consumption of watermelon originating from Brazil.
    Euro surveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin 08/2014; 19(31). · 5.49 Impact Factor
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    ABSTRACT: Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multi-drug resistance of this species. We show a remarkable intra-species genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of ca. 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.
    Genome Biology and Evolution 07/2014; · 4.76 Impact Factor
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    ABSTRACT: Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century.
    PLoS neglected tropical diseases. 07/2014; 8(7):e2981.
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    ABSTRACT: Shigella flexneri is an important human pathogen that has to adapt to the anaerobic environment in the gastrointestinal tract to cause dysentery. To define the influence of anaerobiosis on the virulence of Shigella, we performed deep RNA sequencing to identify transcriptomic differences that are induced by anaerobiosis and modulated by the anaerobic Fumarate and Nitrate Reduction regulator, FNR.
    BMC genomics. 06/2014; 15(1):438.
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    ABSTRACT: The native plasmid of both Chlamydia muridarum and C. trachomatis has been shown to control virulence and infectivity in mice and in lower primates. We have recently described the development of a plasmid-based genetic transformation protocol for Chlamydia trachomatis that for the first time provides a platform for the molecular dissection of the function of the chlamydial plasmid and its individual genes or coding sequences (CDS). In the present study, we transformed a plasmid-free lymphogranuloma venereum isolate of C. trachomatis, serovar L2, with either the original shuttle vector (pGFP::SW2) or a derivative of pGFP::SW2 carrying a deletion of the plasmid CDS5 gene (pCDS5KO). Female mice were inoculated with these strains either intravaginally or transcervically. We found that transformation of the plasmid-free isolate with the intact pGFP::SW2 vector significantly enhanced infectivity and induction of host inflammatory responses when compared to the plasmid-free parental isolate. Transformation with pCDS5KO resulted in infection courses and inflammatory responses not significantly different from those observed in mice infected with the plasmid-free isolate. These results indicate a critical role of plasmid CDS5 in in vivo fitness and in induction of inflammatory responses. To our knowledge, these are the first in vivo observations ascribing infectivity and virulence to a specific plasmid gene.
    Infection and immunity. 05/2014;
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    ABSTRACT: Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination-repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in E. coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasises the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains.
    Environmental Microbiology 05/2014; · 6.24 Impact Factor
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    ABSTRACT: The genus Yersinia has been used as a model system to study pathogen evolution. Using whole-genome sequencing of all Yersinia species, we delineate the gene complement of the whole genus and define patterns of virulence evolution. Multiple distinct ecological specializations appear to have split pathogenic strains from environmental, nonpathogenic lineages. This split demonstrates that contrary to hypotheses that all pathogenic Yersinia species share a recent common pathogenic ancestor, they have evolved independently but followed parallel evolutionary paths in acquiring the same virulence determinants as well as becoming progressively more limited metabolically. Shared virulence determinants are limited to the virulence plasmid pYV and the attachment invasion locus ail. These acquisitions, together with genomic variations in metabolic pathways, have resulted in the parallel emergence of related pathogens displaying an increasingly specialized lifestyle with a spectrum of virulence potential, an emerging theme in the evolution of other important human pathogens.
    Proceedings of the National Academy of Sciences 04/2014; 111(18):6768-73. · 9.81 Impact Factor
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    ABSTRACT: The development of genetic transformation technology for Chlamydia trachomatis using its endogenous plasmid has recently been described. C. muridarum cannot be transformed by the C. trachomatis plasmid indicating a barrier between chlamydial species. To determine which regions of the plasmid conferred the species specificity we used the novel approach of transforming wild-type C. muridarum carrying the endogenous plasmid pNigg and forced recombination with the C. trachomatis vector pGFP::SW2 which carries the complete C.trachomatis plasmid (pSW2). Penicillin and chloramphenicol resistant transformants expressing the green fluorescent protein were selected. Recovery of plasmids from these transformants showed they were recombinants. The differences between the pSW2 and pNigg allowed identification of the recombination breakpoints and showed that pGFP::SW2 had exchanged a ~1kbp region with pNigg covering CDS 2. The recombinant plasmid (pSW2NiggCDS2) is maintained under antibiotic selection when transformed into plasmid-cured C. muridarum. The ability to select for recombinants in C. muridarum shows that the barrier is not at transformation but at the level of plasmid replication or maintenance. Our studies show that CDS 2, together with adjoining sequences, is the main determinant of plasmid tropism.This article is protected by copyright. All rights reserved.
    Pathogens and Disease. 04/2014;
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    ABSTRACT: Since 1817, seven cholera pandemics have plagued mankind. As the causative agent, Vibrio cholerae, is autochthonous in the aquatic ecosystem and some studies have revealed links between outbreaks and flux in climate and aquatic conditions, it has been widely presumed that cholera epidemics are triggered by environmental factors that promote growth of local bacterial reservoirs. However, mounting epidemiological findings and genome sequence analysis of clinical isolates indicate that epidemics are largely unassociated with most of the V. cholerae strains in aquatic ecosystems. Instead, only a specific subset of V. cholerae El Tor 'types' appears to be responsible for current epidemics. A recent report examining the evolution of a variety of V. cholerae strains indicates that the current pandemic is monophyletic and originated from a single ancestral clone that has spread globally in successive waves. In this review, we examine the clonal nature of the disease with the example of the recent history of cholera in the Americas. Epidemiological data and genome sequence-based analysis of V. cholerae isolates demonstrate that cholera epidemics of the 1990s in South America were triggered by the importation of a pathogenic V. cholerae strain that gradually spread throughout the region until local outbreaks ceased in 2001. Latin America remained virtually unaffected by the disease until a new toxigenic V. cholerae clone was imported into Haiti in 2010. Overall, cholera appears to be largely due to a subset of specific V. cholerae clones rather than the vast diversity of V. cholerae strains in the environment. This article is protected by copyright. All rights reserved.
    Clinical Microbiology and Infection 02/2014; · 4.58 Impact Factor
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    ABSTRACT: In August 2010, Pakistan experienced major floods and a subsequent cholera epidemic. To clarify the population dynamics and transmission of Vibrio cholerae in Pakistan, we sequenced the genomes of all V. cholerae O1 El Tor isolates and compared the sequences to a global collection of 146 V. cholerae strains. Within the global phylogeny, all isolates from Pakistan formed 2 new subclades (PSC-1 and PSC-2), lying in the third transmission wave of the seventh-pandemic lineage that could be distinguished by signature deletions and their antimicrobial susceptibilities. Geographically, PSC-1 isolates originated from the coast, whereas PSC-2 isolates originated from inland areas flooded by the Indus River. Single-nucleotide polymorphism accumulation analysis correlated river flow direction with the spread of PSC-2. We found at least 2 sources of cholera in Pakistan during the 2010 epidemic and illustrate the value of a global genomic data bank in contextualizing cholera outbreaks.
    Emerging Infectious Diseases 01/2014; 20(1):13-20. · 6.79 Impact Factor
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    ABSTRACT: The genus Yersinia contains three species pathogenic for humans, one of which is the enteropathogen Yersinia pseudotuberculosis. A recent analysis by Multi Locus Sequence Typing (MLST) of the ‘Y. pseudotuberculosis complex’ revealed that this complex comprises three distinct populations: the Y. pestis/Y. pseudotuberculosis group, the recently described species Yersinia similis, and a third not yet characterized population designated ‘Korean Group’, because most strains were isolated in Korea. The aim of this study was to perform an in depth phenotypic and genetic characterization of the three populations composing the Y. pseudotuberculosis complex (excluding Y. pestis, which belonged to the Y. pseudotuberculosis cluster in the MLST analysis). Using a set of strains representative of each group, we found that the three populations had close metabolic properties, but were nonetheless distinguishable based on D-raffinose and D-melibiose fermentation, and on pyrazinamidase activity. Moreover, high-resolution electrospray mass spectrometry highlighted protein peaks characteristic of each population. Their 16S rRNA gene sequences shared high identity (≥99.5%), but specific nucleotide signatures for each group were identified. Multi-Locus Sequence Analysis also identified three genetically closely related but distinct populations. Finally, an Average Nucleotide Identity (ANI) analysis performed after sequencing the genomes of a subset of strains of each group also showed that intragroup identity (average for each group ≥99%) was higher than intergroup diversity (94.6% to 97.4%). Therefore, all phenotypic and genotypic traits studied concurred with the initial MLST data indicating that the Y. pseudotuberculosis complex comprises a third and clearly distinct population of strains forming a novel Yersinia species that we propose to designate Yersinia wautersii sp. nov. The isolation of some strains from humans, the detection of virulence genes (on the pYV and pVM82 plasmids, or encoding the superantigen ypmA) in some isolates, and the absence of pyrazinamidase activity (a hallmark of pathogenicity in the genus Yersinia) argue for the pathogenic potential of Y. wautersii.
    International journal of medical microbiology: IJMM 01/2014; · 4.54 Impact Factor
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    Proceedings of the National Academy of Sciences 01/2014; 111:6768. · 9.81 Impact Factor
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    ABSTRACT: The complete genomes of two virulent phages infecting Citrobacter rodentium are reported here for the first time. Both bacteriophages were isolated from local sewage treatment plant effluents. Genome analyses revealed a close relationship between both phages and allowed their classification as members of the Autographivirinae subfamily in the T7-like genus.
    Genome announcements. 01/2014; 2(3).
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    ABSTRACT: The study of bacterial populations using whole-genome sequencing is of considerable scientific and clinical interest. However, obtaining bacterial genomic information is not always trivial: the target bacteria may be difficult to culture or uncultured, and they may be found within samples containing complex mixtures of other contaminating microbes and/or host cells, from which it is very difficult to derive robust sequencing data. Here we describe our procedure to generate sufficient DNA for whole-genome sequencing from clinical samples and without the need for culture, as successfully used on the difficult-to-culture, obligate intracellular pathogen Chlamydia trachomatis. Our protocol combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification (WGA), which is followed by high-throughput sequencing. Compared with other techniques that might be used to generate such data, IMS-MDA is an inexpensive, low-technology and highly transferable process that provides amplified genomic DNA for sequencing from target bacteria in under 5 h, with little hands-on time.
    Nature Protocol 12/2013; 8(12):2404-12. · 8.36 Impact Factor
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    ABSTRACT: ABSTRACT Salmonella enterica serovar Typhimurium definitive type 2 (DT2) is host restricted to Columba livia (rock or feral pigeon) but is also closely related to S. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster within S. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 and S. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely related S. Typhimurium strains. We report a novel in silico approach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartate in vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility. IMPORTANCE Whereas Salmonella enterica serovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within a Salmonella serovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2) S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.
    mBio 11/2013; 4(5). · 5.62 Impact Factor
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    ABSTRACT: 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.
    Proceedings of the National Academy of Sciences 09/2013; · 9.81 Impact Factor
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    ABSTRACT: The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associationsof the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.
    Science 09/2013; · 31.20 Impact Factor
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    ABSTRACT: We hypothesized that the plasmid of urogenital isolates of Chlamydia trachomatis would modulate infectivity and virulence in a mouse model. To test this hypothesis, we infected female mice in the respiratory or urogenital tract with graded doses of a human urogenital isolate of C. trachomatis, serovar F, possessing the cognate plasmid. For comparison, we inoculated mice with a plasmid-free serovar F isolate. Following urogenital inoculation, the plasmid-free isolate displayed significantly reduced infectivity compared with the wild-type strain with the latter yielding a 17-fold lower infectious dose to yield 50% infection. When inoculated via the respiratory tract, the plasmid-free isolate exhibited reduced infectivity and virulence (as measured by weight change) when compared to the wild-type isolate. Further, differences in infectivity, but not in virulence were observed in a C. trachomatis, serovar E isolate with a deletion within the plasmid coding sequence 1 when compared to a serovar E isolate with no mutations in the plasmid. We conclude that plasmid loss reduces virulence and infectivity in this mouse model. These findings further support a role for the chlamydial plasmid in infectivity and virulence in vivo.
    Pathogens and disease. 08/2013;
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    ABSTRACT: The immunodominant lipopolysaccharide is a key antigenic factor for Gram-negative pathogens such as salmonellae where it plays key roles in host adaptation, virulence, immune evasion, and persistence. Variation in the lipopolysaccharide is also the major differentiating factor that is used to classify Salmonella into over 2600 serovars as part of the Kaufmann-White scheme. While lipopolysaccharide diversity is generally associated with sequence variation in the lipopolysaccharide biosynthesis operon, extraneous genetic factors such as those encoded by the glucosyltransferase (gtr) operons provide further structural heterogeneity by adding additional sugars onto the O-antigen component of the lipopolysaccharide. Here we identify and examine the O-antigen modifying glucosyltransferase genes from the genomes of Salmonella enterica and Salmonella bongori serovars. We show that Salmonella generally carries between 1 and 4 gtr operons that we have classified into 10 families on the basis of gtrC sequence with apparent O-antigen modification detected for five of these families. The gtr operons localize to bacteriophage-associated genomic regions and exhibit a dynamic evolutionary history driven by recombination and gene shuffling events leading to new gene combinations. Furthermore, evidence of Dam- and OxyR-dependent phase variation of gtr gene expression was identified within eight gtr families. Thus, as O-antigen modification generates significant intra- and inter-strain phenotypic diversity, gtr-mediated modification is fundamental in assessing Salmonella strain variability. This will inform appropriate vaccine and diagnostic approaches, in addition to contributing to our understanding of host-pathogen interactions.
    PLoS Genetics 06/2013; 9(6):e1003568. · 8.52 Impact Factor
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    ABSTRACT: The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C. trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C. trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C. trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA in conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern.
    Genome Research 03/2013; · 14.40 Impact Factor

Publication Stats

10k Citations
1,546.29 Total Impact Points

Institutions

  • 2001–2014
    • Wellcome Trust Sanger Institute
      • Pathogen Genomics Group
      Cambridge, England, United Kingdom
    • Institut Pasteur
      Lutetia Parisorum, Île-de-France, France
  • 2013
    • University of Southampton
      Southampton, England, United Kingdom
  • 2012–2013
    • University of Melbourne
      • • Department of Biochemistry and Molecular Biology
      • • Department of Microbiology and Immunology
      Melbourne, Victoria, Australia
  • 2011–2012
    • Oxford University Clinical Research Unit
      Thành phố Hồ Chí Minh, Ho Chi Minh City, Vietnam
    • The University of Edinburgh
      • Royal (Dick) School of Veterinary Studies
      Edinburgh, SCT, United Kingdom
    • Erasmus MC
      • Department of Medical Microbiology and Infectious Diseases
      Rotterdam, South Holland, Netherlands
  • 2010
    • Örebro University Hospital
      • Department of Laboratory Medicine
      Örebro, Örebro, Sweden
    • Hospital for Tropical Diseases, Ho Chi Minh City
      Thành phố Hồ Chí Minh, Ho Chi Minh City, Vietnam
  • 2009
    • Biotechnology and Biological Sciences Research Council
      Swindon, England, United Kingdom
    • Universitetet i Tromsø
      Tromsø, Troms, Norway
    • Tufts University
      • Department of Developmental, Molecular and Chemical Biology
      Medford, MA, United States
  • 2003–2009
    • Imperial College London
      • • Division of Cell and Molecular Biology
      • • Centre for Molecular Microbiology and Infection
      Londinium, England, United Kingdom
  • 2008
    • University of Oxford
      Oxford, England, United Kingdom
    • University of Birmingham
      • School of Biosciences
      Birmingham, England, United Kingdom
    • EMBL-EBI
      Cambridge, England, United Kingdom
    • Cardiff University
      Cardiff, Wales, United Kingdom
  • 1997–2008
    • University of Cambridge
      • • Department of Veterinary Medicine
      • • Department of Biochemistry
      Cambridge, England, United Kingdom
  • 2006
    • The University of York
      • Department of Biology
      York, ENG, United Kingdom