Professor Nick Thomson


of Bacterial Genomics and Evolution


Keppel Street
United Kingdom

Nicholas Thomson is Professor of Bacterial Genomics and Evolution in the department of Pathogen Molecular Biology, at the London School Of Hygiene & Tropical Medicine. He is also a Principal Scientist at the Wellcome Trust Sanger Institute within the Pathogen Genomics and Biology Program and holds an Honorary Chair at School of Medicine, University of St Andrews. He graduated in Microbiology and Microbial Technology from Warwick University in 1991 and then worked as a Research Technician before pursuing a PhD also at Warwick University reading global regulation of virulence and secondary metabolism in enteric bacteria. After receiving his Doctorate in 1995 he worked as a Post Doctoral Research Fellow at the University of Cambridge, Biochemistry Department and L’Institut National des Sciences Appliquées (INSA) de Lyon, France. He joined the Wellcome Trust Sanger Institute in 1999 as a Senior Computer Biologist and is now a Principal Scientist and runs a group focussed on bacterial genomics. In 2012 he received an Honorary chair at the University of St Andrews and joined the LSHTM recently in 2013. 


Faculty of Infectious and Tropical Diseases
Department of Pathogen Molecular Biology


Much of his work involves extended international networks of scientist, clinicians and clinical scientists. To support these collaborations and increase access to genomic data he, along with the Wellcome trust Advanced Courses and LSHTM, has established and continues to develop genomics courses. The Pathogens Advanced Course alone reaching over 410 participants from 63 different countries.


His research has focused on members of the Enterobacteriaceae including Vibrio cholerae, Salmonella sp & subsp, pathogenic E. coli, Shigella sp, Citrobacter and Yersinia. In addition, he also studied the genetic makeup and diversity of other non-enteric bacteria ranging from Chlamydia to Burkholderia. For Chlamydia his group led the work to produce the first reference genome sequence of a lymphogranuloma venereum (LGV) C. trachomatis isolate and has gone to show that the epidemic LGV isolates (LGV L2b) thought to represent a new more infectious form on LGV was in fact an old strain causing a new disease. Since this time his work has broadened to focus on understanding and defining the population structure of all three disease-causing variants of C. trachomatis. For along time it has been assumed that Chlamydia do not recombine. However, recent work by his group and collaborators has shown conclusively that the ompA gene used to subtype C. trachomatis isolates is a chimera formed by a ‘mix and match’ process of recombination. This work has also provided evidence of widespread DNA exchange throughout the genome between clinical isolates affecting different body sites and causing sexually transmitted or ocular infections, showing that C. trachomatis are able to recombine freely and that there are in fact few barriers to recombination. This fact alone challenges much of our understanding of the population structure of C. trachomatis. To facilitate this work his group has developed methods to sequence Chlamydia directly from uncultured discarded clinical swabs enabling his group to extend their population studies. This methodology has broad applications in clinical microbiology.

 His research on Salmonella has focused on the diversity and genotypic differences between salmonellae with different host-ranges and disease outcomes. This has resulted in the generation of whole genome reference sequences for many of the major human and animal pathogenic serotypes of S. enterica. His early genomic research focused on patterns of evolution involving gene acquisition mediated by phage or other mobile genetic elements and identified serotype-specific genes that plot the evolutionary divergence both within the salmonellae as well as from broader members of the Enterobacteriaceae. However, it soon became clear from this work that gene loss was as important to pathogen evolution as gene gain with a clear association between host restriction in the salmonellae and concomitant functional gene loss.

 In addition his group has contributed to a ‘One Health’ look at the flow of antimicrobial resistance and the zoonotic pathogen Salmonella Typhimurium DT104 (DT104) that carries these determinant by considering isolates from both humans and farm animals over the same 22-year period in Scotland. Contrary to popular belief this study showed that DT104 and antibiotic resistance genes found in it were largely maintained separately within the local animals (mainly cattle) and the human population, with only a small amount of spillover between the two hosts. It was also evident that the combination and array of resistance genes seen in humans was different to that found in local animals. He considers studies of this nature and resolution to be essential if we are to identify the sources and sinks of both food borne pathogens such as DT104 and AMR. AMR being considered by many as one of the most important threats to public health.

 He has also worked to determine the phylogenetic makeup and contemporary and historical distribution of species within the genus Shigella and pandemic seven Vibrio cholerae. His work on cholera used modern techniques and genomic data to identify a global source for pandemic cholera. This work not only concentrates on determining their global distribution but also attempts to understand the drivers for this and the patterns of continued spread between countries and within communities. More recent work in this area has looked more deeply into plotting the national spread of V. cholerae clones, showing firstly that this can be done by genomic approaches with isolates separated by only a few weeks and that it can practical information that can be used to inform public health measures.


Current research

Current Research interests include linking phenotype to genotype: Using Phylogenomics of isolates competing within their natural host to identify novel and known factors associated with ‘fitness’ and onward transmission. Understanding how pathogen variation may impact on host-pathogen interactions and continuing to use genomics towards a better understanding of infectious disease and global health.

Research Area
Drug resistance
Public health
Sexual health
Disease control
Global Health
Molecular biology
Disease and Health Conditions
Eye diseases
Infectious disease
Sexually transmitted disease
Emerging Infectious Disease
Hospital acquired infection
Neglected Tropical Diseases (NTDs)
Sexually transmitted infection
Tropical diseases
Costa Rica
Dominican Republic
United Kingdom
Gambia, The
New Zealand
Korea, Dem. Rep.
Solomon Islands
Venezuela, RB
South Africa
Caribbean small states
East Asia & Pacific (all income levels)
Europe & Central Asia (all income levels)
Latin America & Caribbean (all income levels)
Middle East & North Africa (all income levels)
Sub-Saharan Africa (all income levels)

Selected Publications

Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.
Andersson, P. ; Harris, S.R. ; Smith, H.M. ; Hadfield, J. ; O'Neill, C. ; Cutcliffe, L.T. ; Douglas, F.P. ; Asche, L.V. ; Mathews, J.D. ; Hutton, S.I. ; Sarovich, D.S. ; Tong, S.Y. ; Clarke, I.N. ; Thomson, N.R. ; Giffard, P.M. ;
Nat Commun
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.
Baker, K.S.; Dallman, T.J.; Ashton, P.M.; Day, M.; Hughes, G.; Crook, P.D.; Gilbart, V.L.; Zittermann, S.; Allen, V.G.; Howden, B.P.; Tomita, T.; Valcanis, M.; Harris, S.R.; Connor, T.R.; Sintchenko, V.; Howard, P.; Brown, J.D.; Petty, N.K.; Gouali, M.; Thanh, D.P.; Keddy, K.H.; Smith, A.M.; Talukder, K.A.; Faruque, S.M.; Parkhill, J.; Baker, S.; Weill, F.X.; Jenkins, C.; Thomson, N.R.;
Lancet Infect Dis
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.
Wong, V.K.; Baker, S.; Pickard, D.J.; Parkhill, J.; Page, A.J.; Feasey, N.A.; Kingsley, R.A.; Thomson, N.R.; Keane, J.A.; Weill, F.X.; Edwards, D.J.; Hawkey, J.; Harris, S.R.; Mather, A.E.; Cain, A.K.; Hadfield, J.; Hart, P.J.; Thieu, N.T.; Klemm, E.J.; Glinos, D.A.; Breiman, R.F.; Watson, C.H.; Kariuki, S.; Gordon, M.A.; Heyderman, R.S.; Okoro, C.; Jacobs, J.; Lunguya, O.; Edmunds, W.J.; Msefula, C.; Chabalgoity, J.A.; Kama, M.; Jenkins, K.; Dutta, S.; Marks, F.; Campos, J.; Thompson, C.; Obaro, S.; MacLennan, C.A.; Dolecek, C.; Keddy, K.H.; Smith, A.M.; Parry, C.M.; Karkey, A.; Mulholland, E.K.; Campbell, J.I.; Dongol, S.; Basnyat, B.; Dufour, M.; Bandaranayake, D.; Naseri, T.T.; Singh, S.P.; Hatta, M.; Newton, P.; Onsare, R.S.; Isaia, L.; Dance, D.; Davong, V.; Thwaites, G.; Wijedoru, L.; Crump, J.A.; De Pinna, E.; Nair, S.; Nilles, E.J.; Thanh, D.P.; Turner, P.; Soeng, S.; Valcanis, M.; Powling, J.; Dimovski, K.; Hogg, G.; Farrar, J.; Holt, K.E.; Dougan, G.;
Nat Genet
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.
Holt, K.E.; Wertheim, H.; Zadoks, R.N.; Baker, S.; Whitehouse, C.A.; Dance, D.; Jenney, A.; Connor, T.R.; Hsu, L.Y.; Severin, J.; Brisse, S.; Cao, H.; Wilksch, J.; Gorrie, C.; Schultz, M.B.; Edwards, D.J.; Nguyen, K.V.; Nguyen, T.V.; Dao, T.T.; Mensink, M.; Minh, V.L.; Nhu, N.T.; Schultsz, C.; Kuntaman, K.; Newton, P.N.; Moore, C.E.; Strugnell, R.A.; Thomson, N.R.;
Proc Natl Acad Sci U S A
Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri
Connor, T.R.; Barker, C.R.; Baker, K.S.; Weill, F.-X.; Talukder, K.A.; Smith, A.M.; Stephen, B.; Gouali, M.; Duy Pham, T.; Azmi, I.J.; da Silveira, W.D.; Semmler, T.; Wieler, L.H.; Jenkins, C.; Cravioto, A.; Faruque, S.M.; Parkhill, J.; Kim, D.W.; Keddy, K.H.; Thomson, N.R.
Vibrio cholerae Serogroup O139: Isolation from Cholera Patients and Asymptomatic Household Family Members in Bangladesh between 2013 and 2014.
Chowdhury, F. ; Mather, A.E. ; Begum, Y.A. ; Asaduzzaman, M. ; Baby, N. ; Sharmin, S. ; Biswas, R. ; Ikhtear Uddin, M. ; LaRocque, R.C. ; Harris, J.B. ; Calderwood, S.B. ; Ryan, E.T. ; Clemens, J.D. ; Thomson, N.R. ; Qadri, F. ;
PLoS Negl Trop Dis
The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.
Baker, K.S. ; Mather, A.E. ; McGregor, H. ; Coupland, P. ; Langridge, G.C. ; Day, M. ; Deheer-Graham, A. ; Parkhill, J. ; Russell, J.E. ; Thomson, N.R. ;
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture.
Seth-Smith, H.M. ; Harris, S.R. ; Skilton, R.J. ; Radebe, F.M. ; Golparian, D. ; Shipitsyna, E. ; Duy, P.T. ; Scott, P. ; Cutcliffe, L.T. ; O'Neill, C. ; Parmar, S. ; Pitt, R. ; Baker, S. ; Ison, C.A. ; Marsh, P. ; Jalal, H. ; Lewis, D.A. ; Unemo, M. ; Clarke, I.N. ; Parkhill, J. ; Thomson, N.R. ;
Genome Res
See all Professor Nick Thomson's Publications