Prof. Rob Kingsley

Group Leader

Contact via email

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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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri AN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang'a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Shumba E, El Fahime, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O'Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, de Oliveira Martins L, Tyers L, Ramuth M, Mastouri M, Aouni M, El Hefnawi, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der, Mashe T, Aanniz T, Mohale T, Le Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent, Sall AA, Rebai A, von Gottberg, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira. (2021)

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

Science (New York, N.Y.)


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Mashe T, Takawira FT, de Oliveira Martins L, Gudza-Mugabe M, Chirenda J, Munyanyi M, Chaibva BV, Tarupiwa A, Gumbo H, Juru A, Nyagupe C, Ruhanya V, Phiri I, Manangazira P, Goredema A, Danda S, Chabata I, Jonga J, Munharira R, Masunda K, Mukeredzi I, Mangwanya D, Trotter A, Le Viet T, Rudder S, Kay G, Baker D, Thilliez G, Gutierrez AV, O'Grady J, Hove M, Mutapuri-Zinyowera S, Page AJ, Kingsley RA, Mhlanga G. (2021)

Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.

The Lancet. Global health


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

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases


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Page AJ, Mather AE, Le Viet T, Meader EJ, Alikhan NF, Kay GL, de Oliveira Martins L, Aydin A, Baker DJ, Trotter AJ, Rudder S, Tedim AP, Kolyva A, Stanley R, Yasir M, Diaz M, Potter W, Stuart C, Meadows L, Bell A, Gutierrez AV, Thomson NM, Adriaenssens EM, Swingler T, Gilroy RAJ, Griffith L, Sethi DK, Aggarwal D, Brown CS, Davidson RK, Kingsley RA, Bedford L, Coupland LJ, Charles IG, Elumogo N, Wain J, Prakash R, Webber MA, Smith SJL, Chand M, Dervisevic S, O'Grady J. (2021)

Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.

Microbial genomics


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Abd El, Barquist L, Clare S, Brandt C, Mayho M, Joffre E, Sjöling Å, Turner AK, Klena JD, Kingsley R, Hill-Cawthorne GA, Dougan G, Pickard D. (2021)

Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization.

Microbial genomics


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