Publications

Mutational spectra are associated with bacterial niche


Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Nature Communications. 2023.

The human blood fluke, Schistosoma mansoni, harbours bacteria throughout the parasite’s life cycle


Formenti F, Cortés A, Deiana M, Salter S, Parkhill J, Berriman M, Rinaldi G, Cantacessi C. The Journal of Infectious Diseases. 2023.

Complete Genome Sequence of Ornithobacterium hominis Type Strain MSHR-COH1 (ATCC TSD-185)


Salter SJ, Marsh RL, Parkhill J. Microbiology Resource Announcements. 2023.

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. Microbial Genomics. 2023.

Colonization and transmission of Staphylococcus aureus in schools: a citizen science project


van Tonder AJ, McCullagh F, McKeand H, Thaw S, Bellis K, Raisen C, Lay E, Aggarwal D, Holmes M, Parkhill J, Harrison EM, Kucharski A, Conlan A. Microbial Genomics. 2023.

Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study


Hadjirin NF, van Tonder AJ, Blane B, Lees JA, Kumar N, Delappe N, Brennan W, McGrath E, Parkhill J, Cormican M, Peacock SJ, Ludden C. Microbial Genomics. 2023.

Mycobacterium avium complex (MAC) genomics and transmission in a London hospital


van Tonder AJ, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, Parkhill J, Moffatt MF, Loebinger MR, Cookson WO. European Respiratory Journal. 2022.

Mycobacterium abscessus pathogenesis identified by phenogenomic analyses


Boeck L, Burbaud S, Skwark M, Pearson WH, Sangen J, Wuest AW, Marshall EKP, Weimann A, Everall I, Bryant JM, Malhotra S, Bannerman BP, Kierdorf K, Blundell TL, Dionne MS, Parkhill J, Andres Floto R. Nature Microbiology. 2022.

Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis


Lefrancq N, Bouchez V, Fernandes N, Barkoff AM, Bosch T, Dalby T, Åkerlund T, Darenberg J, Fabianova K, Vestrheim DF, Fry NK, González-López JJ, Gullsby K, Habington A, He Q, Litt D, Martini H, Piérard D, Stefanelli P, Stegger M, Zavadilova J, Armatys N, Landier A, Guillot S, Hong SL, Lemey P, Parkhill J, Toubiana J, Cauchemez S, Salje H, Brisse S. Science Translational Medicine. 2022.

Genomic insights into the mechanism of carbapenem resistance dissemination in Enterobacterales from a tertiary public heath setting in South Asia


Farzana R, Jones LS, Rahman MA, Sands K, van Tonder AJ, Portal E, Criollo JM, Parkhill J, Guest MF, John Watkins W, Pervin M, Boostrom I, Hassan B, Mathias J, Kalam MA, Walsh TR. Clinical Infectious Diseases. 2022.

PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies


Coll F, Gouliouris T, Bruchmann S, Phelan J, Raven KE, Clark TG, Parkhill J, Peacock SJ. Communications Biology. 2022.

Conservation of vaccine antigen sequences encoded by sequenced strains of Streptococcus equi subsp. equi


Frosth S, Morris ERA, Wilson H, Frykberg L, Jacobsson K, Parkhill J, Flock JI, Wood T, Guss B, Aanensen DM, Boyle AG, Riihimäki M, Cohen ND, Waller AS. Equine Veterinary Journal. 2022.

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 Pathogens. 2021.

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. Nature Microbiology. 2021.

Genomic and temporal analyses of Mycobacterium bovis in southern Brazil


Rodrigues RA, Ribeiro Araújo F, Rivera Dávila AM, Etges RN, Parkhill J, van Tonder AJ. Microbial Genomics. 2021.

Population structure and transmission of Mycobacterium bovis in Ethiopia


Almaw G, Mekonnen GA, Mihret A, Aseffa A, Taye H, Conlan AJK, Gumi B, Zewude A, Aliy A, Tamiru M, Olani A, Lakew M, Sombo M, Gebre S, Diguimbaye C, Hilty M, Fané A, Müller B, Hewinson RG, Ellis RJ, Nunez-Garcia J, Palkopoulou E, Abebe T, Ameni G, Parkhill J, Wood JLN, The Ethicobots Consortium, Berg S, van Tonder AJ. Microbial Genomics. 2021.

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.

Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella


Bruchmann S, Feltwell T, Parkhill J, Short FL. Pathogens and Disease. 2021.

Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses


Mitchell C, Steward KF, Charbonneau ARL, Walsh S, Wilson H, Timoney JF, Wernery U, Joseph M, Craig D, van Maanen K, Hoogkamer-van Gennep A, Leon A, Witkowski L, Rzewuska M, Stefańska I, Żychska M, van Loon G, Cursons R, Patty O, Acke E, Gilkerson JR, El-Hage C, Allen J, Bannai H, Kinoshita Y, Niwa H, Becú T, Pringle J, Guss B, Böse R, Abbott Y, Katz L, Leggett B, Buckley TC, Blum SE, Cruz López F, Fernández Ros A, Marotti Campi MC, Preziuso S, Robinson C, Newton JR, Schofield E, Brooke B, Boursnell M, de Brauwere N, Kirton R, Barton CK, Abudahab K, Taylor B, Yeats CA, Goater R, Aanensen DM, Harris SR, Parkhill J, Holden MTG, Waller AS. Microbial Genomics. 2021.

Freshwater monitoring by nanopore sequencing


Urban L, Holzer A, Baronas JJ, Hall MB, Braeuninger-Weimer P, Scherm MJ, Kunz DJ, Perera SN, Martin-Herranz DE, Tipper ET, Salter SJ, Stammnitz MR. Elife. 2021.

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 Biology. 2020.

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia


Gaccioli F, Lager S, de Goffau MC, Sovio U, Dopierala J, Gong S, Cook E, Sharkey A, Moffett A, Lee WK, Delles C, Venturini C, Breuer J, Parkhill J, Peacock SJ, Charnock-Jones DS, Smith GCS. Nature Microbiology. 2020.

Increasing incidence of group B Streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23


Jamrozy D, Bijlsma MW, de Goffau MC, van de Beek D, Kuijpers TW, Parkhill J, van der Ende A, Bentley SD. Scientific Reports. 2020.

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center


Ellington MJ, Heinz E, Wailan AM, Dorman MJ, de Goffau M, Cain AK, Henson SP, Gleadall N, Boinett CJ, Dougan G, Brown NM, Woodford N, Parkhill J, Török ME, Peacock SJ, Thomson NR. Genome Biology. 2019.

Multi-Compartment Profiling of Bacterial and Host Metabolites Identifies Intestinal Dysbiosis and Its Functional Consequences in the Critically Ill Child


Wijeyesekera A, Wagner J, De Goffau M, Thurston S, Rodrigues Sabino A, Zaher S, White D, Ridout J, Peters MJ, Ramnarayan P, Branco RG, Torok ME, Valla F, Meyer R, Klein N, Frost G, Parkhill J, Holmes E, Pathan N. Critical Care Medicine. 2019.

Human placenta has no microbiome but can contain potential pathogens


de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Nature. 2019.