Prof. Justin O'Grady

Group Leader

Contact via email

Rapid infectious disease and foodborne pathogen diagnosis/detection

I gained my B.Sc. in Microbiology, M.Sc. (Res) in infectious diseases molecular diagnostics and Ph.D. in molecular diagnosis of bacterial pathogens in food all at the National University of Ireland Galway (NUIG).  I stayed at NUIG for my first post-doc, continuing in food microbiology research. This was followed by a two-year stint in industry (Beckman Coulter) developing real-time PCR based molecular diagnostics assays for infectious diseases including Mycobacterium tuberculosis.

I then returned to academia, taking up a post-doc position at University College London on TB diagnostics. In January 2013 I was appointed Lecturer in Medical Microbiology at UEA, was promoted to Senior Lecturer in August 2016, and Professor of Medical Microbiology in February 2021.

I joined the Quadram Institute as a Group Leader in April 2018 while maintaining my affiliation with the University of East Anglia (UEA). My research continues to focus on the molecular diagnosis of pathogens with the aim of translating this research broadly, in different sectors and diseases, to maximise community/patient benefit.


Key publications

Schmidt K, Mwaigwisya S, Crossman LC, Doumith M, Munroe D, Pires C, Khan AM, Woodford N, Saunders NJ, Wain J, O’Grady J (joint last and corresponding), Livermore DM. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother 2017 Jan;72(1):104-114.  doi: 10.1093/jac/dkw397

Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018. doi: 10.1038/nbt.4060

Burnham CD, Leeds J, Nordmann P, O’Grady J (all authors contributed equally), Patel J. Diagnosing antimicrobial resistance. Nat Rev Microbiol. 2017;15(11):697-703.  doi: 10.1038/nrmicro.2017.103

Ashton, P.M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J., and O’Grady, J. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nature Biotech, 2015, 33(3):296-300. doi: 10.1038/nbt.3103

Bates M, O’Grady J (joint first author) et al: Assessment of the Xpert MTB/RIF assay for diagnosis of tuberculosis with gastric lavage aspirates in children in sub-Saharan Africa: a prospective descriptive study. Lancet Infect Dis 2013, 13(1):36-42. doi: 10.1016/S1473-3099(12)70245-1

Baker DJ,Aydin A,Le Viet T,Kay GL,Rudder S,de Oliveira Martins L,Tedim AP,Kolyva A,Diaz M,Alikhan NF,Meadows L,Bell A,Gutierrez AV,Trotter AJ,Thomson NM,Gilroy R,Griffith L,Adriaenssens EM,Stanley R,Charles IG,Elumogo N,Wain J,Prakash R,Meader E,Mather AE,Webber M,Dervisevic S,Page AJ,O J. (2021)

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.

Genome medicine


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Foster-Nyarko E,Alikhan NF,Ikumapayi UN,Sarwar G,Okoi C,Tientcheu PM,Defernez M,O J,Antonio M,Pallen MJ. (2021)

Genomic diversity of Escherichia coli from healthy children in rural Gambia.

PeerJ


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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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Foster-Nyarko E,Alikhan NF,Ravi A,Thilliez G,Thomson N,Baker D,Kay G,Antonio M,O J,Pallen MJ. (2020)

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Microbial Genomics, 6


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Trotter AJ,Dean R,Whitehouse CE,Mikalsen J,Hill C,Brunton-Sim R,Kay GL,Shakokani M,Durst AZE,Wain J,McNamara I,O'Grady J. (2020)

Preliminary evaluation of a rapid lateral flow calprotectin test for the diagnosis of prosthetic joint infection.

Bone & joint research


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Phelan J. E., O'Sullivan D. M., Machado D., Ramos J., Oppong Y. E. A., Campino S., O'Grady J., McNerney R., Hibberd M. L., Viveiros M., Huggett J. F., Clark T. G.. (2019)

Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs.

Genome medicine, 11, 41


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Trotter A. J., Aydin A., Strinden M. J., O'Grady J.. (2019)

Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance.

Current Opinion in Microbiology, 51, 39-45


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Charalampous T., Kay G. L., Richardson H., Aydin A., Baldan R., Jeanes C., Rae D., Grundy S., Turner D. J., Wain J., Leggett R. M., Livermore D. M., O'Grady J.. (2019)

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection.

Nature Biotechnology, 37, 783-792


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