Dr Rob Kingsley

Research Leader

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I am a Research Leader at the Institute, overseeing a research programme that combines bioinformatics, genomics, molecular microbiology and models of infection to investigate the evolution of interactions between pathogens, the environment and the host. Much of my early career was focused on investigation of iron metabolism in bacterial pathogens, and later on molecular mechanisms by which they colonise the host and cause disease.

I have always been interested in using information about the naturally occurring variation in the genetic makeup of bacterial pathogens in order to infer function and evolutionary history of colonization and virulence factors. This led to the discovery of intestinal colonisation and persistence mechanisms specific to subtypes of Salmonella that account for the vast majority of human disease, likely because they enabled expansion in host range to include domesticated animals that form the zoonotic reservoir of this pathogen.

Around the year 2005, next generation sequencing changed the potential of whole genome sequencing of bacteria to enable discrimination of genetic variants of bacterial pathogens with exquisite resolution. My interest therefore moved to the use of this technology to investigate variation on a whole genome level, and in particular, closely related variants that exhibit differences in host range, pathogenicity and risk to food safety.

I now use these approaches to understand how new pathogens emerge and evolve, how epidemics spread, and how we can use this information to improve surveillance and risk assessment of foodborne pathogens.


Key Publications

Liljana Petrovska, Alison E. Mather, Manal AbuOun, Priscilla Branchu, Simon R. Harris, Thomas Connor, K. L. Hopkins, A. Underwood, Antonia A Lettini, Andrew Page, Mary Bagnall, John Wain, Julian Parkhill, Gordon Dougan, Robert Davies, Robert A. Kingsley (2016) Microevolution during the emergence of a monophasic Salmonella Typhimurium epidemic in the United Kingdom. Emerging Infectious Diseases. ;22(4):617-24.

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, Hill J, Harcourt K, Parkhill J, Dougan G, Kingsley RA (2015) Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa. PLoS Negl Trop Dis. Mar14;9(3):e0003611

Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S, Hale C, Seshasayee A, Harris S, Thomson NR, Gardner P, Rabsch W, Wigley P, Humphrey T, Parkhill J, Dougan G. (2013) Genome and transcriptome adaptation accompanying emergence of the DT2 host-restricted Salmonella Typhimurium pathovar. MBio 27:4(5):e00565-13.

Chinyere K. Okoro, Robert A. Kingsley, Thomas R. Connor, Simon R. Harris, Christopher M. Parry, Manar N Al-Mashhadani, Samuel Kariuki, Chisomo L. Msefula, Melita A. Gordon, Elizabeth de Pinna, John Wain, Robert S. Heyderman, Stephen Obaro, Pedro L. Alonso Inacio Mandomando, Calman A. MacLennan, Milagritos D. Tapia, Myron M. Levine, Sharon M. Tennant Julian Parkhill, Gordon Dougan. (2012) Intra-continental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa.  Nature Genetics. 30 September 2012;

Robert A. Kingsley, Chisomo L. Msefula, Nicholas R. Thomson, Samuel Kariuki, Kathryn E. Holt, Melita A. Gordon, David Harris, Louise Clarke, Sally Whitehead, Vartul Sangal, Kevin Marsh,  Mark Achtman, Malcolm E. Molyneux, Martin Cormican, Julian Parkhill, Calman A. MacLennan, Robert S. Heyderman and Gordon Dougan. (2009) Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in Sub-Saharan Africa have a distinct genotype.  Genome Research, 9(12), 2279-87.

Ondari E. M., Heath J. N., Klemm E. J., Langridge G., Barquist L., Goulding D. A., Clare S., Dougan G., Kingsley R. A., MacLennan C. A.. (2017)

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

Infection and immunity, 85, 2017 Aug 18;85(9)


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Metris A., Sudhakar P., Fazekas D., Demeter A., Eszter A., Olbei M., Branchu P., Kingsley R., Baranyi J., Korcsmaros T.. (2017)

SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation

Nature Partner Journals Systems Biology and Applications, 3, Article number: 31 (2017)


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Zhang Y., Dominguez-Medina C., Cumley N. J., Heath J. N., Essex S. J., Bobat S., Schager A., Goodall M., Kracker S., Buckley C. D., May R. C., Kingsley R. A., MacLennan C. A., López-Macías C., Cunningham A. F., Toellner K. M.. (2017)

IgG1 Is Required for Optimal Protection after Immunization with the Purified Porin OmpD from Salmonella Typhimurium.

Journal of immunology (Baltimore, Md. : 1950), 199, 4103-4109


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Wheeler N. E., Barquist L., Kingsley R. A., Gardner P. P.. (2016)

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Bioinformatics, 32, 3566-3574


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Wong V. K., Baker S., Connor T. R., Pickard D., Page A. J., Dave J., Murphy N., Holliman R., Sefton A., Millar M., Dyson Z. A., Dougan G., Holt K. E., Kingsley R. A.. (2016)

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

Nature communications, 7, 12827


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Feasey N. A., Hadfield J., Keddy K. H., Dallman T. J., Jacobs J., Deng X., Wigley P., Barquist Barquist L., Langridge G. C., Feltwell T., Harris S. R., Mather A. E., Fookes M., Aslett M., Msefula C., Kariuki S., Maclennan C. A., Onsare R. S., Weill F. X., Le Hello S., Smith A. M., McClelland M., Desai P., Parry C. M., Cheesbrough J., French N., Campos J., Chabalgoity J. A., Betancor L., Hopkins K. L., Nair S., Humphrey T. J., Lunguya O., Cogan T. A., Tapia M. D., Sow S. O., Tennant S. M., Bornstein K., Levine M. M., Lacharme-Lora L., Everett D. B., Kingsley R. A., Parkhill J., Heyderman R. S., Dougan G., Gordon M. A., Thomson N. R.. (2016)

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

Nature Genetics, 48, 1211-7


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Darton T. C., Jones C., Blohmke C. J., Waddington C. S., Zhou L., Peters A., Haworth K., Sie R., Green C. A., Jeppesen C. A., Moore M., Thompson B. A., John T., Kingsley R., Yu L. M., Voysey M., Hindle Z., Lockhart S., Sztein M. B., Dougan G., Angus B., Levine M. M., Pollard A. J.. (2016)

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

PLoS neglected tropical diseases, 10, e0004926


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