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.

Devaraj A,González JF,Eichar B,Thilliez G,Kingsley RA,Baker S,Allard MW,Bakaletz LO,Gunn JS,Goodman SD. (2021)

Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi.

PLoS pathogens


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Volz E,Hill V,McCrone JT,Price A,Jorgensen D,O'Toole Á,Southgate J,Johnson R,Jackson B,Nascimento FF,Rey SM,Nicholls SM,Colquhoun RM,da Silva,Shepherd J,Pascall DJ,Shah R,Jesudason N,Li K,Jarrett R,Pacchiarini N,Bull M,Geidelberg L,Siveroni I,Goodfellow I,Loman NJ,Pybus OG,Robertson DL,Thomson EC,Rambaut A,Connor TR,Koshy C,Wise E,Cortes N,Lynch J,Kidd S,Mori M,Fairley DJ,Curran T,McKenna JP,Adams H,Fraser C,Golubchik T,Bonsall D,Moore C,Caddy SL,Khokhar FA,Wantoch M,Reynolds N,Warne B,Maksimovic J,Spellman K,McCluggage K,John M,Beer R,Afifi S,Morgan S,Marchbank A,Price A,Kitchen C,Gulliver H,Merrick I,Southgate J,Guest M,Munn R,Workman T,Connor TR,Fuller W,Bresner C,Snell LB,Charalampous T,Nebbia G,Batra R,Edgeworth J,Robson SC,Beckett A,Loveson KF,Aanensen DM,Underwood AP,Yeats CA,Abudahab K,Taylor BEW,Menegazzo M,Clark G,Smith W,Khakh M,Fleming VM,Lister MM,Howson-Wells HC,Berry L,Boswell T,Joseph A,Willingham I,Bird P,Helmer T,Fallon K,Holmes C,Tang J,Raviprakash V,Campbell S,Sheriff N,Loose MW,Holmes N,Moore C,Carlile M,Wright V,Sang F,Debebe J,Coll F,Signell AW,Betancor G,Wilson HD,Feltwell T,Houldcroft CJ,Eldirdiri S,Kenyon A,Davis T,Pybus O,du Plessis,Zarebski A,Raghwani J,Kraemer M,Francois S,Attwood S,Vasylyeva T,Torok ME,Hamilton WL,Goodfellow IG,Hall G,Jahun AS,Chaudhry Y,Hosmillo M,Pinckert ML,Georgana I,Yakovleva A,Meredith LW,Moses S,Lowe H,Ryan F,Fisher CL,Awan AR,Boyes J,Breuer J,Harris KA,Brown JR,Shah D,Atkinson L,Lee JCD,Alcolea-Medina A,Moore N,Cortes N,Williams R,Chapman MR,Levett LJ,Heaney J,Smith DL,Bashton M,Young GR,Allan J,Loh J,Randell PA,Cox A,Madona P,Holmes A,Bolt F,Price J,Mookerjee S,Rowan A,Taylor GP,Ragonnet-Cronin M,Nascimento FF,Jorgensen D,Siveroni I,Johnson R,Boyd O,Geidelberg L,Volz EM,Brunker K,Smollett KL,Loman NJ,Quick J,McMurray C,Stockton J,Nicholls S,Rowe W,Poplawski R,Martinez-Nunez RT,Mason J,Robinson TI,O'Toole E,Watts J,Breen C,Cowell A,Ludden C,Sluga G,Machin NW,Ahmad SSY,George RP,Halstead F,Sivaprakasam V,Thomson EC,Shepherd JG,Asamaphan P,Niebel MO,Li KK,Shah RN,Jesudason NG,Parr YA,Tong L,Broos A,Mair D,Nichols J,Carmichael SN,Nomikou K,Aranday-Cortes E,Johnson N,Starinskij I,da Silva,Robertson DL,Orton RJ,Hughes J,Vattipally S,Singer JB,Hale AD,Macfarlane-Smith LR,Harper KL,Taha Y,Payne BAI,Burton-Fanning S,Waugh S,Collins J,Eltringham G,Templeton KE,McHugh MP,Dewar R,Wastenge E,Dervisevic S,Stanley R,Prakash R,Stuart C,Elumogo N,Sethi DK,Meader EJ,Coupland LJ,Potter W,Graham C,Barton E,Padgett D,Scott G,Swindells E,Greenaway J,Nelson A,Yew WC,Resende Silva,Andersson M,Shaw R,Peto T,Justice A,Eyre D,Crooke D,Hoosdally S,Sloan TJ,Duckworth N,Walsh S,Chauhan AJ,Glaysher S,Bicknell K,Wyllie S,Butcher E,Elliott S,Lloyd A,Impey R,Levene N,Monaghan L,Bradley DT,Allara E,Pearson C,Muir P,Vipond IB,Hopes R,Pymont HM,Hutchings S,Curran MD,Parmar S,Lackenby A,Mbisa T,Platt S,Miah S,Bibby D,Manso C,Hubb J,Chand M,Dabrera G,Ramsay M,Bradshaw D,Thornton A,Myers R,Schaefer U,Groves N,Gallagher E,Lee D,Williams D,Ellaby N,Harrison I,Hartman H,Manesis N,Patel V,Bishop C,Chalker V,Osman H,Bosworth A,Robinson E,Holden MTG,Shaaban S,Birchley A,Adams A,Davies A,Gaskin A,Plimmer A,Gatica-Wilcox B,McKerr C,Moore C,Williams C,Heyburn D,De Lacy,Hilvers E,Downing F,Shankar G,Jones H,Asad H,Coombes J,Watkins J,Evans JM,Fina L,Gifford L,Gilbert L,Graham L,Perry M,Morgan M,Bull M,Cronin M,Pacchiarini N,Craine N,Jones R,Howe R,Corden S,Rey S,Kumziene-Summerhayes S,Taylor S,Cottrell S,Jones S,Edwards S,O'Grady J,Page AJ,Wain J,Webber MA,Mather AE,Baker DJ,Rudder S,Yasir M,Thomson NM,Aydin A,Tedim AP,Kay GL,Trotter AJ,Gilroy RAJ,Alikhan NF,de Oliveira,Le Viet T,Meadows L,Kolyva A,Diaz M,Bell A,Gutierrez AV,Charles IG,Adriaenssens EM,Kingsley RA,Casey A,Simpson DA,Molnar Z,Thompson T,Acheson E,Masoli JAH,Knight BA,Hattersley A,Ellard S,Auckland C,Mahungu TW,Irish-Tavares D,Haque T,Bourgeois Y,Scarlett GP,Partridge DG,Raza M,Evans C,Johnson K,Liggett S,Baker P,Essex S,Lyons RA,Caller LG,Castellano S,Williams RJ,Kristiansen M,Roy S,Williams CA,Dyal PL,Tutill HJ,Panchbhaya YN,Forrest LM,Niola P,Findlay J,Brooks TT,Gavriil A,Mestek-Boukhibar L,Weeks S,Pandey S,Berry L,Jones K,Richter A,Beggs A,Smith CP,Bucca G,Hesketh AR,Harrison EM,Peacock SJ,Palmer S,Churcher CM,Bellis KL,Girgis ST,Naydenova P,Blane B,Sridhar S,Ruis C,Forrest S,Cormie C,Gill HK,Dias J,Higginson EE,Maes M,Young J,Kermack LM,Hadjirin NF,Aggarwal D,Griffith L,Swingler T,Davidson RK,Rambaut A,Williams T,Balcazar CE,Gallagher MD,O'Toole Á,Rooke S,Jackson B,Colquhoun R,Ashworth J,Hill V,McCrone JT,Scher E,Yu X,Williamson KA,Stanton TD,Michell SL,Bewshea CM,Temperton B,Michelsen ML,Warwick-Dugdale J,Manley R,Farbos A,Harrison JW,Sambles CM,Studholme DJ,Jeffries AR,Darby AC,Hiscox JA,Paterson S,Iturriza-Gomara M,Jackson KA,Lucaci AO,Vamos EE,Hughes M,Rainbow L,Eccles R,Nelson C,Whitehead M,Turtle L,Haldenby ST,Gregory R,Gemmell M,Kwiatkowski D,de Silva,Smith N,Angyal A,Lindsey BB,Groves DC,Green LR,Wang D,Freeman TM,Parker MD,Keeley AJ,Parsons PJ,Tucker RM,Brown R,Wyles M,Constantinidou C,Unnikrishnan M,Ott S,Cheng JKJ,Bridgewater HE,Frost LR,Taylor-Joyce G,Stark R,Baxter L,Alam MT,Brown PE,McClure PC,Chappell JG,Tsoleridis T,Ball J,Gramatopoulos D,Buck D,Todd JA,Green A,Trebes A,MacIntyre-Cockett G,de Cesare,Langford C,Alderton A,Amato R,Goncalves S,Jackson DK,Johnston I,Sillitoe J,Palmer S,Lawniczak M,Berriman M,Danesh J,Livett R,Shirley L,Farr B,Quail M,Thurston S,Park N,Betteridge E,Weldon D,Goodwin S,Nelson R,Beaver C,Letchford L,Jackson DA,Foulser L,McMinn L,Prestwood L,Kay S,Kane L,Dorman MJ,Martincorena I,Puethe C,Keatley JP,Tonkin-Hill G,Smith C,Jamrozy D,Beale MA,Patel M,Ariani C,Spencer-Chapman M,Drury E,Lo S,Rajatileka S,Scott C,James K,Buddenborg SK,Berger DJ,Patel G,Garcia-Casado MV,Dibling T,McGuigan S,Rogers HA,Hunter AD,Souster E,Neaverson AS. (2021)

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Cell


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Kingsley R,Tassinari E,Bawn M,Thilliez G,Charity O,Acton L,Kirkwood M,Petrovska L,Dallman T,Burgess C,Hall N,Duffy G. (2020)

Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella Typhimurium clone

Microbial Genomics


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Mashe T,Leekitcharoenphon P,Mtapuri-Zinyowera S,Kingsley R,Robertson V,Tarupiwa A,Kock MM,Makombe EP,Chaibva BV,Manangazira P,Phiri I,Nyadundu S,Chigwena CT,Mufoya LP,Thilliez G,Midzi S,Mwamakamba LW,Hamblion EL,Matheu J,Jensen JD,Aarestrup FM,Hendriksen RS,Ehlers MM. (2020)

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

The Journal of antimicrobial chemotherapy


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Tambassi M,Berni M,Bracchi C,Scaltriti E,Morganti M,Bolzoni L,Tanner JR,Thilliez G,Kingsley R,Pongolini S,Casadei G. (2020)

Mutation of hilD in a Salmonella Derby lineage linked to swine adaptation and reduced risk to human health.

Scientific reports


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