Prof. Rob Kingsley

Group Leader

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Pathogen variation

I am a Group 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.

Khan MM, Sidorczuk K, Becker J, Aleksandrowicz A, Baraniewicz K, Ludwig C, Ali A, Kingsley R, Schierack P, Kolenda . (2024)

Characterization of clumpy adhesion of Escherichia coli to human cells and associated factors influencing antibiotic sensitivity

Microbiology spectrum


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Acton L, Pye HV, Thilliez G, Kolenda R, Matthews M, Turner AK, Yasir M, Holden E, Al-Khanaq H, Webber M, Adriaenssens EM, Kingsley . (2024)

Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica

Journal of Virology


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Elek C, Brown T, Le Viet T, Evans R, Baker D, Telatin A, Tiwari S, Al-Khanaq H, Thilliez G, Kingsley R, Hall L, Webber M, Adriaenssens . (2023)

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Microbial Genomics, 9


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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva, De A, de Ligt, Diaz Guevara, Dolecek C, Dutta S, Ehlers MM, Francois Watkins, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley R, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE, Aaby P, Abbas A, Ahmed N, Andleeb S, Aseffa A, Baker KS, Bentsi-Enchill A, Breiman RF, Britto C, Campos J, Chen CJ, Chiou CS, Davong V, Faiz A, Gul D, Hasan R, Hatta M, Ikram A, Isaia L, Jacobs J, Kariuki S, Khokhar F, Klemm E, Kuijpers LMF, Langridge G, Lim K, Lunguya O, Luquero F, MacLennan CA, Marks F, Morita M, Muchimba M, Mwansa JCL, Mwape K, Mwenda JM, Nash J, Neuzil KM, Newton P, Obaro S, Octavia S, Ohnishi M, Owusu M, Owusu-Dabo E, Park SE, Parkhill J, Pham DT, Phoba MF, Pickard DJ, Rakotozandrindrainy R, Ramon-Pardo P, Rasheed F, Rokney A, Rupali P, Sah R, Shakoor S, Simuyand M, Sooka A, Stanaway JD, Steele AD, Tack B, Tall A, Taneja N, Teferi M, Tessema S, Thilliez G, Turner P, Ussher JE, Villanueva AM, Weimer B, Wong VK, Founou R. (2023)

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

eLife


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Thilliez G, Mashe T, Chaibva BV, Robertson V, Bawn M, Tarupiwa A, Takawira FT, Kock MM, Midzi S, Mwamakamba LW, Matheu J, Juru A, Kingsley R, Ehlers M. (2023)

Population structure of Salmonella enterica Typhi in Harare, Zimbabwe (2012-19) before typhoid conjugate vaccine roll-out: a genomic epidemiology study.

The Lancet. Microbe


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Van Puyvelde, de Block, Sridhar S, Bawn M, Kingsley R, Ingelbeen B, Beale MA, Barbé B, Jeon HJ, Mbuyi-Kalonji L, Phoba MF, Falay D, Martiny D, Vandenberg O, Affolabi D, Rutanga JP, Ceyssens PJ, Mattheus W, Cuypers WL, van der, Park SE, Kariuki S, Otieno K, Lusingu JPA, Mbwana JR, Adjei S, Sarfo A, Agyei SO, Asante KP, Otieno W, Otieno L, Tahita MC, Lompo P, Hoffman IF, Mvalo T, Msefula C, Hassan-Hanga F, Obaro S, Mackenzie G, Deborggraeve S, Feasey N, Marks F, MacLennan CA, Thomson NR, Jacobs J, Dougan G, Kariuki S, Lunguya . (2023)

A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa.

Nature communications


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Mashe T, Thilliez G, Chaibva B, Leekitcharoenphon P, Bawn M, Nyanzunda M, Tarupiwa A, Al-Khanaq H, Baker D, Kock M, Weill X, Hendriksen R, Ehlers M, Kingsley . (2023)

Highly drug resistant clone of Salmonella Kentucky ST198 in clinical infections and poultry in Zimbabwe

NPJ Antimicrobials & Resistance, 1, 6


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Nyagupe C, de Oliveira Martins L, Gumbo H, Mashe T, Takawira T, Maeka KK, Juru A, Chikanda LK, Tauya AR, Page AJ, Kingsley RA, Simbi R, Chirenda J, Manasa J, Ruhanya V, Mavenyengwa R. (2023)

SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis.

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde


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