Sanger Institute, Genome Research Limited

People

Parkhill, Julian
Julian Parkhill, FMedSci FRS
Group Leader

Julian is the Board of Management representative for the Infection Genomics Programme at the Sanger Institute. He uses high-throughput sequencing and phenotyping to study pathogen diversity and variation, how they affect virulence and transmission, and what they tell us about the evolution of pathogenicity and host interactions.

Key Projects, Collaborations, Tools & Data

Research Programmes

Partners and Funders

Internal Partners

Publications

  • Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis.

    Lees JA, Brouwer M, van der Ende A, Parkhill J, van de Beek D and Bentley SD

    Infection and immunity 2017;85;3

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

    Moradigaravand D, Martin V, Peacock SJ and Parkhill J

    mBio 2017;8;1

  • Seeding and establishment of Legionella pneumophila in hospitals; implications for genomic investigations of nosocomial Legionnaires' disease.

    David S, Afshar B, Mentasti M, Ginevra C, Podglajen I et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017

  • The secondary resistome of multidrug-resistant Klebsiella pneumoniae.

    Jana B, Cain AK, Doerrler WT, Boinett CJ, Fookes MC et al.

    Scientific reports 2017;7;42483

  • Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape.

    Esson D, Gupta S, Bailey D, Wigley P, Wedley A et al.

    Microbial pathogenesis 2017;104;202-211

  • Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae.

    Runcharoen C, Moradigaravand D, Blane B, Paksanont S, Thammachote J et al.

    Genome medicine 2017;9;1;6

  • Genomic variations leading to alterations in cell morphology of Campylobacter spp.

    Esson D, Mather AE, Scanlan E, Gupta S, de Vries SP et al.

    Scientific reports 2016;6;38303

  • Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania.

    Seni J, Mshana SE, Msigwa F, Matee M, Mazigo H et al.

    Genome announcements 2016;4;6

  • Rapid detection and evolutionary analysis of Legionella pneumophila serogroup 1 sequence type 47.

    Mentasti M, Cassier P, David S, Ginevra C, Gomez-Valero L et al.

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2016

  • Microbial genome-wide association studies: lessons from human GWAS.

    Power RA, Parkhill J and de Oliveira T

    Nature reviews. Genetics 2016

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

    Bryant JM, Grogono DM, Rodriguez-Rincon D, Everall I, Brown KP et al.

    Science (New York, N.Y.) 2016;354;6313;751-757

  • Understanding pneumococcal serotype 1 biology through population genomic analysis.

    Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L et al.

    BMC infectious diseases 2016;16;1;649

  • Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

    Fazal MA, Alexander S, Burnett E, Deheer-Graham A, Oliver K et al.

    Genome announcements 2016;4;6

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

    David S, Rusniok C, Mentasti M, Gomez-Valero L, Harris SR et al.

    Genome research 2016;26;11;1555-1564

  • An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.

    Wong VK, Baker S, Connor TR, Pickard D, Page AJ et al.

    Nature communications 2016;7;12827

  • Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks.

    Harrison EM, Ludden C, Brodrick HJ, Blane B, Brennan G et al.

    Genome medicine 2016;8;1;102

  • Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study.

    Casali N, Broda A, Harris SR, Parkhill J, Brown T and Drobniewski F

    PLoS medicine 2016;13;10;e1002137

  • Genomic analysis of Salmonella enterica serovar Typhimurium from wild passerines in England and Wales.

    Mather AE, Lawson B, de Pinna E, Wigley P, Parkhill J et al.

    Applied and environmental microbiology 2016

  • Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.

    Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J et al.

    Nature genetics 2016

  • A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland.

    Raven KE, Reuter S, Reynolds R, Brodrick HJ, Russell JE et al.

    Genome research 2016

  • Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland.

    Moradigaravand D, Boinett CJ, Martin V, Peacock SJ and Parkhill J

    Genome research 2016;26;8;1101-9

  • Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana.

    Lamelas A, Ampah KA, Aboagye S, Kerber S, Danso E et al.

    PLoS neglected tropical diseases 2016;10;7;e0004856

  • Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid.

    Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J et al.

    Environmental microbiology 2016;18;7;2214-25

  • Mycobacterium tuberculosis wild-type and non-wild-type MIC distributions for the novel fluoroquinolone antofloxacin compared with ofloxacin, levofloxacin, and moxifloxacin.

    Yu X, Wang G, Chen S, Wei G, Shang Y et al.

    Antimicrobial agents and chemotherapy 2016

  • Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168.

    Anjum A, Brathwaite KJ, Aidley J, Connerton PL, Cummings NJ et al.

    Nucleic acids research 2016;44;10;4581-94

  • dfrA thyA Double Deletion in para-Aminosalicylic Acid-Resistant Mycobacterium tuberculosis Beijing Strains.

    Moradigaravand D, Grandjean L, Martinez E, Li H, Zheng J et al.

    Antimicrobial agents and chemotherapy 2016;60;6;3864-7

  • Whole-genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates from Myanmar.

    Aung HL, Tun T, Moradigaravand D, Köser CU, Nyunt WW et al.

    Journal of global antimicrobial resistance 2016;6;113-117

  • Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers.

    Einarsson GG, Comer DM, McIlreavey L, Parkhill J, Ennis M et al.

    Thorax 2016

  • Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.

    Cuthbertson L, Rogers GB, Walker AW, Oliver A, Green LE et al.

    The ISME journal 2016;10;5;1081-91

  • Systematic surveillance detects multiple silent introductions and household transmission of methicillin-resistant Staphylococcus aureus USA300 in the east of England.

    Toleman MS, Reuter S, Coll F, Harrison EM, Blane B et al.

    The Journal of infectious diseases 2016

  • The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries.

    Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ et al.

    Bioinformatics (Oxford, England) 2016;32;7;1109-11

  • Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

    Petrovska L, Mather AE, AbuOun M, Branchu P, Harris SR et al.

    Emerging infectious diseases 2016;22;4;617-24

  • Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR et al.

    Nature microbiology 2016;1;3

  • Genome-based characterization of hospital-adapted Enterococcus faecalis lineages.

    Raven KE, Reuter S, Gouliouris T, Reynolds R, Russell JE et al.

    Nature microbiology 2016;1;3

  • Genomes on ice.

    Parkhill J

    Nature reviews. Microbiology 2016;14;3;134

  • Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

    Reuter S, Török ME, Holden MT, Reynolds R, Raven KE et al.

    Genome research 2016;26;2;263-70

  • The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity.

    Warne B, Harkins CP, Harris SR, Vatsiou A, Stanley-Wall N et al.

    BMC genomics 2016;17;1;222

  • Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon.

    Bernardo D, Durant L, Mann ER, Bassity E, Montalvillo E et al.

    Cellular and molecular gastroenterology and hepatology 2016;2;1;22-39.e5

  • Genomic Analysis of Companion Rabbit Staphylococcus aureus.

    Holmes MA, Harrison EM, Fisher EA, Graham EM, Parkhill J et al.

    PloS one 2016;11;3;e0151458

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

  • Genomic perspectives on the evolution and spread of bacterial pathogens.

    Bentley SD and Parkhill J

    Proceedings. Biological sciences / The Royal Society 2015;282;1821;20150488

  • Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis.

    Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA et al.

    Journal of clinical microbiology 2015;53;12;3812-21

  • Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study.

    Hill DM, Lucidarme J, Gray SJ, Newbold LS, Ure R et al.

    The Lancet. Infectious diseases 2015;15;12;1420-8

  • Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

    Ba X, Harrison EM, Lovering AL, Gleadall N, Zadoks R et al.

    Antimicrobial agents and chemotherapy 2015;59;12;7396-404

  • Genomic and Proteomic Studies on the Mode of Action of Oxaboroles against the African Trypanosome.

    Jones DC, Foth BJ, Urbaniak MD, Patterson S, Ong HB et al.

    PLoS neglected tropical diseases 2015;9;12;e0004299

  • Roary: rapid large-scale prokaryote pan genome analysis.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al.

    Bioinformatics (Oxford, England) 2015;31;22;3691-3

  • Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

    Walker TM, Kohl TA, Omar SV, Hedge J, Del Ojo Elias C et al.

    The Lancet. Infectious diseases 2015;15;10;1193-202

  • Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome.

    Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR et al.

    Infection and immunity 2015;83;10;4165-73

  • Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera.

    Sun Z, Harris HM, McCann A, Guo C, Argimón S et al.

    Nature communications 2015;6;8322

  • The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource.

    Baker KS, Burnett E, McGregor H, Deheer-Graham A, Boinett C et al.

    Genome medicine 2015;7;97

  • Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection.

    Harris SR, Robinson C, Steward KF, Webb KS, Paillot R et al.

    Genome research 2015;25;9;1360-71

  • Essential roles of methionine and S-adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis.

    Berney M, Berney-Meyer L, Wong KW, Chen B, Chen M et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;32;10008-13

  • Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study.

    Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G et al.

    The Lancet. Infectious diseases 2015;15;8;913-21

  • Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation.

    Powell N, Lo JW, Biancheri P, Vossenkämper A, Pantazi E et al.

    Gastroenterology 2015;149;2;456-67.e15

  • Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.

    Sealey KL, Harris SR, Fry NK, Hurst LD, Gorringe AR et al.

    The Journal of infectious diseases 2015;212;2;294-301

  • Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

    Panagea T, Pincus DH, Grogono D, Jones M, Bryant J et al.

    Journal of clinical microbiology 2015;53;7;2355-8

  • Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses.

    Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hoffman LR et al.

    Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2015;14;4;464-7

  • Complete Genome Sequence of Bordetella pertussis D420.

    Boinett CJ, Harris SR, Langridge GC, Trainor EA, Merkel TJ and Parkhill J

    Genome announcements 2015;3;3

  • Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al.

    Nature genetics 2015;47;6;632-9

  • Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon.

    Bolz M, Bratschi MW, Kerber S, Minyem JC, Um Boock A et al.

    PLoS neglected tropical diseases 2015;9;6;e0003802

  • Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri.

    Baker KS, Parkhill J and Thomson NR

    Genome announcements 2015;3;3

  • Emergent and evolving antimicrobial resistance cassettes in community-associated fusidic acid and meticillin-resistant Staphylococcus aureus.

    Ellington MJ, Reuter S, Harris SR, Holden MT, Cartwright EJ et al.

    International journal of antimicrobial agents 2015;45;5;477-84

  • Staphylococcus aureus adapts to oxidative stress by producing H2O2-resistant small-colony variants via the SOS response.

    Painter KL, Strange E, Parkhill J, Bamford KB, Armstrong-James D and Edwards AM

    Infection and immunity 2015;83;5;1830-44

  • Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

    Hsu LY, Harris SR, Chlebowicz MA, Lindsay JA, Koh TH et al.

    Genome biology 2015;16;81

  • Rapid emergence of multidrug resistant, H58-lineage Salmonella typhi in Blantyre, Malawi.

    Feasey NA, Gaskell K, Wong V, Msefula C, Selemani G et al.

    PLoS neglected tropical diseases 2015;9;4;e0003748

  • Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: a whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up.

    Guerra-Assunção JA, Houben RM, Crampin AC, Mzembe T, Mallard K et al.

    The Journal of infectious diseases 2015;211;7;1154-63

  • Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission.

    Paterson GK, Harrison EM, Murray GG, Welch JJ, Warland JH et al.

    Nature communications 2015;6;6560

  • Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area.

    Guerra-Assunção JA, Crampin AC, Houben RM, Mzembe T, Mallard K et al.

    eLife 2015;4

  • Selective and genetic constraints on pneumococcal serotype switching.

    Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD et al.

    PLoS genetics 2015;11;3;e1005095

  • Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

    Okoro CK, Barquist L, Connor TR, Harris SR, Clare S et al.

    PLoS neglected tropical diseases 2015;9;3;e0003611

  • Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al.

    Nucleic acids research 2015;43;3;e15

  • TLR signaling modulates side effects of anticancer therapy in the small intestine.

    Frank M, Hennenberg EM, Eyking A, Rünzi M, Gerken G et al.

    Journal of immunology (Baltimore, Md. : 1950) 2015;194;4;1983-95

  • Microbiota that affect risk for shigellosis in children in low-income countries.

    Lindsay B, Oundo J, Hossain MA, Antonio M, Tamboura B et al.

    Emerging infectious diseases 2015;21;2;242-50

  • Patterns of genome evolution that have accompanied host adaptation in Salmonella.

    Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N et al.

    Proceedings of the National Academy of Sciences of the United States of America 2015;112;3;863-8

  • 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

    Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ and Scott KP

    Microbiome 2015;3;26

  • Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66.

    Hahn C, Harrison EM, Parkhill J, Holmes MA and Paterson GK

    Genome announcements 2015;3;3

  • Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting.

    Tong SY, Holden MT, Nickerson EK, Cooper BS, Köser CU et al.

    Genome research 2015;25;1;111-8

  • Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.

    Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J et al.

    Nature communications 2015;6;6740

  • Identification of antigen-specific B cell receptor sequences using public repertoire analysis.

    Trück J, Ramasamy MN, Galson JD, Rance R, Parkhill J et al.

    Journal of immunology (Baltimore, Md. : 1950) 2015;194;1;252-61

  • Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis.

    Landy J, Walker AW, Li JV, Al-Hassi HO, Ronde E et al.

    Scientific reports 2015;5;12955

  • Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.

    Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR et al.

    Frontiers in microbiology 2015;6;1191

  • Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy.

    De Smet B, Sarovich DS, Price EP, Mayo M, Theobald V et al.

    Journal of clinical microbiology 2015;53;1;323-6

  • Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi.

    Glynn JR, Guerra-Assunção JA, Houben RM, Sichali L, Mzembe T et al.

    PloS one 2015;10;7;e0132840

  • Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.

    Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S et al.

    Genome biology and evolution 2014;6;12;3281-94

  • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.

    Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO et al.

    BMC biology 2014;12;87

  • Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection.

    Mather AE, Baker KS, McGregor H, Coupland P, Mather PL et al.

    Lancet (London, England) 2014;384;9955;1720

  • Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals.

    Cavanagh JP, Hjerde E, Holden MT, Kahlke T, Klingenberg C et al.

    The Journal of antimicrobial chemotherapy 2014;69;11;2920-7

  • Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

    Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N et al.

    Nature 2014;514;7523;494-7

  • Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

    Lamelas A, Harris SR, Röltgen K, Dangy JP, Hauser J et al.

    mBio 2014;5;5;e01974-14

  • Comment on: characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array.

    Köser CU, Bryant JM, Comas I, Feuerriegel S, Niemann S et al.

    The Journal of antimicrobial chemotherapy 2014;69;8;2298-9

  • 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 et al.

    PLoS genetics 2014;10;8;e1004547

  • Defining the estimated core genome of bacterial populations using a Bayesian decision model.

    van Tonder AJ, Mistry S, Bray JE, Hill DM, Cody AJ et al.

    PLoS computational biology 2014;10;8;e1003788

  • Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

    Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y et al.

    Genome biology and evolution 2014;6;8;2096-110

  • Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M et al.

    PLoS biology 2014;12;8;e1001920

  • Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections.

    Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hafiz T et al.

    Journal of clinical microbiology 2014;52;8;3011-6

  • Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?

    Török ME, Harris SR, Cartwright EJ, Raven KE, Brown NM et al.

    The Journal of antimicrobial chemotherapy 2014;69;8;2238-45

  • Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape.

    Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L et al.

    Genome biology and evolution 2014;6;7;1589-602

  • Parallel independent evolution of pathogenicity within the genus Yersinia.

    Reuter S, Connor TR, Barquist L, Walker D, Feltwell T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;18;6768-73

  • PolyTB: a genomic variation map for Mycobacterium tuberculosis.

    Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D et al.

    Tuberculosis (Edinburgh, Scotland) 2014;94;3;346-54

  • Rapid single-colony whole-genome sequencing of bacterial pathogens.

    Köser CU, Fraser LJ, Ioannou A, Becq J, Ellington MJ et al.

    The Journal of antimicrobial chemotherapy 2014;69;5;1275-81

  • Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

    Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK et al.

    Molecular ecology 2014;23;10;2442-51

  • Global population structure and evolution of Bordetella pertussis and their relationship with vaccination.

    Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D et al.

    mBio 2014;5;2;e01074

  • A novel hybrid SCCmec-mecC region in Staphylococcus sciuri.

    Harrison EM, Paterson GK, Holden MT, Ba X, Rolo J et al.

    The Journal of antimicrobial chemotherapy 2014;69;4;911-8

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al.

    Nature genetics 2014;46;3;305-9

  • Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene.

    Ba X, Harrison EM, Edwards GF, Holden MT, Larsen AR et al.

    The Journal of antimicrobial chemotherapy 2014;69;3;594-7

  • Prevalence and properties of mecC methicillin-resistant Staphylococcus aureus (MRSA) in bovine bulk tank milk in Great Britain.

    Paterson GK, Morgan FJ, Harrison EM, Peacock SJ, Parkhill J et al.

    The Journal of antimicrobial chemotherapy 2014;69;3;598-602

  • Evolution and transmission of drug-resistant tuberculosis in a Russian population.

    Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O et al.

    Nature genetics 2014;46;3;279-86

  • Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study.

    Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR et al.

    The Lancet. Infectious diseases 2014;14;3;220-6

  • The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.

    Kennedy NA, Walker AW, Berry SH, Duncan SH, Farquarson FM et al.

    PloS one 2014;9;2;e88982

  • The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis.

    Howell KJ, Weinert LA, Chaudhuri RR, Luan SL, Peters SE et al.

    BMC genomics 2014;15;1179

  • Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

    Shah MA, Mutreja A, Thomson N, Baker S, Parkhill J et al.

    Emerging infectious diseases 2014;20;1;13-20

  • Novel determinants of antibiotic resistance: identification of mutated loci in highly methicillin-resistant subpopulations of methicillin-resistant Staphylococcus aureus.

    Dordel J, Kim C, Chung M, Pardos de la Gándara M, Holden MT et al.

    mBio 2014;5;2;e01000

  • Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

    Seth-Smith HM, Harris SR, Scott P, Parmar S, Marsh P et al.

    Nature protocols 2013;8;12;2404-12

  • Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study.

    Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH et al.

    The Lancet. Respiratory medicine 2013;1;10;786-92

  • Tracking the establishment of local endemic populations of an emergent enteric pathogen.

    Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW et al.

    Proceedings of the National Academy of Sciences of the United States of America 2013;110;43;17522-7

  • Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

    Comas I, Coscolla M, Luo T, Borrell S, Holt KE et al.

    Nature genetics 2013;45;10;1176-82

  • Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

    Lindsay B, Pop M, Antonio M, Walker AW, Mai V et al.

    Journal of clinical microbiology 2013;51;10;3263-9

  • Transcriptional regulation of Culex pipiens mosquitoes by Wolbachia influences cytoplasmic incompatibility.

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  • Genome flexibility in Neisseria meningitidis.

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  • Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain.

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  • DNAPlotter: circular and linear interactive genome visualization.

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  • Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.

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    Nature reviews. Microbiology 2003;1;1;11-2

  • Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica.

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  • The complete genome sequence of Mycobacterium bovis.

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  • Genomics: Relative pathogenic values.

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  • Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei.

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  • Restricting genome data won't stop bioterrorism.

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  • Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

    Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR et al.

    Nature 2002;417;6885;141-7

  • Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.

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  • Genome sequence of Yersinia pestis, the causative agent of plague.

    Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT et al.

    Nature 2001;413;6855;523-7

  • Massive gene decay in the leprosy bacillus.

    Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR et al.

    Nature 2001;409;6823;1007-11

  • Artemis: sequence visualization and annotation.

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  • In defense of complete genomes.

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  • Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491.

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    Nature 2000;404;6777;502-6

  • The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences.

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  • Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

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