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An Interdisciplinary Research Centre at the University of Cambridge


The research of my group focusses on the evolution of bacterial pathogens; their origin, transmission and adaptation to selective pressure. I primarily use genomic and phylogenetic approaches to address these, and over the last few years my group has used large-scale population genomics to identify the global origin and routes of spread of many human and animal pathogens. Overlaid on the phylogeny, we look for signatures of adaptation to the host, to antibiotics and to vaccine pressure, most recently developing bacterial genome-wide association approaches to identify genetic determinants responsible for this adaptation. In addition to informatics approaches, we develop and apply genome-wide experimental tools, studying interaction with the host and antimicrobial resistance mechanisms. We have an interest in metagenomics, currently studying the microbiota in the gut, the lung, the nasopharynx and the placenta (which doesn’t have one). We often work at an international level, with many collaborations in Low- and Middle-Income countries. Our work has clear translational benefits for tracking transmission at the hospital level and more broadly. To enable this translation, we have been collaborating with local hospitals, and national and international health-protection agencies, as well as the commercial sector.


Key publications: 

Google Scholar:

A lung-specific mutational signature enables inference of viral and bacterial respiratory niche.

Ruis C, Peacock TP, Polo LM, Masone D, Alvarez MS, Hinrichs AS, Turakhia Y, Cheng Y, McBroome J, Corbett-Detig R, Parkhill J, Floto RA.Microb Genom. 2023 May;9(5):mgen001018. doi: 10.1099/mgen.0.001018.

A scalable analytical approach from bacterial genomes to epidemiology.

Didelot X, Parkhill J.Philos Trans R Soc Lond B Biol Sci. 2022 Oct 10;377(1861):20210246. doi: 10.1098/rstb.2021.0246. 

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial.

van Tonder AJ, Thornton MJ, Conlan AJK, Jolley KA, Goolding L, Mitchell AP, Dale J, Palkopoulou E, Hogarth PJ, Hewinson RG, Wood JLN, Parkhill J.PLoS Pathog. 2021 Nov 29;17(11):e1010075. doi: 10.1371/journal.ppat.1010075

Dissemination of Mycobacterium abscessus via global transmission networks.

Ruis C, Bryant JM, Bell SC, Thomson R, Davidson RM, Hasan NA, van Ingen J, Strong M, Floto RA, Parkhill J. Nat Microbiol. (2021) doi: 10.1038/s41564-021-00963-3

Stepwise pathogenic evolution of Mycobacterium abscessus.

Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, Grogono DM, Peterson CM, Verma D, Evans IE, Ruis C, Weimann A, Arora D, Malhotra S, Bannerman B, Passemar C, Templeton K, MacGregor G, Jiwa K, Fisher AJ, Blundell TL, Ordway DJ, Jackson M, Parkhill J, Floto RA. Science. (2021) 372(6541):eabb8699. doi: 10.1126/science.abb8699.

Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.

Gouliouris T, Coll F, Ludden C, Blane B, Raven KE, Naydenova P, Crawley C, Török ME, Enoch DA, Brown NM, Harrison EM, Parkhill J, Peacock SJ. Nat Microbiol. (2021) 6:103-111. doi: 10.1038/s41564-020-00806-7

Producing polished prokaryotic pangenomes with the Panaroo pipeline.

Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J.
Genome Biol. 2020 Jul 22;21(1):180. doi: 10.1186/s13059-020-02090-4.


Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions.
Lees JA, Mai TT, Galardini M, Wheeler NE, Horsfield ST, Parkhill J, Corander J.
mBio. 2020 Jul 7;11(4):e01344-20. doi: 10.1128/mBio.01344-20.


Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.

Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D, Parkhill J, Peacock SJ.
Commun Biol. 2019 Nov 22;2:428. doi: 10.1038/s42003-019-0678-x.


Kime L, Randall CP, Banda FI, Coll F, Wright J, Richardson J, Empel J, Parkhill J, O'Neill AJ.
mBio. 2019 Oct 29;10(5):e01755-19. doi: 10.1128/mBio.01755-19.


de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS.
Nature. 2019 Aug;572(7769):329-334. doi: 10.1038/s41586-019-1451-5.


Ludden C, Moradigaravand D, Jamrozy D, Gouliouris T, Blane B, Naydenova P, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Crawley C, Brown NM, Holmes M, Parkhill J, Peacock SJ.
Clin Infect Dis. 2020 Jan 2;70(2):219-226. doi: 10.1093/cid/ciz174.


Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B, Coll F, de Goffau M, Naydenova P, Horner C, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Brown NM, Holmes M, Parkhill J, Peacock SJ.
mBio. 2019 Jan 22;10(1):e02693-18. doi: 10.1128/mBio.02693-18.


The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISort.

Dorman MJ, Feltwell T, Goulding DA, Parkhill J, Short FL. MBio. (2018) 9(6). pii: e01863-18

Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.

Gouliouris T, Raven KE, Ludden C, Blane B, Corander J, Horner CS, Hernandez-Garcia J, Wood P, Hadjirin NF, Radakovic M, Holmes MA, de Goffau M, Brown NM, Parkhill J, Peacock SJ.

MBio. (2018) 9(6). pii: e01780-18

Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.

Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ. Sci Transl Med. (2017) 9(413). pii: eaak9745.

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM, Martin V, Peacock SJ, Parkhill J.

Genome Res. (2017) 27: 1437-1449

Evolution and Epidemiology of Multidrug-Resistant Klebsiella pneumoniae in the United Kingdom and Ireland.

Moradigaravand D, Martin V, Peacock SJ, Parkhill J. MBio. (2017) 8(1). pii: e01976-16

Global and regional dissemination and evolution of Burkholderia pseudomallei.

Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z, Harris SR, Mather AE, Tuanyok A, De Smet B, Le Hello S, Bizet C, Mayo M, Wuthiekanun V, Limmathurotsakul D, Phetsouvanh R, Spratt BG, Corander J, Keim P, Dougan G, Dance DA, Currie BJ, Parkhill J, Peacock SJ. Nat Microbiol. (2017) 2:16263

Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.

Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP, Moreno P, Verma D, Hill E, Drijkoningen J, Gilligan P, Esther CR, Noone PG, Giddings O, Bell SC, Thomson R, Wainwright CE, Coulter C, Pandey S, Wood ME, Stockwell RE, Ramsay KA, Sherrard LJ, Kidd TJ, Jabbour N, Johnson GR, Knibbs LD, Morawska L, Sly PD, Jones A, Bilton D, Laurenson I, Ruddy M, Bourke S, Bowler IC, Chapman SJ, Clayton A, Cullen M, Daniels T, Dempsey O, Denton M, Desai M, Drew RJ, Edenborough F, Evans J, Folb J, Humphrey H, Isalska B, Jensen-Fangel S, Jönsson B, Jones AM, Katzenstein TL, Lillebaek T, MacGregor G, Mayell S, Millar M, Modha D, Nash EF, O'Brien C, O'Brien D, Ohri C, Pao CS, Peckham D, Perrin F, Perry A, Pressler T, Prtak L, Qvist T, Robb A, Rodgers H, Schaffer K, Shafi N, van Ingen J, Walshaw M, Watson D, West N, Whitehouse J, Haworth CS, Harris SR, Ordway D, Parkhill J, Floto RA.

Science. (2016) 354(6313):751-757

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently.

David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR, Lechat P, Lees J, Ginevra C, Glaser P, Ma L, Bouchier C, Underwood A, Jarraud S, Harrison TG, Parkhill J, Buchrieser C.

Genome Res. (2016) 26(11):1555-1564

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.

Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, Honkela A, Parkhill J, Bentley SD, Corander J.

Nat Commun. (2016) 7:12797

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.

Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J.

PLoS Genet. (2014) 10(8):e1004547

Professor of Bacterial Evolution, Department of Veterinary Medicine
The emergence, transmission and evolution of bacterial pathogens
Professor Julian  Parkhill
Takes PhD students
Available for consultancy


Person keywords: 
Molecular Biology
Host-Pathogen Interaction
Pathogen Evolution