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Cambridge Immunology Network



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.


Key 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, Smith AM, Baker S, Gouali M, Pham Thanh D, Jahan Azmi I et al. eLife 2015;4;e07335

PUBMED: 26238191; PMC: 4522646; DOI: 10.7554/eLife.07335


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, Dance D, Jenney A, Connor TR, Hsu LY, Severin J et al. Proceedings of the National Academy of Sciences of the United States of America 2015;112;27;E3574-81

PUBMED: 26100894 PMC: 4500264 DOI: 10.1073/pnas.1501049112


Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G, Crook PD, Gilbart VL, Zittermann S, Allen VG, Howden BP et al. The Lancet. Infectious diseases 2015;15;8;913-21

PUBMED: 25936611 DOI: 10.1016/S1473-3099(15)00002-X


The extant World War 1 dysentery bacillus NCTC1: a genomic analysis. Baker KS, Mather AE, McGregor H, Coupland P, Langridge GC, Day M, Deheer-Graham A, Parkhill J, Russell JE and Thomson NR. Lancet (London, England) 2014;384;9955;1691-7

PUBMED: 25441199 PMC: 4226921 DOI: 10.1016/S0140-6736(14)61789-X


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, Deheer-Graham A, Parkhill J, Bracegirdle P, Russell JE and Thomson NR. Lancet (London, England) 2014;384;9955;1720

PUBMED: 25441203 DOI: 10.1016/S0140-6736(14)61790-6


Genomic Investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen. Gillespie SH, Ling CL, Oravcova K, Pinheiro M, Wells L, Bryant JM, McHugh TD, Bébéar C, Webster D, Harris SR et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2014;60;3;381-8

PUBMED: 25344534; PMC: 4293396; DOI: 10.1093/cid/ciu820


Parallel independent evolution of pathogenicity within the genus Yersinia. Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM et al. Proceedings of the National Academy of Sciences of the United States of America 2014;111;18;6768-73

PUBMED: 24753568 PMC: 4020045 DOI: 10.1073/pnas.1317161111


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, Unemo M, Clarke IN, Parkhill J and Thomson NR. Nature protocols 2013;8;12;2404-12

PUBMED: 24202554 DOI: 10.1038/nprot.2013.147


Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Mather AE, Reid SW, Maskell DJ, Parkhill J, Fookes MC, Harris SR, Brown DJ, Coia JE, Mulvey MR, Gilmour MW et al. Science (New York, N.Y.) 2013;341;6153;1514-7.

PUBMED: 24030491 PMC: 4012302 DOI: 10.1126/science.1240578


Evidence for several waves of global transmission in the seventh cholera pandemic. Mutreja A, Kim DW, Thomson NR, Connor TR, Lee JH, Kariuki S, Croucher NJ, Choi SY, Harris SR, Lebens M et al. Nature 2011;477;7365;462-5

PUBMED: 21866102 PMC: 3736323 DOI: 10.1038/nature10392

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