Professor Nicholas Robert Thomson | Group Leader

Thomson, Nicholas Robert

Nick is a microbiologist and bioinformatician and is interested in bacterial evolution and spread with a focus on sexually transmitted and diarrhoeal diseases. He is also Professor of Bacterial Genomics and Evolution at the London School of Hygiene and Tropical Medicine.

Nick's lab uses genomic approaches to investigate how variation in bacterial genomes relates to their hosts/niche, changes over time and geography, or in response to therapeutic interventions. His group also focuses on accessing genome data directly from clinical samples without the need for culture.

Nick graduated from Warwick University in 1991 with a degree in Microbiology and Microbial Technology and then went on to earn a PhD in global regulation of virulence and secondary metabolism in enteric bacteria.

Before joining the Sanger Institute, Nick worked as a Postdoctoral Fellow at the University of Cambridge Biochemistry Department and L'Institut National des Sciences Appliquées (INSA) de Lyon, France.

In 1999, Nick moved to the Institute as a Senior Computer Biologist, subsequently became a Principal Staff Scientist and was promoted to Group Leader and member of Faculty in 2014. Nick has and is very proud of an honorary chair he received in 2012 from the University of St Andrews, School of Medicine. Equally proud of, at the end of 2013 Nick took up a joint appointment between the Sanger Institute and the London School of Hygiene and Tropical Medicine where he is Chair of Bacterial Genomics and Evolution. These appointments are at the heart of Nicks approach to research: multidisciplinary teams, scientist, modelers and clinicians alike, with a broad global reach and focus. Of course at the absolute core of his work is enthusiasm, a love of investigative research, willingness to collaborate, communicate and teach science as well as the most important piece, a great young team of investigators, current and past.

Publications

  • Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

    Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA et al.

    eLife 2015;4;e07335

  • Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.

    Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;27;E3574-81

  • Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.

    Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G et al.

    The Lancet. Infectious diseases 2015;15;8;913-21

  • The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.

    Baker KS, Mather AE, McGregor H, Coupland P, Langridge GC et al.

    Lancet (London, England) 2014;384;9955;1691-7

  • Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection.

    Mather AE, Baker KS, McGregor H, Coupland P, Mather PL et al.

    Lancet (London, England) 2014;384;9955;1720

  • Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen.

    Gillespie SH, Ling CL, Oravcova K, Pinheiro M, Wells L et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015;60;3;381-8

  • Parallel independent evolution of pathogenicity within the genus Yersinia.

    Reuter S, Connor TR, Barquist L, Walker D, Feltwell T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;18;6768-73

  • Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

    Seth-Smith HM, Harris SR, Scott P, Parmar S, Marsh P et al.

    Nature protocols 2013;8;12;2404-12

  • Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

    Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC et al.

    Science (New York, N.Y.) 2013;341;6153;1514-7

  • 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

  • Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya.

    Henson SP, Boinett CJ, Ellington MJ, Kagia N, Mwarumba S et al.

    International journal of medical microbiology : IJMM 2017

  • Galleria mellonella is low cost and suitable surrogate host for studying virulence of human pathogenic Vibrio cholerae.

    Bokhari H, Ali A, Noreen Z, Thomson N and Wren BW

    Gene 2017

  • Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing.

    Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S et al.

    PLoS neglected tropical diseases 2017;11;6;e0005671

  • Brucella neotomae Infection in Humans, Costa Rica.

    Suárez-Esquivel M, Ruiz-Villalobos N, Jiménez-Rojas C, Barquero-Calvo E, Chacón-Díaz C et al.

    Emerging infectious diseases 2017;23;6;997-1000

  • European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

    Seth-Smith HMB, Busó LS, Livingstone M, Sait M, Harris SR et al.

    BMC genomics 2017;18;1;344

  • 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

  • Concern regarding the alleged spread of hypervirulent lymphogranuloma venereum Chlamydia trachomatis strain in Europe.

    Seth-Smith HM, Galán JC, Goldenberger D, Lewis DA, Peuchant O et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2017;22;15

  • Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

    Baker KS, Campos J, Pichel M, Della Gaspera A, Duarte-Martínez F et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2017

  • Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients.

    Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017

  • Genomic landscape of extended-spectrum β-lactamase resistance in Escherichia coli from an urban African setting.

    Musicha P, Feasey NA, Cain AK, Kallonen T, Chaguza C et al.

    The Journal of antimicrobial chemotherapy 2017

  • A Clostridium difficile lineage endemic to Costa Rican hospitals is multidrug-resistant by acquisition of chromosomal mutations and novel mobile genetic elements.

    Ramírez-Vargas G, Quesada-Gómez C, Acuña-Amador L, López-Ureña D, Murillo T et al.

    Antimicrobial agents and chemotherapy 2017

  • Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape.

    Esson D, Gupta S, Bailey D, Wigley P, Wedley A et al.

    Microbial pathogenesis 2017;104;202-211

  • Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice.

    Oshota O, Conway M, Fookes M, Schreiber F, Chaudhuri RR et al.

    PloS one 2017;12;8;e0181365

  • Genomic variations leading to alterations in cell morphology of Campylobacter spp.

    Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP et al.

    Scientific reports 2016;6;38303

  • A genomic island in Vibrio cholerae with VPI-1 site-specific recombination characteristics contains CRISPR-Cas and type VI secretion modules.

    Labbate M, Orata FD, Petty NK, Jayatilleke ND, King WL et al.

    Scientific reports 2016;6;36891

  • The type III secretion system effector SeoC of Salmonella enterica subspecies salamae and arizonae ADP-ribosylates Src and inhibits opsono-phagocytosis.

    Pollard DJ, Young JC, Covarelli V, Herrera-León S, Connor TR et al.

    Infection and immunity 2016

  • 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

  • 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

  • Genomic analysis of Salmonella enterica serovar Typhimurium from wild passerines in England and Wales.

    Mather AE, Lawson B, de Pinna E, Wigley P, Parkhill J et al.

    Applied and environmental microbiology 2016

  • Travel- and Community-Based Transmission of Multidrug-Resistant Shigella sonnei Lineage among International Orthodox Jewish Communities.

    Baker KS, Dallman TJ, Behar A, Weill FX, Gouali M et al.

    Emerging infectious diseases 2016;22;9;1545-53

  • The diversity of Klebsiella pneumoniae surface polysaccharides.

    Follador R, Heinz E, Wyres KL, Ellington MJ, Kowarik M et al.

    Microbial genomics 2016;2;8;e000073

  • South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study.

    Chung The H, Rabaa MA, Pham Thanh D, De Lappe N, Cormican M et al.

    PLoS medicine 2016;13;8;e1002055

  • Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

    Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N et al.

    Nature microbiology 2016;1;16027

  • Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.

    Andersson P, Harris SR, Seth Smith HM, Hadfield J, O'Neill C et al.

    Nature communications 2016;7;10688

  • 'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution.

    McNally A, Thomson NR, Reuter S and Wren BW

    Nature reviews. Microbiology 2016;14;3;177-90

  • Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria.

    Seth-Smith HM, Dourala N, Fehr A, Qi W, Katharios P et al.

    The ISME journal 2016

  • 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

  • Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution.

    Jelocnik M, Bachmann NL, Seth-Smith H, Thomson NR, Timms P and Polkinghorne AM

    PeerJ 2016;4;e1661

  • Quantitative Proteomics of the Infectious and Replicative Forms of Chlamydia trachomatis.

    Skipp PJ, Hughes C, McKenna T, Edwards R, Langridge J et al.

    PloS one 2016;11;2;e0149011

  • Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014.

    Chowdhury F, Mather AE, Begum YA, Asaduzzaman M, Baby N et al.

    PLoS neglected tropical diseases 2015;9;11;e0004183

  • A putative, novel coli surface antigen 8B (CS8B) of enterotoxigenic Escherichia coli.

    Njoroge SM, Boinett CJ, Madé LF, Ouko TT, Fèvre EM et al.

    Pathogens and disease 2015;73;7

  • The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource.

    Baker KS, Burnett E, McGregor H, Deheer-Graham A, Boinett C et al.

    Genome medicine 2015;7;97

  • Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri.

    Connor TR, Barker CR, Baker KS, Weill FX, Talukder KA et al.

    eLife 2015;4;e07335

  • Genetic characterization of three qnrS1-harbouring multidrug-resistance plasmids and qnrS1-containing transposons circulating in Ho Chi Minh City, Vietnam.

    Le V, Nhu NT, Cerdeno-Tarraga A, Campbell JI, Tuyen HT et al.

    Journal of medical microbiology 2015;64;8;869-78

  • Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.

    Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G et al.

    The Lancet. Infectious diseases 2015;15;8;913-21

  • Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.

    Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;27;E3574-81

  • Whole genome analysis to detect potential vaccine-induced changes on Shigella sonnei genome.

    Behar A, Fookes MC, Goren S, Thomson NR and Cohen D

    Vaccine 2015;33;26;2978-83

  • The genetic characterization of three qnrS1 harbouring multi-drug resistance plasmids and qnrS1-containing transposons circulating in Ho Chi Minh City, Vietnam.

    Le V, Khanh Nhu NT, Cerdeno-Tarraga A, Campbell JI, Tuyen HT et al.

    Journal of medical microbiology 2015

  • Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis.

    Hjerde E, Karlsen C, Sørum H, Parkhill J, Willassen NP and Thomson NR

    BMC genomics 2015;16;447

  • 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

  • Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.

    Baker KS, Parkhill J and Thomson NR

    Genome announcements 2015;3;3

  • Antimicrobial Drug Resistance of Vibrio cholerae, Democratic Republic of the Congo.

    Miwanda B, Moore S, Muyembe JJ, Nguefack-Tsague G, Kabangwa IK et al.

    Emerging infectious diseases 2015;21;5;847-51

  • Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

    Weerdenburg EM, Abdallah AM, Rangkuti F, Abd El Ghany M, Otto TD et al.

    Infection and immunity 2015;83;5;1778-88

  • A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.

    Rapa RA, Islam A, Monahan LG, Mutreja A, Thomson N et al.

    Environmental microbiology 2015;17;4;1090-102

  • A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae.

    Chung The H, Karkey A, Pham Thanh D, Boinett CJ, Cain AK et al.

    EMBO molecular medicine 2015;7;3;227-39

  • 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

  • Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Infantis Strains from Healthy Broiler Chicks in Hungary and in the United Kingdom.

    Olasz F, Nagy T, Szabó M, Kiss J, Szmolka A et al.

    Genome announcements 2015;3;1

  • A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster.

    Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K et al.

    DNA research : an international journal for rapid publication of reports on genes and genomes 2015;22;1;101-7

  • Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen.

    Gillespie SH, Ling CL, Oravcova K, Pinheiro M, Wells L et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2015;60;3;381-8

  • 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

  • Multi-scale mechanical characterization of highly swollen photo-activated collagen hydrogels.

    Tronci G, Grant CA, Thomson NH, Russell SJ and Wood DJ

    Journal of the Royal Society, Interface / the Royal Society 2015;12;102;20141079

  • Draft genomes of Shigella strains used by the STOPENTERICS consortium.

    Rossi O, Baker KS, Phalipon A, Weill FX, Citiulo F et al.

    Gut pathogens 2015;7;14

  • Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp.

    Katharios P, Seth-Smith HM, Fehr A, Mateos JM, Qi W et al.

    Scientific reports 2015;5;17609

  • Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates.

    Moore S, Miwanda B, Sadji AY, Thefenne H, Jeddi F et al.

    PLoS neglected tropical diseases 2015;9;6;e0003817

  • Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels.

    Hall M, Chattaway MA, Reuter S, Savin C, Strauch E et al.

    Journal of clinical microbiology 2015;53;1;35-42

  • 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

  • The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.

    Baker KS, Mather AE, McGregor H, Coupland P, Langridge GC et al.

    Lancet (London, England) 2014;384;9955;1691-7

  • Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection.

    Mather AE, Baker KS, McGregor H, Coupland P, Mather PL et al.

    Lancet (London, England) 2014;384;9955;1720

  • The genetic basis of plasmid tropism between Chlamydia trachomatis and Chlamydia muridarum.

    Wang Y, Cutcliffe LT, Skilton RJ, Ramsey KH, Thomson NR and Clarke IN

    Pathogens and disease 2014;72;1;19-23

  • Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

    Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W et al.

    PLoS computational biology 2014;10;10;e1003907

  • A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012.

    Byrne L, Fisher I, Peters T, Mather A, Thomson N et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2014;19;31;6-13

  • Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

    Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y et al.

    Genome biology and evolution 2014;6;8;2096-110

  • Plasmid CDS5 influences infectivity and virulence in a mouse model of Chlamydia trachomatis urogenital infection.

    Ramsey KH, Schripsema JH, Smith BJ, Wang Y, Jham BC et al.

    Infection and immunity 2014;82;8;3341-9

  • 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

  • RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri.

    Vergara-Irigaray M, Fookes MC, Thomson NR and Tang CM

    BMC genomics 2014;15;438

  • 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

  • Parallel independent evolution of pathogenicity within the genus Yersinia.

    Reuter S, Connor TR, Barquist L, Walker D, Feltwell T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;18;6768-73

  • The Yersinia pseudotuberculosis complex: characterization and delineation of a new species, Yersinia wautersii.

    Savin C, Martin L, Bouchier C, Filali S, Chenau J et al.

    International journal of medical microbiology : IJMM 2014;304;3-4;452-63

  • Widespread epidemic cholera caused by a restricted subset of Vibrio cholerae clones.

    Moore S, Thomson N, Mutreja A and Piarroux R

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2014;20;5;373-9

  • Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.

    Ashton PM, Baker KS, Gentle A, Wooldridge DJ, Thomson NR et al.

    Gut pathogens 2014;6;1;7

  • Plasmid deficiency in urogenital isolates of Chlamydia trachomatis reduces infectivity and virulence in a mouse model.

    Sigar IM, Schripsema JH, Wang Y, Clarke IN, Cutcliffe LT et al.

    Pathogens and disease 2014;70;1;61-9

  • 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

  • Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

    Seth-Smith HM, Harris SR, Scott P, Parmar S, Marsh P et al.

    Nature protocols 2013;8;12;2404-12

  • Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.

    McDonnell J, Dallman T, Atkin S, Turbitt DA, Connor TR et al.

    Epidemiology and infection 2013;141;12;2568-75

  • Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi.

    Bronowski C, Fookes MC, Gilderthorp R, Ashelford KE, Harris SR et al.

    PLoS neglected tropical diseases 2013;7;11;e2557

  • 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

  • Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

    Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC et al.

    Science (New York, N.Y.) 2013;341;6153;1514-7

  • Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.

    Seth-Smith HM, Harris SR, Skilton RJ, Radebe FM, Golparian D et al.

    Genome research 2013;23;5;855-66

  • Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.

    O'Neill CE, Seth-Smith HM, Van Der Pol B, Harris SR, Thomson NR et al.

    Microbiology (Reading, England) 2013;159;Pt 4;748-56

  • Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms.

    Dziva F, Hauser H, Connor TR, van Diemen PM, Prescott G et al.

    Infection and immunity 2013;81;3;838-49

  • Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians.

    Seth-Smith HM and Thomson NR

    Current opinion in infectious diseases 2013;26;1;90-8

  • 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

  • The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

    Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;20;E1277-86

  • Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.

    Harris SR, Clarke IN, Seth-Smith HM, Solomon AW, Cutcliffe LT et al.

    Nature genetics 2012;44;4;413-9, S1

  • Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.

    Seth-Smith HM, Fookes MC, Okoro CK, Baker S, Harris SR et al.

    Journal of bacteriology 2012;194;6;1494-504

  • Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae.

    Stecher B, Denzler R, Maier L, Bernet F, Sanders MJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;4;1269-74

  • Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis.

    Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI et al.

    PLoS pathogens 2011;7;11;e1002342

  • 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

  • Salmonella bongori provides insights into the evolution of the Salmonellae.

    Fookes M, Schroeder GN, Langridge GC, Blondel CJ, Mammina C et al.

    PLoS pathogens 2011;7;8;e1002191

  • Genome sequences of Salmonella enterica serovar typhimurium, Choleraesuis, Dublin, and Gallinarum strains of well- defined virulence in food-producing animals.

    Richardson EJ, Limaye B, Inamdar H, Datta A, Manjari KS et al.

    Journal of bacteriology 2011;193;12;3162-3

  • Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.

    Petty NK, Feltwell T, Pickard D, Clare S, Toribio AL et al.

    PLoS pathogens 2011;7;4;e1002018

  • Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding blaCTX-M-14.

    Cottell JL, Webber MA, Coldham NG, Taylor DL, Cerdeño-Tárraga AM et al.

    Emerging infectious diseases 2011;17;4;645-52

  • Differential phenotypic and genotypic characteristics of qnrS1-harboring plasmids carried by hospital and community commensal enterobacteria.

    Vien le TM, Abuoun M, Morrison V, Thomson N, Campbell JI et al.

    Antimicrobial agents and chemotherapy 2011;55;4;1798-802

  • Genome sequence of the zoonotic pathogen Chlamydophila psittaci.

    Seth-Smith HM, Harris SR, Rance R, West AP, Severin JA et al.

    Journal of bacteriology 2011;193;5;1282-3

  • Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.

    Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P et al.

    Nature genetics 2010;42;12;1140-3

  • A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.

    Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M et al.

    Journal of bacteriology 2010;192;21;5822-31

  • 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

  • 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

  • Studying bacterial transcriptomes using RNA-seq.

    Croucher NJ and Thomson NR

    Current opinion in microbiology 2010;13;5;619-24

  • Prevalence of Salmonella enterica in poultry and eggs in Uruguay during an epidemic due to Salmonella enterica serovar Enteritidis.

    Betancor L, Pereira M, Martinez A, Giossa G, Fookes M et al.

    Journal of clinical microbiology 2010;48;7;2413-23

  • The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization.

    Unemo M, Seth-Smith HM, Cutcliffe LT, Skilton RJ, Barlow D et al.

    Microbiology (Reading, England) 2010;156;Pt 5;1394-404

  • Chlamydia trachomatis: small genome, big challenges.

    Thomson NR and Clarke IN

    Future microbiology 2010;5;4;555-61

  • Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.

    Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL et al.

    PloS one 2010;5;1;e8801

  • 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

  • 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

  • Genomics. Genome project standards in a new era of sequencing.

    Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J et al.

    Science (New York, N.Y.) 2009;326;5950;236-7

  • 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

  • Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain.

    Seth-Smith HM, Harris SR, Persson K, Marsh P, Barron A et al.

    BMC genomics 2009;10;239

  • Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever.

    Phan MD, Kidgell C, Nair S, Holt KE, Turner AK et al.

    Antimicrobial agents and chemotherapy 2009;53;2;716-27

  • 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

  • The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.

    Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD et al.

    Journal of bacteriology 2009;191;1;261-77

  • 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

  • DNAPlotter: circular and linear interactive genome visualization.

    Carver T, Thomson N, Bleasby A, Berriman M and Parkhill J

    Bioinformatics (Oxford, England) 2009;25;1;119-20

  • Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.

    Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW et al.

    Genome biology 2009;10;5;R51

  • Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.

    Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C et al.

    Genome research 2009;19;1;12-23

  • The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.

    Hjerde E, Lorentzen MS, Holden MT, Seeger K, Paulsen S et al.

    BMC genomics 2008;9;616

  • Characterization of the genomes of a diverse collection of Salmonella enterica serovar Typhimurium definitive phage type 104.

    Cooke FJ, Brown DJ, Fookes M, Pickard D, Ivens A et al.

    Journal of bacteriology 2008;190;24;8155-62

  • Rapid Virulence Annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts.

    Waterfield NR, Sanchez-Contreras M, Eleftherianos I, Dowling A, Yang G et al.

    Proceedings of the National Academy of Sciences of the United States of America 2008;105;41;15967-72

  • 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

  • The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.

    Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF et al.

    Journal of bacteriology 2008;190;20;6881-93

  • Genome evolution of Wolbachia strain wPip from the Culex pipiens group.

    Klasson L, Walker T, Sebaihia M, Sanders MJ, Quail MA et al.

    Molecular biology and evolution 2008;25;9;1877-87

  • Vive la différence.

    Thomson NR

    Nature reviews. Microbiology 2008;6;7;502-3

  • Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.

    Pearson MM, Sebaihia M, Churcher C, Quail MA, Seshasayee AS et al.

    Journal of bacteriology 2008;190;11;4027-37

  • Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.

    Field D, Garrity GM, Sansone SA, Sterk P, Gray T et al.

    Omics : a journal of integrative biology 2008;12;2;109-13

  • Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.

    Field D, Glöckner FO, Garrity GM, Gray T, Sterk P et al.

    Omics : a journal of integrative biology 2008;12;2;101-8

  • Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.

    Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al.

    Omics : a journal of integrative biology 2008;12;2;137-41

  • The minimum information about a genome sequence (MIGS) specification.

    Field D, Garrity G, Gray T, Morrison N, Selengut J et al.

    Nature biotechnology 2008;26;5;541-7

  • The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants.

    Crossman LC, Gould VC, Dow JM, Vernikos GS, Okazaki A et al.

    Genome biology 2008;9;4;R74

  • 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

  • Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids.

    Revilla C, Garcillán-Barcia MP, Fernández-López R, Thomson NR, Sanders M et al.

    Antimicrobial agents and chemotherapy 2008;52;4;1472-80

  • Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates.

    Thomson NR, Holden MT, Carder C, Lennard N, Lockey SJ et al.

    Genome research 2008;18;1;161-71

  • A generalized transducing phage for the murine pathogen Citrobacter rodentium.

    Petty NK, Toribio AL, Goulding D, Foulds I, Thomson N et al.

    Microbiology (Reading, England) 2007;153;Pt 9;2984-8

  • Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates.

    Cooke FJ, Wain J, Fookes M, Ivens A, Thomson N et al.

    Journal of clinical microbiology 2007;45;8;2590-8

  • Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes.

    Sebaihia M, Peck MW, Minton NP, Thomson NR, Holden MT et al.

    Genome research 2007;17;7;1082-92

  • 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

  • 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

  • Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction.

    Sebaihia M, Preston A, Maskell DJ, Kuzmiak H, Connell TD et al.

    Journal of bacteriology 2006;188;16;6002-15

  • 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

  • Bacterial home from home.

    Thomson N, Crossman L and Bentley S

    Nature reviews. Microbiology 2006;4;3;168-70

  • The genome of Rhizobium leguminosarum has recognizable core and accessory components.

    Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF et al.

    Genome biology 2006;7;4;R34

  • Microbial mariners.

    Holden M, Thomson N and Bentley S

    Nature reviews. Microbiology 2005;3;10;748-9

  • Massive attack.

    Thomson N, Cerdeño-Tárraga A and Bentley S

    Nature reviews. Microbiology 2005;3;8;586-7

  • The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.

    Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD et al.

    Genome research 2005;15;5;629-40

  • GI genomes.

    Cerdeño-Tárraga A, Claesson MJ, Sebaihia M and Thomson NR

    Nature reviews. Microbiology 2005;3;5;368-9

  • Livelihood hazards.

    Sebaihia M, Thomson NR, Crossman L and Parkhill J

    Nature reviews. Microbiology 2005;3;4;278-9

  • The influence of smoking on the treatment response in patients with asthma.

    Thomson NC and Spears M

    Current opinion in allergy and clinical immunology 2005;5;1;57-63

  • Brothers in arms.

    Thomson N, Holden M and Parkhill J

    Nature reviews. Microbiology 2005;3;2;100-1

  • The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number.

    Collins NE, Liebenberg J, de Villiers EP, Brayton KA, Louw E et al.

    Proceedings of the National Academy of Sciences of the United States of America 2005;102;3;838-43

  • Microevolution and history of the plague bacillus, Yersinia pestis.

    Achtman M, Morelli G, Zhu P, Wirth T, Diehl I et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;51;17837-42

  • The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics.

    Gilmour MW, Thomson NR, Sanders M, Parkhill J and Taylor DE

    Plasmid 2004;52;3;182-202

  • Pathogens in decay.

    Cerdeño-Tárraga A, Thomson N and Parkhill J

    Nature reviews. Microbiology 2004;2;10;774-5

  • Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.

    Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;39;14240-5

  • Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.

    Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;30;11105-10

  • Chalk and cheese.

    Crossman L, Cerdeño-Tárraga A and Thomson NR

    Nature reviews. Microbiology 2004;2;7;528-9

  • Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate.

    Kapatral V, Campbell JW, Minnich SA, Thomson NR, Matsumura P and Prüss BM

    Microbiology (Reading, England) 2004;150;Pt 7;2289-300

  • The role of prophage-like elements in the diversity of Salmonella enterica serovars.

    Thomson N, Baker S, Pickard D, Fookes M, Anjum M et al.

    Journal of molecular biology 2004;339;2;279-300

  • The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

    Cerdeño-Tárraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M et al.

    Nucleic acids research 2003;31;22;6516-23

  • Fitting the niche by genomic adaptation.

    Thomson N, Bentley S, Holden M and Parkhill J

    Nature reviews. Microbiology 2003;1;2;92-3

  • The value of comparison.

    Thomson N, Sebaihia M, Cerdeño-Tárraga A, Bentley S, Crossman L and Parkhill J

    Nature reviews. Microbiology 2003;1;1;11-2

  • Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

    Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N et al.

    Nature genetics 2003;35;1;32-40

  • Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7.

    Pickard D, Wain J, Baker S, Line A, Chohan S et al.

    Journal of bacteriology 2003;185;17;5055-65

  • A bad combination.

    Sebaihia M, Bentley S, Crossman L, Thomson N and Parkhill J

    Trends in microbiology 2003;11;7;297-9

  • The devil is in the detail.

    Bentley SD, Thomson NR, Sebaihia M, Crossman LC and Parkhill J

    Trends in microbiology 2003;11;6;256-8

  • All walks of life.

    Thomson NR, Cerdeño-Tárraga A, Crossman L, Sebaihia M and Parkhill J

    Trends in microbiology 2003;11;4;159-60

  • The building blocks of pathogenicity.

    Thomson NR and Parkhill J

    Trends in microbiology 2003;11;2;66-7

  • Microbial genomics: spot the difference. . .

    Thomson NR, Sebaihia M and Parkhill J

    Trends in microbiology 2002;10;11;489-90

  • Sibling rivalry.

    Thomson N, Sebaihia M, Cerdeño-Tárraga A and Parkhill J

    Trends in microbiology 2002;10;9;396-7

  • Genome giants.

    Sebaihia M, Bentley S, Thomson N, Holden M and Parkhill J

    Trends in microbiology 2002;10;7;309-10

  • Tales of the unexpected.

    Sebaihia M, Bentley S, Thomson N, Holden M and Parkhill J

    Trends in microbiology 2002;10;6;261-2

  • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

    Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR et al.

    Nature 2002;417;6885;141-7

  • Armed to the teeth.

    Bentley S, Holden M, Thomson N and Parkhill J

    Trends in microbiology 2002;10;4;163-4

  • The decaying genome of Mycobacterium leprae.

    Eiglmeier K, Parkhill J, Honoré N, Garnier T, Tekaia F et al.

    Leprosy review 2001;72;4;387-98

  • Microbial genomics. Dynamic duos.

    Sebaihia M, Thomson N, Holden M and Parkhill J

    Trends in microbiology 2001;9;12;579

  • Lost and found.

    Cerdeño-Tárraga A, Thomson N, Holden M, Sebaihia M and Parkhill J

    Trends in microbiology 2001;9;11;526-7

  • 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

  • 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

  • The full monty.

    Thomson N, Holden M, Sebaihia M, Cerdeño-Tárraga A and Parkhill J

    Trends in microbiology 2001;9;9;411-2

  • Size matters?

    Thomson N, Sebaihia M, Holden M, Cerdeño-Tárraga A and Parkhill J

    Trends in microbiology 2001;9;8;359

  • Of staphs, streps and other things.

    Sebaihia M, Cerdeño-Tárraga A, Thomson N and Parkhill J

    Trends in microbiology 2001;9;7;309

  • Massive gene decay in the leprosy bacillus.

    Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR et al.

    Nature 2001;409;6823;1007-11

  • Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control.

    Thomson NR, Crow MA, McGowan SJ, Cox A and Salmond GP

    Molecular microbiology 2000;36;3;539-56

  • Erwinia carotovora has two KdgR-like proteins belonging to the IciR family of transcriptional regulators: identification and characterization of the RexZ activator and the KdgR repressor of pathogenesis.

    Thomson NR, Nasser W, McGowan S, Sebaihia M and Salmond GP

    Microbiology (Reading, England) 1999;145 ( Pt 7);1531-45

  • The rap and hor proteins of Erwinia, Serratia and Yersinia: a novel subgroup in a growing superfamily of proteins regulating diverse physiological processes in bacterial pathogens.

    Thomson NR, Cox A, Bycroft BW, Stewart GS, Williams P and Salmond GP

    Molecular microbiology 1997;26;3;531-44

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Thomson, Nicholas Robert
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