Dougan Group | Microbial Pathogenesis

Dougan Group | Microbial Pathogenesis

Dougan Group

dougan-group.jpgSanger Institute, Genome Research Limited

Our Research and Approach

Background

Infectious diseases still pose a threat at a global and local level, particularly as disease agents can evolve so quickly. For example, bacteria such as Salmonella and Shigella cause intestinal infections that can have devastating consequences particularly in developing countries, but bacterial strains such as these can be resistant to almost all antibiotics.

New approaches are needed to treat bacterial infections, one of which is focusing on understanding the methods by which the body's natural systems fight off the tens of thousands of potentially pathogenic bacteria to which it is exposed in ordinary everyday life.

A complementary challenge is investigating how disease agents change to prevent human intervention. Understanding the molecular basis of infection could assist in attempts to develop vaccines and other therapies to protect against infections.

This information will be exploited towards developing methods of controlling infection, including vaccines and antibiotics, in the continuing fight against disease that is crucial for populations worldwide.

The team is also investigating the relationships between different members of the family of bacteria that cause typhoid, Salmonella Typhi, in order to explain their evolution, antibiotic resistance and transmission within the human population.

Finally the team is involved in a number of major high profile collaborations worldwide investigating methods for developing vaccines against typhoid, dysentery, malaria, and tuberculosis, all critically important diseases particularly in developing countries.

Read More

People

Professor Gordon Dougan
Group Leader

Professor Gordon Dougan's research focuses on the genetic analysis of host/pathogen interactions during infection, particularly those involving enteric bacteria. He has worked extensively in both academia and industry, making important contributions in the field of vaccinology where he has worked to improve vaccine delivery to poorly resourced regions.

Show Alumni

Alumni

Key Projects, Collaborations, Tools & Data

Faculty Programme Overview: We are focusing our research around the biology of intestinal bacterial infections, with a strong emphasis on invasive Salmonella disease. We work closely with other Faculty Groups in this and other Programmes of the Sanger Institute and have generated information on the genome sequences of a number of different Salmonella species or serovars including Bongori, Typhi, Typhimurium, Enteritidis, Gallinarum, Hadar, Infantis, Senftenberg and Paratyphi A that cause potentially lethal diseases such as typhoid and salmonella food poisoning. With Dr Trevor Lawley's Faculty Group, we have also determined the phylogenetic structure of C. difficile. We are using the information to investigate, at the genetic level, what makes different species of bacteria more potent (or virulent), in terms of their ability to cause disease, than others. To complement this research we are creating 'libraries' of pathogen strains that have single genes disabled in order to investigate their (the genes') functions and effects on virulence.We are also undertaking an analysis of microbial population structure in collaboration with Dr Mark Achtman at the Max Planck Institute for Infection Biology, Berlin, and Dr Stephen Baker at the Wellcome Unit in Ho Chi Minh City. We are concentrating efforts on Salmonella Typhi, which causes typhoid, and C. difficile, a common cause of infection in hospitals but have projects on other pathogens including Vibrio cholerae. We use DNA sequencing and gene-functionality based approaches, and exploit this information for biological experimentation. Another key study involves the analysis of the genome of S. typhimurium, responsible for invasive bacterial disease throughout Africa. This is run in collaboration with Dr Sam Kariuki in Nairobi and the Wellcome Unit in Blantyre, Malawi.Mouse genetic infection susceptibility project (Deputy Head, Dr Simon Clare): We run a mouse genetics project in which mice with an artificially disabled gene are challenged with certain pathogens. The aim is to identify mammalian genes that contribute to controlling susceptibility to infection. The main infectious agents used in this screen are currently S. typhimurium and Citrobacter rodentium, although other pathogens can be exploited to investigate genetic effects in detail.

Research Programmes and Faciltites

We are a part of:

Parasites and Microbes

We are using genomics to get at important problems in infectious disease, with a strong desire to translate this into tools for disease control and elimination, but we are also at the forefront of basic research into microbial ecology, evolutionary genetics and the biology of parasitism.

Show Previous Research Programmes and Facilities
Archive Page: Infection Genomics

The Infection Genomics Programme investigates the common underpinning mechanisms of evolution, infection and resistance to therapy in viruses, bacteria and parasites. The Programme also focuses on the genetics of host response to infection and the role of the microbiota in health and disease.

Partners and Funders

Internal Partners
Aanensen Group

Our group consistis of a mix of genomic epidemiologists, computational biologists and web software engineers within The Centre for Genomic Pathogen Surveillance (CGPS) a collaboration with imperial College London.

Within CGPS, broad aims are to provide data and tools for local, national and international utility focused on antimicrobial resistance and genomic surveillance. We are addressing the utility of large-scale structured pathogen surveys to provide contextual WGS datasets and population structure. Key aims are to enable the identification of high risk clones of public health importance, their risk assessment (eg resistance, virulence and transmissibility) and ultimately management.

Hancock Group

We are collaborating with Gordon Dougan's team on high-throughout phenotyping of host and bacterial cells, as well as the development of new therapeutic strategies based on an understanding of antibiotic resistance.

Lawley Lab

The host-microbiota Interactions laboratory studies the mechanisms that underlie how micro-organisms in the gut, nasopharynx and uro-gential tract interact with their host during periods of health and disease. In particular the team seek to develop novel ways to treat diseases that are associated with unwanted imbalances in the micro-organism population.

Liu Group

We use various approaches including genetics, genomics and cell biology to study gene functions in normal development and disease such as cancer. We are particularly interested in stem cell self-renewal, differentiation, and lineage choice.

Parkhill Group

The Pathogen genomics team, headed by Julian Parkhill, uses high-throughput genomic and phenotypic analysis of bacteria to understand their virulence, evolution, transmission and host-interactions.

Parkhill Group

The Pathogen genomics team, headed by Julian Parkhill, uses high-throughput genomic and phenotypic analysis of bacteria to understand their virulence, evolution, transmission and host-interactions.

Pathogen Informatics

The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the pathogen group. We develop and maintain scalable and robust automated tools for sequence and annotation tracking and analysis and provide ad-hoc informatics support and training to the researchers in the pathogen group.

Pathogen Informatics

The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the pathogen group. We develop and maintain scalable and robust automated tools for sequence and annotation tracking and analysis and provide ad-hoc informatics support and training to the researchers in the pathogen group.

Pathogen Informatics

The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the pathogen group. We develop and maintain scalable and robust automated tools for sequence and annotation tracking and analysis and provide ad-hoc informatics support and training to the researchers in the pathogen group.

Pathogen Informatics

The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the pathogen group. We develop and maintain scalable and robust automated tools for sequence and annotation tracking and analysis and provide ad-hoc informatics support and training to the researchers in the pathogen group.

Wright Group

The Cell Surface Signalling Laboratory investigates the molecular basis of cellular recognition processes to identify new therapeutic targets for both genetic and infectious diseases.

Publications

  • Requirement of bic/microRNA-155 for normal immune function.

    Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P et al.

    Science (New York, N.Y.) 2007;316;5824;608-11

    PUBMED: 17463290; PMC: 2610435; DOI: 10.1126/science.1139253

  • A new stage, a new life: individual success in quitting smoking.

    Willms DG

    Social science & medicine (1982) 1991;33;12;1365-71

    PUBMED: 1776050

  • A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

    Baker S, Holt K, Whitehead S, Goodhead I, Perkins T et al.

    Molecular microbiology 2007;66;5;1207-18

    PUBMED: 17976161; PMC: 2652032; DOI: 10.1111/j.1365-2958.2007.05995.x

  • The neglected role of antibody in protection against bacteremia caused by nontyphoidal strains of Salmonella in African children.

    MacLennan CA, Gondwe EN, Msefula CL, Kingsley RA, Thomson NR et al.

    The Journal of clinical investigation 2008;118;4;1553-62

    PUBMED: 18357343; PMC: 2268878; DOI: 10.1172/JCI33998

  • Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.

    Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM et al.

    Nature genetics 2012;44;11;1215-21

    PUBMED: 23023330; PMC: 3491877; DOI: 10.1038/ng.2423

  • IFITM3 restricts the morbidity and mortality associated with influenza.

    Everitt AR, Clare S, Pertel T, John SP, Wash RS et al.

    Nature 2012;484;7395;519-23

    PUBMED: 22446628; PMC: 3648786; DOI: 10.1038/nature10921

  • Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.

    Lawley TD, Clare S, Walker AW, Stares MD, Connor TR et al.

    PLoS pathogens 2012;8;10;e1002995

    PUBMED: 23133377; PMC: 3486913; DOI: 10.1371/journal.ppat.1002995

  • Evidence for several waves of global transmission in the seventh cholera pandemic.

    Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH et al.

    Nature 2011;477;7365;462-5

    PUBMED: 21866102; PMC: 3736323; DOI: 10.1038/nature10392

  • Localization of ATPase activity in dendritic spines of the cerebral cortex.

    Cohen RS and Kriho V

    Journal of neurocytology 1991;20;9;703-15

    PUBMED: 1835734

  • Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance.

    Davies MR, Holden MT, Coupland P, Chen JH, Venturini C et al.

    Nature genetics 2015;47;1;84-7

    PUBMED: 25401300; DOI: 10.1038/ng.3147

  • Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.

    von Mentzer A, Connor TR, Wieler LH, Semmler T, Iguchi A et al.

    Nature genetics 2014;46;12;1321-6

    PUBMED: 25383970; DOI: 10.1038/ng.3145

  • CD28 expression is required after T cell priming for helper T cell responses and protective immunity to infection.

    Linterman MA, Denton AE, Divekar DP, Zvetkova I, Kane L et al.

    eLife 2014;3

    PUBMED: 25347065; PMC: 4241536; DOI: 10.7554/eLife.03180

  • Drug resistance in Salmonella enterica ser. Typhimurium bloodstream infection, Malawi.

    Feasey NA, Cain AK, Msefula CL, Pickard D, Alaerts M et al.

    Emerging infectious diseases 2014;20;11;1957-9

    PUBMED: 25340988; PMC: 4214322; DOI: 10.3201/eid2011.141175

  • Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

    Lamelas A, Harris SR, Röltgen K, Dangy JP, Hauser J et al.

    mBio 2014;5;5;e01974-14

    PUBMED: 25336458; PMC: 4212839; DOI: 10.1128/mBio.01974-14

  • Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever.

    Dougan G and Baker S

    Annual review of microbiology 2014;68;317-36

    PUBMED: 25208300; DOI: 10.1146/annurev-micro-091313-103739

  • Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.

    Zhou Z, McCann A, Weill FX, Blin C, Nair S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;33;12199-204

    PUBMED: 25092320; PMC: 4143038; DOI: 10.1073/pnas.1411012111

  • Corrigendum: Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

    Da Cunha V, Davies MR, Douarre PE, Rosinski-Chupin I, Margarit I et al.

    Nature communications 2015;6;6108

    PUBMED: 25629801; PMC: 4317489; DOI: 10.1038/ncomms7108

  • Typhoid fever in Fiji: a reversible plague?

    Thompson CN, Kama M, Acharya S, Bera U, Clemens J et al.

    Tropical medicine & international health : TM & IH 2014;19;10;1284-92

    PUBMED: 25066005; PMC: 4285329; DOI: 10.1111/tmi.12367

  • The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.

    Abd El Ghany M, Chander J, Mutreja A, Rashid M, Hill-Cawthorne GA et al.

    PLoS neglected tropical diseases 2014;8;7;e2981

    PUBMED: 25058483; PMC: 4109905; DOI: 10.1371/journal.pntd.0002981

  • The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design.

    van Sorge NM, Cole JN, Kuipers K, Henningham A, Aziz RK et al.

    Cell host & microbe 2014;15;6;729-740

    PUBMED: 24922575; PMC: 4078075; DOI: 10.1016/j.chom.2014.05.009

  • Global dissemination of a multidrug resistant Escherichia coli clone.

    Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;15;5694-9

    PUBMED: 24706808; PMC: 3992628; DOI: 10.1073/pnas.1322678111

  • Antibacterial resistance in sub-Saharan Africa: an underestimated emergency.

    Kariuki S and Dougan G

    Annals of the New York Academy of Sciences 2014;1323;43-55

    PUBMED: 24628272; PMC: 4159419; DOI: 10.1111/nyas.12380

  • New Variant of Multidrug-Resistant <i>Salmonella enterica</i> Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam.

    Mather AE, Phuong TLT, Gao Y, Clare S, Mukhopadhyay S et al.

    mBio 2018;9;5

    PUBMED: 30181247; DOI: 10.1128/mBio.01056-18

  • FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.

    Grinter R, Hay ID, Song J, Wang J, Teng D et al.

    PLoS biology 2018;16;8;e2006026

    PUBMED: 30071011; DOI: 10.1371/journal.pbio.2006026

  • Point prevalence survey of carbapenemase-producing Enterobacteriaceae (CPE) and vancomycin-resistant enterococci (VRE) in adult inpatients in a University teaching hospital in the United Kingdom.

    Wilson HJ, Khokhar F, Enoch DA, Brown NM, Ahluwalia J et al.

    The Journal of hospital infection 2018

    PUBMED: 29969691; DOI: 10.1016/j.jhin.2018.06.024

  • Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses.

    Napolitani G, Kurupati P, Teng KWW, Gibani MM, Rei M et al.

    Nature immunology 2018

    PUBMED: 29925993; DOI: 10.1038/s41590-018-0133-z

  • An investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis.

    Torres VVL, Heinz E, Stubenrauch CJ, Wilksch JJ, Cao H et al.

    Molecular microbiology 2018

    PUBMED: 29873128; DOI: 10.1111/mmi.13990

  • Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy.

    Britto CD, Dyson ZA, Duchene S, Carter MJ, Gurung M et al.

    PLoS neglected tropical diseases 2018;12;4;e0006408

    PUBMED: 29684021; DOI: 10.1371/journal.pntd.0006408

  • PlasmidTron: assembling the cause of phenotypes and genotypes from NGS data.

    Page AJ, Wailan A, Shao Y, Judge K, Dougan G et al.

    Microbial genomics 2018

    PUBMED: 29533742; PMC: 5885016; DOI: 10.1099/mgen.0.000164

  • Outer membrane vesicles from Neisseria gonorrhoeae target PorB to mitochondria and induce apoptosis.

    Deo P, Chow SH, Hay ID, Kleifeld O, Costin A et al.

    PLoS pathogens 2018;14;3;e1006945

    PUBMED: 29601598; PMC: 5877877; DOI: 10.1371/journal.ppat.1006945

  • Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.

    Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL et al.

    Nature genetics 2018;50;3;424-431

    PUBMED: 29379200; DOI: 10.1038/s41588-018-0046-7

  • Emergence of an Extensively Drug-Resistant <i>Salmonella enterica</i> Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins.

    Klemm EJ, Shakoor S, Page AJ, Qamar FN, Judge K et al.

    mBio 2018;9;1

    PUBMED: 29463654; PMC: 5821095; DOI: 10.1128/mBio.00105-18

  • Comparison of Salmonella enterica serovars Typhi and Typhimurium reveals typhoidal-specific responses to bile.

    Johnson R, Ravenhall M, Pickard D, Dougan G, Byrne A and Frankel G

    Infection and immunity 2017

    PUBMED: 29229736; DOI: 10.1128/IAI.00490-17

  • DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.

    Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J et al.

    Gut 2017

    PUBMED: 29141958; DOI: 10.1136/gutjnl-2017-314817

  • Genomic history of the seventh pandemic of cholera in Africa.

    Weill FX, Domman D, Njamkepo E, Tarr C, Rauzier J et al.

    Science (New York, N.Y.) 2017;358;6364;785-789

    PUBMED: 29123067; DOI: 10.1126/science.aad5901

  • Integrated view of <i>Vibrio cholerae</i> in the Americas.

    Domman D, Quilici ML, Dorman MJ, Njamkepo E, Mutreja A et al.

    Science (New York, N.Y.) 2017;358;6364;789-793

    PUBMED: 29123068; DOI: 10.1126/science.aao2136

  • Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

    Stubenrauch CJ, Dougan G, Lithgow T and Heinz E

    Open biology 2017;7;11

    PUBMED: 29142104; DOI: 10.1098/rsob.170144

  • Phylogenetic Analysis of Klebsiella pneumoniae from Hospitalized Children, Pakistan.

    Ejaz H, Wang N, Wilksch JJ, Page AJ, Cao H et al.

    Emerging infectious diseases 2017;23;11;1872-1875

    PUBMED: 29048298; PMC: 5652443; DOI: 10.3201/eid2311.170833

  • Complete Genome Sequence of Serotype III Streptococcus agalactiae Sequence Type 17 Strain 874391.

    Sullivan MJ, Forde BM, Prince DW, Ipe DS, Ben Zakour NL et al.

    Genome announcements 2017;5;42

    PUBMED: 29051249; PMC: 5646402; DOI: 10.1128/genomeA.01107-17

  • Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo.

    Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D et al.

    Cell metabolism 2017

    PUBMED: 28988824; DOI: 10.1016/j.cmet.2017.09.003

  • Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).

    Mentzer AV, Tobias J, Wiklund G, Nordqvist S, Aslett M et al.

    Scientific reports 2017;7;1;12514

    PUBMED: 28970563; DOI: 10.1038/s41598-017-12743-3

  • Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights.

    Kiu R, Caim S, Alcon-Giner C, Belteki G, Clarke P et al.

    Genome biology and evolution 2017;9;10;2707-2714

    PUBMED: 29044436; DOI: 10.1093/gbe/evx210

  • Salmonella enterica serovar Typhi Producing CTX-M-15 Extended Spectrum β-Lactamase in the Democratic Republic of the Congo.

    Phoba MF, Barbé B, Lunguya O, Masendu L, Lulengwa D et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;65;7;1229-1231

    PUBMED: 29136410; PMC: 5849100; DOI: 10.1093/cid/cix342

  • NBEAL2 is required for neutrophil and NK cell function and pathogen defense.

    Sowerby JM, Thomas DC, Clare S, Espéli M, Guerrero JA et al.

    The Journal of clinical investigation 2017;127;9;3521-3526

    PUBMED: 28783043; DOI: 10.1172/JCI91684

  • Role of <i>sapA</i> and <i>yfgA</i> in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium.

    Ondari EM, Heath JN, Klemm EJ, Langridge G, Barquist L et al.

    Infection and immunity 2017;85;9

    PUBMED: 28674031; PMC: 5563563; DOI: 10.1128/IAI.00419-17

  • The Typhoid Vaccine Acceleration Consortium (TyVAC): Vaccine effectiveness study designs: Accelerating the introduction of typhoid conjugate vaccines and reducing the global burden of enteric fever. Report from a meeting held on 26-27 October 2016, Oxford, UK.

    Meiring JE, Gibani M and TyVAC Consortium Meeting Group

    Vaccine 2017

    PUBMED: 28802757; DOI: 10.1016/j.vaccine.2017.08.001

  • Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2.

    Tchasovnikarova IA, Timms RT, Douse CH, Roberts RC, Dougan G et al.

    Nature genetics 2017

    PUBMED: 28581500; DOI: 10.1038/ng.3878

  • Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis.

    Yeung ATY, Hale C, Lee AH, Gill EE, Bushell W et al.

    Nature communications 2017;8;15013

    PUBMED: 28440293; PMC: 5414054; DOI: 10.1038/ncomms15013

  • Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.

    Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK et al.

    The Journal of experimental medicine 2017;214;4;1111-1128

    PUBMED: 28351984; PMC: 5379978; DOI: 10.1084/jem.20161382

  • Typhoid in Africa and vaccine deployment.

    Dougan G

    The Lancet. Global health 2017;5;3;e236-e237

    PUBMED: 28193381; DOI: 10.1016/S2214-109X(17)30045-1

  • The Type III Secretion System Effector SptP of Salmonella enterica Serovar Typhi.

    Johnson R, Byrne A, Berger CN, Klemm E, Crepin VF et al.

    Journal of bacteriology 2017;199;4

    PUBMED: 27920299; PMC: 5287405; DOI: 10.1128/JB.00647-16

  • Induction of Cell Cycle and NK Cell Responses by Live-Attenuated Oral Vaccines against Typhoid Fever.

    Blohmke CJ, Hill J, Darton TC, Carvalho-Burger M, Eustace A et al.

    Frontiers in immunology 2017;8;1276

    PUBMED: 29075261; PMC: 5643418; DOI: 10.3389/fimmu.2017.01276

  • Combined immunodeficiency with severe inflammation and allergy caused by ARPC1B deficiency.

    Kuijpers TW, Tool AT, van der Bijl I, de Boer M, van Houdt M et al.

    The Journal of allergy and clinical immunology 2016

    PUBMED: 27965109; DOI: 10.1016/j.jaci.2016.09.061

  • Mitochondrial Protein Lipoylation and the 2-Oxoglutarate Dehydrogenase Complex Controls HIF1α Stability in Aerobic Conditions.

    Burr SP, Costa AS, Grice GL, Timms RT, Lobb IT et al.

    Cell metabolism 2016;24;5;740-752

    PUBMED: 27923773; DOI: 10.1016/j.cmet.2016.09.015

  • New Approaches for Needed Vaccines: Bacteria

    MacLennan,C.A., Mutreja,A. and Dougan,G.

    The Vaccine Book: Second Edition 2016;311-29

    DOI: 10.1016/B978-0-12-802174-3.00016-3; URL: http://dx.doi.org/10.1016/B97...8-0-12-802174-3.00016-3

  • Single-cell RNA-seq identifies a PD-1<sup>hi</sup> ILC progenitor and defines its development pathway.

    Yu Y, Tsang JC, Wang C, Clare S, Wang J et al.

    Nature 2016;539;7627;102-106

    PUBMED: 27749818; DOI: 10.1038/nature20105

  • ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex.

    Timms RT, Tchasovnikarova IA, Antrobus R, Dougan G and Lehner PJ

    Cell reports 2016;17;3;653-659

    PUBMED: 27732843; DOI: 10.1016/j.celrep.2016.09.050

  • An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.

    Wong VK, Baker S, Connor TR, Pickard D, Page AJ et al.

    Nature communications 2016;7;12827

    PUBMED: 27703135; DOI: 10.1038/ncomms12827

  • Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

    Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J et al.

    Nature genetics 2016;48;10;1211-7

    PUBMED: 27548315; PMC: 5047355; DOI: 10.1038/ng.3644

  • Retrospective Analysis of Serotype Switching of Vibrio cholerae O1 in a Cholera Endemic Region Shows It Is a Non-random Process.

    Karlsson SL, Thomson N, Mutreja A, Connor T, Sur D et al.

    PLoS neglected tropical diseases 2016;10;10;e0005044

    PUBMED: 27706170; DOI: 10.1371/journal.pntd.0005044

  • C13orf31 (FAMIN) is a central regulator of immunometabolic function.

    Cader MZ, Boroviak K, Zhang Q, Assadi G, Kempster SL et al.

    Nature immunology 2016;17;9;1046-56

    PUBMED: 27478939; DOI: 10.1038/ni.3532

  • Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa.

    International Typhoid Consortium, Wong VK, Holt KE, Okoro C, Baker S et al.

    PLoS neglected tropical diseases 2016;10;9;e0004781

    PUBMED: 27657909; DOI: 10.1371/journal.pntd.0004781

  • Derivation of Intestinal Organoids from Human Induced Pluripotent Stem Cells for Use as an Infection System.

    Forbester JL, Hannan N, Vallier L and Dougan G

    Methods in molecular biology (Clifton, N.J.) 2016

    PUBMED: 27576565; DOI: 10.1007/7651_2016_7

  • Using a Human Challenge Model of Infection to Measure Vaccine Efficacy: A Randomised, Controlled Trial Comparing the Typhoid Vaccines M01ZH09 with Placebo and Ty21a.

    Darton TC, Jones C, Blohmke CJ, Waddington CS, Zhou L et al.

    PLoS neglected tropical diseases 2016;10;8;e0004926

    PUBMED: 27533046; PMC: 4988630; DOI: 10.1371/journal.pntd.0004926

  • Binding of Plasmodium falciparum Merozoite Surface Proteins DBLMSP and DBLMSP2 to Human Immunoglobulin M Is Conserved among Broadly Diverged Sequence Variants.

    Crosnier C, Iqbal Z, Knuepfer E, Maciuca S, Perrin AJ et al.

    The Journal of biological chemistry 2016;291;27;14285-99

    PUBMED: 27226583; PMC: 4933183; DOI: 10.1074/jbc.M116.722074

  • Infection Susceptibility in Gastric Intrinsic Factor (Vitamin B12)-Defective Mice Is Subject to Maternal Influences.

    Mottram L, Speak AO, Selek RM, Cambridge EL, McIntyre Z et al.

    mBio 2016;7;3

    PUBMED: 27329747; PMC: 4916386; DOI: 10.1128/mBio.00830-16

  • Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family.

    Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW et al.

    Genome biology and evolution 2016;8;6;1690-705

    PUBMED: 27190006; PMC: 4943183; DOI: 10.1093/gbe/evw112

  • Genetic dissection of mammalian ERAD through comparative haploid and CRISPR forward genetic screens.

    Timms RT, Menzies SA, Tchasovnikarova IA, Christensen LC, Williamson JC et al.

    Nature communications 2016;7;11786

    PUBMED: 27283361; PMC: 4906395; DOI: 10.1038/ncomms11786

  • The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

    Pham Thanh D, Thompson CN, Rabaa MA, Sona S, Sopheary S et al.

    PLoS neglected tropical diseases 2016;10;6;e0004785

    PUBMED: 27331909; DOI: 10.1371/journal.pntd.0004785

  • Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.

    Blohmke CJ, Darton TC, Jones C, Suarez NM, Waddington CS et al.

    The Journal of experimental medicine 2016;213;6;1061-77

    PUBMED: 27217537; PMC: 4886356; DOI: 10.1084/jem.20151025

  • Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics.

    Klemm E and Dougan G

    Cell host & microbe 2016;19;5;599-610

    PUBMED: 27173928; DOI: 10.1016/j.chom.2016.04.015

  • Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

    Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR et al.

    Emerging infectious diseases 2016;22;4;617-24

    PUBMED: 26982594; PMC: 4806966; DOI: 10.3201/eid2204.150531

  • T cell fate and clonality inference from single-cell transcriptomes.

    Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO et al.

    Nature methods 2016;13;4;329-332

    PUBMED: 26950746; PMC: 4835021; DOI: 10.1038/nmeth.3800

  • Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain.

    Pérez-Vázquez M, Oteo J, García-Cobos S, Aracil B, Harris SR et al.

    The Journal of antimicrobial chemotherapy 2016;71;4;887-96

    PUBMED: 26769896; PMC: 4790626; DOI: 10.1093/jac/dkv458

  • Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR et al.

    Nature microbiology 2016;1;3

    PUBMED: 27127642; PMC: 4843968; DOI: 10.1038/nmicrobiol.2015.23

  • A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.

    Makendi C, Page AJ, Wren BW, Le Thi Phuong T, Clare S et al.

    PLoS neglected tropical diseases 2016;10;2;e0004446

    PUBMED: 26867150; PMC: 4750946; DOI: 10.1371/journal.pntd.0004446

  • Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.

    Holt K, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ et al.

    Microbial genomics 2016;2;2;e000052

    PUBMED: 28348844; PMC: 5320584; DOI: 10.1099/mgen.0.000052

  • Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.

    Maggiore L, Yu L, Omasits U, Rossi O, Dougan G et al.

    International journal of medical microbiology : IJMM 2016;306;2;99-108

    PUBMED: 26746581; PMC: 4820968; DOI: 10.1016/j.ijmm.2015.12.003

  • Invasive Group A Streptococcus Infection among Children, Rural Kenya.

    Seale AC, Davies MR, Anampiu K, Morpeth SC, Nyongesa S et al.

    Emerging infectious diseases 2016;22;2;224-32

    PUBMED: 26811918; DOI: 10.3201/eid2202.151358

  • Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants.

    Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ et al.

    Nature microbiology 2016;1;15010

    PUBMED: 27571974; DOI: 10.1038/nmicrobiol.2015.10

  • A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure.

    Pham Thanh D, Karkey A, Dongol S, Ho Thi N, Thompson CN et al.

    eLife 2016;5

    PUBMED: 26974227; PMC: 4805543; DOI: 10.7554/eLife.14003

  • Discovery and Characterization of Human-Urine Utilization by Asymptomatic-Bacteriuria-Causing Streptococcus agalactiae.

    Ipe DS, Ben Zakour NL, Sullivan MJ, Beatson SA, Ulett KB et al.

    Infection and immunity 2015;84;1;307-19

    PUBMED: 26553467; PMC: 4694007; DOI: 10.1128/IAI.00938-15

  • Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription.

    Alasoo K, Martinez FO, Hale C, Gordon S, Powrie F et al.

    Scientific reports 2015;5;12524

    PUBMED: 26224331; PMC: 4519778; DOI: 10.1038/srep12524

  • Interaction of Salmonella enterica Serovar Typhimurium with Intestinal Organoids Derived from Human Induced Pluripotent Stem Cells.

    Forbester JL, Goulding D, Vallier L, Hannan N, Hale C et al.

    Infection and immunity 2015;83;7;2926-34

    PUBMED: 25964470; PMC: 4468523; DOI: 10.1128/IAI.00161-15

  • GENE SILENCING. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells.

    Tchasovnikarova IA, Timms RT, Matheson NJ, Wals K, Antrobus R et al.

    Science (New York, N.Y.) 2015;348;6242;1481-5

    PUBMED: 26022416; PMC: 4487827; DOI: 10.1126/science.aaa7227

  • Defining the Roles of TcdA and TcdB in Localized Gastrointestinal Disease, Systemic Organ Damage, and the Host Response during Clostridium difficile Infections.

    Carter GP, Chakravorty A, Pham Nguyen TA, Mileto S, Schreiber F et al.

    mBio 2015;6;3;e00551

    PUBMED: 26037121; PMC: 4453007; DOI: 10.1128/mBio.00551-15

  • The transcription factor Bcl11b is specifically expressed in group 2 innate lymphoid cells and is essential for their development.

    Yu Y, Wang C, Clare S, Wang J, Lee SC et al.

    The Journal of experimental medicine 2015;212;6;865-74

    PUBMED: 25964371; PMC: 4451136; DOI: 10.1084/jem.20142318

  • Non-typhoidal Salmonella Typhimurium ST313 isolates that cause bacteremia in humans stimulate less inflammasome activation than ST19 isolates associated with gastroenteritis.

    Carden S, Okoro C, Dougan G and Monack D

    Pathogens and disease 2015;73;4

    PUBMED: 25808600; PMC: 4399442; DOI: 10.1093/femspd/ftu023

  • Oral Wild-Type Salmonella Typhi Challenge Induces Activation of Circulating Monocytes and Dendritic Cells in Individuals Who Develop Typhoid Disease.

    Toapanta FR, Bernal PJ, Fresnay S, Darton TC, Jones C et al.

    PLoS neglected tropical diseases 2015;9;6;e0003837

    PUBMED: 26065687; PMC: 4465829; DOI: 10.1371/journal.pntd.0003837

  • Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al.

    Nature genetics 2015;47;6;632-9

    PUBMED: 25961941; PMC: 4921243; DOI: 10.1038/ng.3281

  • Ceftriaxone-resistant Salmonella enterica serotype typhimurium sequence type 313 from Kenyan patients is associated with the blaCTX-M-15 gene on a novel IncHI2 plasmid.

    Kariuki S, Okoro C, Kiiru J, Njoroge S, Omuse G et al.

    Antimicrobial agents and chemotherapy 2015;59;6;3133-9

    PUBMED: 25779570; PMC: 4432211; DOI: 10.1128/AAC.00078-15

  • Activation of Salmonella Typhi-specific regulatory T cells in typhoid disease in a wild-type S. Typhi challenge model.

    McArthur MA, Fresnay S, Magder LS, Darton TC, Jones C et al.

    PLoS pathogens 2015;11;5;e1004914

    PUBMED: 26001081; PMC: 4441490; DOI: 10.1371/journal.ppat.1004914

  • Rapid emergence of multidrug resistant, H58-lineage Salmonella typhi in Blantyre, Malawi.

    Feasey NA, Gaskell K, Wong V, Msefula C, Selemani G et al.

    PLoS neglected tropical diseases 2015;9;4;e0003748

    PUBMED: 25909750; PMC: 4409211; DOI: 10.1371/journal.pntd.0003748

  • Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.

    Baltazar M, Ngandjio A, Holt KE, Lepillet E, Pardos de la Gandara M et al.

    Emerging infectious diseases 2015;21;4;655-9

    PUBMED: 25811307; PMC: 4378479; DOI: 10.3201/eid2104.141355

  • Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function.

    Yeung AT, Hale C, Xia J, Tate PH, Goulding D et al.

    Scientific reports 2015;5;8908

    PUBMED: 25752829; PMC: 4354151; DOI: 10.1038/srep08908

  • An O antigen capsule modulates bacterial pathogenesis in Shigella sonnei.

    Caboni M, Pédron T, Rossi O, Goulding D, Pickard D et al.

    PLoS pathogens 2015;11;3;e1004749

    PUBMED: 25794007; PMC: 4368438; DOI: 10.1371/journal.ppat.1004749

  • Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

    Okoro CK, Barquist L, Connor TR, Harris SR, Clare S et al.

    PLoS neglected tropical diseases 2015;9;3;e0003611

    PUBMED: 25803844; PMC: 4372345; DOI: 10.1371/journal.pntd.0003611

  • The Hd, Hj, and Hz66 flagella variants of Salmonella enterica serovar Typhi modify host responses and cellular interactions.

    Schreiber F, Kay S, Frankel G, Clare S, Goulding D et al.

    Scientific reports 2015;5;7947

    PUBMED: 25609312; PMC: 4302301; DOI: 10.1038/srep07947

  • Patterns of genome evolution that have accompanied host adaptation in Salmonella.

    Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;3;863-8

    PUBMED: 25535353; PMC: 4311825; DOI: 10.1073/pnas.1416707112

  • Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance.

    Davies MR, Holden MT, Coupland P, Chen JH, Venturini C et al.

    Nature genetics 2015;47;1;84-7

    PUBMED: 25401300; DOI: 10.1038/ng.3147

  • Induced pluripotent stem cell derived macrophages as a cellular system to study salmonella and other pathogens.

    Hale C, Yeung A, Goulding D, Pickard D, Alasoo K et al.

    PloS one 2015;10;5;e0124307

    PUBMED: 25946027; PMC: 4422593; DOI: 10.1371/journal.pone.0124307

  • Transfer of scarlet fever-associated elements into the group A Streptococcus M1T1 clone.

    Ben Zakour NL, Davies MR, You Y, Chen JH, Forde BM et al.

    Scientific reports 2015;5;15877

    PUBMED: 26522788; PMC: 4629146; DOI: 10.1038/srep15877

  • Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.

    von Mentzer A, Connor TR, Wieler LH, Semmler T, Iguchi A et al.

    Nature genetics 2014;46;12;1321-6

    PUBMED: 25383970; DOI: 10.1038/ng.3145

  • Drug resistance in Salmonella enterica ser. Typhimurium bloodstream infection, Malawi.

    Feasey NA, Cain AK, Msefula CL, Pickard D, Alaerts M et al.

    Emerging infectious diseases 2014;20;11;1957-9

    PUBMED: 25340988; PMC: 4214322; DOI: 10.3201/eid2011.141175

  • CD28 expression is required after T cell priming for helper T cell responses and protective immunity to infection.

    Linterman MA, Denton AE, Divekar DP, Zvetkova I, Kane L et al.

    eLife 2014;3

    PUBMED: 25347065; PMC: 4241536; DOI: 10.7554/eLife.03180

  • Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

    Lamelas A, Harris SR, Röltgen K, Dangy JP, Hauser J et al.

    mBio 2014;5;5;e01974-14

    PUBMED: 25336458; PMC: 4212839; DOI: 10.1128/mBio.01974-14

  • Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

    Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD et al.

    Cell host & microbe 2014;16;4;504-16

    PUBMED: 25263220; PMC: 4190086; DOI: 10.1016/j.chom.2014.08.017

  • Typhoid fever in Fiji: a reversible plague?

    Thompson CN, Kama M, Acharya S, Bera U, Clemens J et al.

    Tropical medicine & international health : TM & IH 2014;19;10;1284-92

    PUBMED: 25066005; PMC: 4285329; DOI: 10.1111/tmi.12367

  • Antibacterial resistance in sub-Saharan Africa: an underestimated emergency.

    Kariuki S and Dougan G

    Annals of the New York Academy of Sciences 2014;1323;43-55

    PUBMED: 24628272; PMC: 4159419; DOI: 10.1111/nyas.12380

  • Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.

    Zhou Z, McCann A, Weill FX, Blin C, Nair S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;33;12199-204

    PUBMED: 25092320; PMC: 4143038; DOI: 10.1073/pnas.1411012111

  • TMEM129 is a Derlin-1 associated ERAD E3 ligase essential for virus-induced degradation of MHC-I.

    van den Boomen DJ, Timms RT, Grice GL, Stagg HR, Skødt K et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;31;11425-30

    PUBMED: 25030448; PMC: 4128144; DOI: 10.1073/pnas.1409099111

  • Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

    Da Cunha V, Davies MR, Douarre PE, Rosinski-Chupin I, Margarit I et al.

    Nature communications 2014;5;4544

    PUBMED: 25088811; PMC: 4538795; DOI: 10.1038/ncomms5544

  • The population structure of Vibrio cholerae from the Chandigarh Region of Northern India.

    Abd El Ghany M, Chander J, Mutreja A, Rashid M, Hill-Cawthorne GA et al.

    PLoS neglected tropical diseases 2014;8;7;e2981

    PUBMED: 25058483; PMC: 4109905; DOI: 10.1371/journal.pntd.0002981

  • Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides.

    Kenyon JJ, Holt KE, Pickard D, Dougan G and Hall RM

    Research in microbiology 2014;165;6;472-5

    PUBMED: 24861001; PMC: 4110982; DOI: 10.1016/j.resmic.2014.05.034

  • Vitamin B₁₂-dependent taurine synthesis regulates growth and bone mass.

    Roman-Garcia P, Quiros-Gonzalez I, Mottram L, Lieben L, Sharan K et al.

    The Journal of clinical investigation 2014;124;7;2988-3002

    PUBMED: 24911144; PMC: 4071367; DOI: 10.1172/JCI72606

  • The classical lancefield antigen of group a Streptococcus is a virulence determinant with implications for vaccine design.

    van Sorge NM, Cole JN, Kuipers K, Henningham A, Aziz RK et al.

    Cell host & microbe 2014;15;6;729-740

    PUBMED: 24922575; PMC: 4078075; DOI: 10.1016/j.chom.2014.05.009

  • Complete Genome Sequences of Two Citrobacter rodentium Bacteriophages, CR8 and CR44b.

    Toribio AL, Pickard D, Cerdeño-Tárraga AM, Petty NK, Thomson N et al.

    Genome announcements 2014;2;3

    PUBMED: 24874665; PMC: 4038870; DOI: 10.1128/genomeA.00146-14

  • An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution.

    Waddington CS, Darton TC, Jones C, Haworth K, Peters A et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2014;58;9;1230-40

    PUBMED: 24519873; PMC: 3982839; DOI: 10.1093/cid/ciu078

  • Global dissemination of a multidrug resistant Escherichia coli clone.

    Petty NK, Ben Zakour NL, Stanton-Cook M, Skippington E, Totsika M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;15;5694-9

    PUBMED: 24706808; PMC: 3992628; DOI: 10.1073/pnas.1322678111

  • Neutrophils recruited by IL-22 in peripheral tissues function as TRAIL-dependent antiviral effectors against MCMV.

    Stacey MA, Marsden M, Pham N TA, Clare S, Dolton G et al.

    Cell host & microbe 2014;15;4;471-83

    PUBMED: 24721575; PMC: 3989063; DOI: 10.1016/j.chom.2014.03.003

  • Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.

    De Chiara M, Hood D, Muzzi A, Pickard DJ, Perkins T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;14;5439-44

    PUBMED: 24706866; PMC: 3986186; DOI: 10.1073/pnas.1403353111

  • A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.

    Hamidian M, Holt KE, Pickard D, Dougan G and Hall RM

    The Journal of antimicrobial chemotherapy 2014;69;4;955-8

    PUBMED: 24235096; PMC: 3956371; DOI: 10.1093/jac/dkt454

  • Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism.

    Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP et al.

    BMC genomics 2014;15;160

    PUBMED: 24568651; PMC: 4028888; DOI: 10.1186/1471-2164-15-160

  • Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii.

    Hamidian M, Wynn M, Holt KE, Pickard D, Dougan G and Hall RM

    The Journal of antimicrobial chemotherapy 2014;69;2;557-8

    PUBMED: 24080502; PMC: 3886933; DOI: 10.1093/jac/dkt379

  • Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

    Shah MA, Mutreja A, Thomson N, Baker S, Parkhill J et al.

    Emerging infectious diseases 2014;20;1;13-20

    PUBMED: 24378019; PMC: 3884714; DOI: 10.3201/.eid2001.130428

  • Salmonella enterica serovar Typhi and the pathogenesis of typhoid fever.

    Dougan G and Baker S

    Annual review of microbiology 2014;68;317-36

    PUBMED: 25208300; DOI: 10.1146/annurev-micro-091313-103739

  • Tracking the establishment of local endemic populations of an emergent enteric pathogen.

    Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW et al.

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;43;17522-7

    PUBMED: 24082120; PMC: 3808646; DOI: 10.1073/pnas.1308632110

  • Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification.

    Pham Thanh D, Tran Vu Thieu N, Tran Thuy C, Lodén M, Tuin K et al.

    Journal of clinical microbiology 2013;51;9;2950-8

    PUBMED: 23824765; PMC: 3754622; DOI: 10.1128/JCM.01010-13

  • The agr locus regulates virulence and colonization genes in Clostridium difficile 027.

    Martin MJ, Clare S, Goulding D, Faulds-Pain A, Barquist L et al.

    Journal of bacteriology 2013;195;16;3672-81

    PUBMED: 23772065; PMC: 3754575; DOI: 10.1128/JB.00473-13

  • Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

    White JK, Gerdin AK, Karp NA, Ryder E, Buljan M et al.

    Cell 2013;154;2;452-64

    PUBMED: 23870131; PMC: 3717207; DOI: 10.1016/j.cell.2013.06.022

  • Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

    Wong VK, Pickard DJ, Barquist L, Sivaraman K, Page AJ et al.

    PloS one 2013;8;12;e84567

    PUBMED: 24386394; PMC: 3875573; DOI: 10.1371/journal.pone.0084567

  • Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model.

    Everitt AR, Clare S, McDonald JU, Kane L, Harcourt K et al.

    PloS one 2013;8;11;e80723

    PUBMED: 24278312; PMC: 3836756; DOI: 10.1371/journal.pone.0080723

  • Emergence and global spread of epidemic healthcare-associated Clostridium difficile.

    He M, Miyajima F, Roberts P, Ellison L, Pickard DJ et al.

    Nature genetics 2013;45;1;109-13

    PUBMED: 23222960; PMC: 3605770; DOI: 10.1038/ng.2478

  • Extensive diversity of Streptococcus pyogenes in a remote human population reflects global-scale transmission rather than localised diversification.

    Towers RJ, Carapetis JR, Currie BJ, Davies MR, Walker MJ et al.

    PloS one 2013;8;9;e73851

    PUBMED: 24066079; PMC: 3774777; DOI: 10.1371/journal.pone.0073851

  • Haploid genetic screens identify an essential role for PLP2 in the downregulation of novel plasma membrane targets by viral E3 ubiquitin ligases.

    Timms RT, Duncan LM, Tchasovnikarova IA, Antrobus R, Smith DL et al.

    PLoS pathogens 2013;9;11;e1003772

    PUBMED: 24278019; PMC: 3836740; DOI: 10.1371/journal.ppat.1003772

  • Mcph1-deficient mice reveal a role for MCPH1 in otitis media.

    Chen J, Ingham N, Clare S, Raisen C, Vancollie VE et al.

    PloS one 2013;8;3;e58156

    PUBMED: 23516444; PMC: 3596415; DOI: 10.1371/journal.pone.0058156

  • RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

    Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ et al.

    BMC genomics 2013;14;822

    PUBMED: 24267595; PMC: 4046660; DOI: 10.1186/1471-2164-14-822

  • RocA truncation underpins hyper-encapsulation, carriage longevity and transmissibility of serotype M18 group A streptococci.

    Lynskey NN, Goulding D, Gierula M, Turner CE, Dougan G et al.

    PLoS pathogens 2013;9;12;e1003842

    PUBMED: 24367267; PMC: 3868526; DOI: 10.1371/journal.ppat.1003842

  • Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.

    Okoro CK, Kingsley RA, Connor TR, Harris SR, Parry CM et al.

    Nature genetics 2012;44;11;1215-21

    PUBMED: 23023330; PMC: 3491877; DOI: 10.1038/ng.2423

  • Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.

    Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A et al.

    Nature genetics 2012;44;9;1056-9

    PUBMED: 22863732; PMC: 3442231; DOI: 10.1038/ng.2369

  • The Clostridium difficile spo0A gene is a persistence and transmission factor.

    Deakin LJ, Clare S, Fagan RP, Dawson LF, Pickard DJ et al.

    Infection and immunity 2012;80;8;2704-11

    PUBMED: 22615253; PMC: 3434595; DOI: 10.1128/IAI.00147-12

  • Molecular characterization of the 2011 Hong Kong scarlet fever outbreak.

    Tse H, Bao JY, Davies MR, Maamary P, Tsoi HW et al.

    The Journal of infectious diseases 2012;206;3;341-51

    PUBMED: 22615319; PMC: 4125623; DOI: 10.1093/infdis/jis362

  • The role of sphingosine-1-phosphate transporter Spns2 in immune system function.

    Nijnik A, Clare S, Hale C, Chen J, Raisen C et al.

    Journal of immunology (Baltimore, Md. : 1950) 2012;189;1;102-11

    PUBMED: 22664872; PMC: 3381845; DOI: 10.4049/jimmunol.1200282

  • A conserved acetyl esterase domain targets diverse bacteriophages to the Vi capsular receptor of Salmonella enterica serovar Typhi.

    Pickard D, Toribio AL, Petty NK, van Tonder A, Yu L et al.

    Journal of bacteriology 2010;192;21;5746-54

    PUBMED: 20817773; PMC: 2953684; DOI: 10.1128/JB.00659-10

  • Legionella pneumophila strain 130b possesses a unique combination of type IV secretion systems and novel Dot/Icm secretion system effector proteins.

    Schroeder GN, Petty NK, Mousnier A, Harding CR, Vogrin AJ et al.

    Journal of bacteriology 2010;192;22;6001-16

    PUBMED: 20833813; PMC: 2976443; DOI: 10.1128/JB.00778-10

  • Use of purified Clostridium difficile spores to facilitate evaluation of health care disinfection regimens.

    Lawley TD, Clare S, Deakin LJ, Goulding D, Yen JL et al.

    Applied and environmental microbiology 2010;76;20;6895-900

    PUBMED: 20802075; PMC: 2953018; DOI: 10.1128/AEM.00718-10

  • Molecular and physiological analysis of three Pseudomonas aeruginosa phages belonging to the "N4-like viruses".

    Ceyssens PJ, Brabban A, Rogge L, Lewis MS, Pickard D et al.

    Virology 2010;405;1;26-30

    PUBMED: 20619867; PMC: 3715699; DOI: 10.1016/j.virol.2010.06.011

  • An investigation of clinical and immunological events following repeated aerodigestive tract challenge infections with live Mycobacterium bovis Bacille Calmette Guérin.

    Schreiber F, Huo Z, Giemza R, Woodrow M, Fenner N et al.

    Vaccine 2010;28;33;5427-31

    PUBMED: 20558246; PMC: 3764428; DOI: 10.1016/j.vaccine.2010.06.005

  • Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion.

    Li P, Burke S, Wang J, Chen X, Ortiz M et al.

    Science (New York, N.Y.) 2010;329;5987;85-9

    PUBMED: 20538915; PMC: 3628452; DOI: 10.1126/science.1188063

  • Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia.

    Kariuki S, Revathi G, Kiiru J, Mengo DM, Mwituria J et al.

    Journal of clinical microbiology 2010;48;6;2171-6

    PUBMED: 20392916; PMC: 2884483; DOI: 10.1128/JCM.01983-09

  • Dysregulated humoral immunity to nontyphoidal Salmonella in HIV-infected African adults.

    MacLennan CA, Gilchrist JJ, Gordon MA, Cunningham AF, Cobbold M et al.

    Science (New York, N.Y.) 2010;328;5977;508-12

    PUBMED: 20413503; DOI: 10.1126/science.1180346

  • Evolutionary dynamics of Clostridium difficile over short and long time scales.

    He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF et al.

    Proceedings of the National Academy of Sciences of the United States of America 2010;107;16;7527-32

    PUBMED: 20368420; PMC: 2867753; DOI: 10.1073/pnas.0914322107

  • The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.

    Petty NK, Bulgin R, Crepin VF, Cerdeño-Tárraga AM, Schroeder GN et al.

    Journal of bacteriology 2010;192;2;525-38

    PUBMED: 19897651; PMC: 2805327; DOI: 10.1128/JB.01144-09

  • Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

    Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G et al.

    BMC genomics 2009;10;606

    PUBMED: 20003482; PMC: 2807441; DOI: 10.1186/1471-2164-10-606

  • A simple method for directional transcriptome sequencing using Illumina technology.

    Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB et al.

    Nucleic acids research 2009;37;22;e148

    PUBMED: 19815668; PMC: 2794173; DOI: 10.1093/nar/gkp811

  • Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants.

    Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L et al.

    Genome research 2009;19;12;2308-16

    PUBMED: 19826075; PMC: 2792183; DOI: 10.1101/gr.097097.109

  • The T3SS effector EspT defines a new category of invasive enteropathogenic E. coli (EPEC) which form intracellular actin pedestals.

    Bulgin R, Arbeloa A, Goulding D, Dougan G, Crepin VF et al.

    PLoS pathogens 2009;5;12;e1000683

    PUBMED: 20011125; PMC: 2782363; DOI: 10.1371/journal.ppat.1000683

  • Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts.

    Lawley TD, Clare S, Walker AW, Goulding D, Stabler RA et al.

    Infection and immunity 2009;77;9;3661-9

    PUBMED: 19564382; PMC: 2737984; DOI: 10.1128/IAI.00558-09

  • Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores.

    Lawley TD, Croucher NJ, Yu L, Clare S, Sebaihia M et al.

    Journal of bacteriology 2009;191;17;5377-86

    PUBMED: 19542279; PMC: 2725610; DOI: 10.1128/JB.00597-09

  • A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

    Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD et al.

    PLoS genetics 2009;5;7;e1000569

    PUBMED: 19609351; PMC: 2704369; DOI: 10.1371/journal.pgen.1000569

  • Public health. The cholera crisis in Africa.

    Bhattacharya S, Black R, Bourgeois L, Clemens J, Cravioto A et al.

    Science (New York, N.Y.) 2009;324;5929;885

    PUBMED: 19443768; DOI: 10.1126/science.1173890

  • Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi.

    Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R et al.

    BMC genomics 2009;10;36

    PUBMED: 19159446; PMC: 2658671; DOI: 10.1186/1471-2164-10-36

  • Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.

    Stabler RA, He M, Dawson L, Martin M, Valiente E et al.

    Genome biology 2009;10;9;R102

    PUBMED: 19781061; PMC: 2768977; DOI: 10.1186/gb-2009-10-9-r102

  • Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69.

    Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T et al.

    Journal of bacteriology 2009;191;1;347-54

    PUBMED: 18952797; PMC: 2612414; DOI: 10.1128/JB.01238-08

  • Typhoid Fever

    Kingsley,R.A. and Dougan,G.;

    Vaccines for Biodefense and Emerging and Neglected Diseases 2009;Chapter 57;1147–1161

    DOI: 10.1016/B978-0-12-369408-9.00057-3; URL: http://www.sciencedirect.com/scien...ce/article/pii/B9780123694089000573

  • Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.

    Thomson NR, Clayton DJ, Windhorst D, Vernikos G, Davidson S et al.

    Genome research 2008;18;10;1624-37

    PUBMED: 18583645; PMC: 2556274; DOI: 10.1101/gr.077404.108

  • High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

    Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX et al.

    Nature genetics 2008;40;8;987-93

    PUBMED: 18660809; PMC: 2652037; DOI: 10.1038/ng.195

  • The neglected role of antibody in protection against bacteremia caused by nontyphoidal strains of Salmonella in African children.

    MacLennan CA, Gondwe EN, Msefula CL, Kingsley RA, Thomson NR et al.

    The Journal of clinical investigation 2008;118;4;1553-62

    PUBMED: 18357343; PMC: 2268878; DOI: 10.1172/JCI33998

  • Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1.

    Pickard D, Thomson NR, Baker S, Wain J, Pardo M et al.

    Journal of bacteriology 2008;190;7;2580-7

    PUBMED: 18192390; PMC: 2293211; DOI: 10.1128/JB.01654-07

  • A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

    Baker S, Holt K, Whitehead S, Goodhead I, Perkins T et al.

    Molecular microbiology 2007;66;5;1207-18

    PUBMED: 17976161; PMC: 2652032; DOI: 10.1111/j.1365-2958.2007.05995.x

  • Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota.

    Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M et al.

    PLoS biology 2007;5;10;2177-89

    PUBMED: 17760501; PMC: 1951780; DOI: 10.1371/journal.pbio.0050244

  • The genome of Salmonella enterica serovar Typhi.

    Baker S and Dougan G

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2007;45 Suppl 1;S29-33

    PUBMED: 17582565; DOI: 10.1086/518143

  • Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.

    Holt KE, Thomson NR, Wain J, Phan MD, Nair S et al.

    Journal of bacteriology 2007;189;11;4257-64

    PUBMED: 17384186; PMC: 1913411; DOI: 10.1128/JB.00232-07

  • Requirement of bic/microRNA-155 for normal immune function.

    Rodriguez A, Vigorito E, Clare S, Warren MV, Couttet P et al.

    Science (New York, N.Y.) 2007;316;5824;608-11

    PUBMED: 17463290; PMC: 2610435; DOI: 10.1126/science.1139253

  • The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

    Thomson NR, Howard S, Wren BW, Holden MT, Crossman L et al.

    PLoS genetics 2006;2;12;e206

    PUBMED: 17173484; PMC: 1698947; DOI: 10.1371/journal.pgen.0020206

  • Evolutionary history of Salmonella typhi.

    Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S et al.

    Science (New York, N.Y.) 2006;314;5803;1301-4

    PUBMED: 17124322; PMC: 2652035; DOI: 10.1126/science.1134933

  • The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.

    Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N et al.

    Nature genetics 2006;38;7;779-86

    PUBMED: 16804543; DOI: 10.1038/ng1830

  • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D et al.

    Nature 2001;413;6858;848-52

    PUBMED: 11677608; DOI: 10.1038/35101607

  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT et al.

    Nature 2001;413;6855;523-7

    PUBMED: 11586360; DOI: 10.1038/35097083