Archive Page: Parkhill Group | Pathogen Genomics

Archive Page: Parkhill Group | Pathogen Genomics

Parkhill Group

In 2019 the Parkhill group moved to the Department of Veterinary Medicine, University of Cambridge. This page is being maintained as historical record of the group's research at the Sanger Institute and is no longer being updated.
team-81-11.jpgSanger Institute, Genome Research Limited

Our Research and Approach

The Pathogen genomics team, headed by Julian Parkhill, used high-throughput genomic and phenotypic analysis of bacteria to understand their virulence, evolution, transmission and host-interactions.

At the Sanger Institute, the team investigated a wide range of human and animal pathogens, and collaborate widely within the UK and global scientific community. The team had previously generated reference genomes of organisms that are of fundamental importance for human health, including the causative agents of tuberculosis, plague, typhoid fever, whooping cough, leprosy, diphtheria and meningitis. We used population genomics to investigate transmission and evolution in many of these pathogens.

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Julian Parkhill, FMedSci FRS
Group Leader

Julian was the Board of Management representative for the Infection Genomics Programme at the Sanger Institute. During his time at the Sanger Institute, he used high-throughput sequencing and phenotyping to study pathogen diversity and variation, how they affected virulence and transmission, and what they told us about the evolution of pathogenicity and host interactions.

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Lees, John

John Lees
Former PhD Student at the Sanger Institute

Key Projects, Collaborations, Tools & Data

Programmes, Associate Research Programmes and Facilities

Partners and Funders

Internal Partners


  • Mechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases.

    McDougall S, Clausen L, Ha HJ, Gibson I, Bryan M et al.

    Veterinary microbiology 2020;242;108592

  • A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England.

    Ludden C, Moradigaravand D, Jamrozy D, Gouliouris T, Blane B et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020;70;2;219-226

  • Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae.

    Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC and Milner JJ

    Plant biotechnology journal 2019

  • The impact of antimicrobials on gonococcal evolution.

    Sánchez-Busó L, Golparian D, Corander J, Grad YH, Ohnishi M et al.

    Nature microbiology 2019;4;11;1941-1950

  • Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological study.

    Lynskey NN, Jauneikaite E, Li HK, Zhi X, Turner CE et al.

    The Lancet. Infectious diseases 2019;19;11;1209-1218

  • Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks.

    Brown NM, Blane B, Raven KE, Kumar N, Leek D et al.

    Journal of clinical microbiology 2019;57;11

  • Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511.

    Turnbull JD, Russell JE, Fazal MA, Grayson NE, Deheer-Graham A et al.

    Microbiology resource announcements 2019;8;44

  • The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study.

    Wagner J, Harrison EM, Martinez Del Pero M, Blane B, Mayer G et al.

    Microbiome 2019;7;1;137

  • Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK.

    Cain AK, Nolan LM, Sullivan GJ, Whitchurch CB, Filloux A and Parkhill J

    Microbiology resource announcements 2019;8;41

  • Genome-wide epistasis and co-selection study using mutual information.

    Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J et al.

    Nucleic acids research 2019;47;18;e112

  • A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis.

    Masschelein J, Sydor PK, Hobson C, Howe R, Jones C et al.

    Nature chemistry 2019;11;10;906-912

  • Genomic characterization of novel Neisseria species.

    Diallo K, MacLennan J, Harrison OB, Msefula C, Sow SO et al.

    Scientific reports 2019;9;1;13742

  • A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages.

    Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N et al.

    Scientific reports 2019;9;1;13718

  • 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 et al.

    Genome biology 2019;20;1;184

  • 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 et al.

    Critical care medicine 2019;47;9;e727-e734

  • The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential.

    Webster G, Mullins AJ, Bettridge AS, Jones C, Cunningham-Oakes E et al.

    Microbiology resource announcements 2019;8;34

  • The speciation and hybridization history of the genus Salmonella.

    Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J et al.

    Microbial genomics 2019;5;8

  • Human placenta has no microbiome but can contain potential pathogens.

    de Goffau MC, Lager S, Sovio U, Gaccioli F, Cook E et al.

    Nature 2019;572;7769;329-334

  • Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.

    Blane B, Raven KE, Leek D, Brown N, Parkhill J and Peacock SJ

    The Journal of antimicrobial chemotherapy 2019;74;8;2153-2156

  • Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis.

    MacFadyen AC, Leroy S, Harrison EM, Parkhill J, Holmes MA and Paterson GK

    International journal of systematic and evolutionary microbiology 2019;69;8;2208-2213

  • Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD.

    Seni J, Mshana SE, Msigwa F, Iddi S, Mazigo H et al.

    Journal of global antimicrobial resistance 2019

  • Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India.

    Munir A, Kumar N, Ramalingam SB, Tamilzhalagan S, Shanmugam SK et al.

    Scientific reports 2019;9;1;10283

  • Complete Whole-Genome Sequences of Two Raoultella terrigena Strains, NCTC 13097 and NCTC 13098, Isolated from Human Cases.

    Fazal MA, Alexander S, Grayson NE, Deheer-Graham A, Oliver K et al.

    Microbiology resource announcements 2019;8;27

  • Domestication of Campylobacter jejuni NCTC 11168.

    Pascoe B, Williams LK, Calland JK, Meric G, Hitchings MD et al.

    Microbial genomics 2019;5;7

  • Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus.

    Harrison EM, Ba X, Coll F, Blane B, Restif O et al.

    Nature microbiology 2019;4;10;1680-1691

  • Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839.

    Fazal MA, Alexander S, Grayson NE, Deheer-Graham A, Oliver K et al.

    Microbiology resource announcements 2019;8;25

  • An unusual Burkholderia gladioli double chain-initiating nonribosomal peptide synthetase assembles 'fungal' icosalide antibiotics.

    Jenner M, Jian X, Dashti Y, Masschelein J, Hobson C et al.

    Chemical science 2019;10;21;5489-5494

  • Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

    Davies MR, McIntyre L, Mutreja A, Lacey JA, Lees JA et al.

    Nature genetics 2019;51;6;1035-1043

  • Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria.

    Mullins AJ, Murray JAH, Bull MJ, Jenner M, Jones C et al.

    Nature microbiology 2019;4;6;996-1005

  • Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory.

    Raven KE, Blane B, Leek D, Churcher C, Kokko-Gonzales P et al.

    Journal of clinical microbiology 2019;57;6

  • Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.

    Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Serón MV et al.

    Nature communications 2019;10;1;2176

  • Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts.

    Decano AG, Ludden C, Feltwell T, Judge K, Parkhill J and Downing T

    mSphere 2019;4;3

  • Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.

    Raven KE, Ludden C, Gouliouris T, Blane B, Naydenova P et al.

    Microbial genomics 2019;5;5

  • Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

    McNally A, Kallonen T, Connor C, Abudahab K, Aanensen DM et al.

    mBio 2019;10;2

  • Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment.

    Gouliouris T, Raven KE, Moradigaravand D, Ludden C, Coll F et al.

    Genome research 2019;29;4;626-634

  • A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC.

    MacFadyen AC, Harrison EM, Drigo I, Parkhill J, Holmes MA and Paterson GK

    The Journal of antimicrobial chemotherapy 2019;74;3;547-552

  • Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.

    Nguyen VT, Jamrozy D, Matamoros S, Carrique-Mas JJ, Ho HM et al.

    The Journal of antimicrobial chemotherapy 2019;74;3;561-570

  • Nasal carriage of Staphylococcus pseudintermedius in patients with granulomatosis with polyangiitis.

    Kronbichler A, Blane B, Holmes MA, Wagner J, Parkhill J et al.

    Rheumatology (Oxford, England) 2019;58;3;548-550

  • O-Antigen-Dependent Colicin Insensitivity of Uropathogenic Escherichia coli.

    Sharp C, Boinett C, Cain A, Housden NG, Kumar S et al.

    Journal of bacteriology 2019;201;4

  • 'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs.

    Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC et al.

    Microbial genomics 2019;5;2

  • Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii.

    Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT et al.

    Microbial genomics 2019;5;2

  • One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock.

    Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B et al.

    mBio 2019;10;1

  • Separating Bacteria by Capsule Amount Using a Discontinuous Density Gradient.

    Feltwell T, Dorman MJ, Goulding DA, Parkhill J and Short FL

    Journal of visualized experiments : JoVE 2019;143

  • Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.

    Chung WSF, Walker AW, Vermeiren J, Sheridan PO, Bosscher D et al.

    FEMS microbiology ecology 2019;95;1

  • Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States.

    Mohamed N, Timofeyeva Y, Jamrozy D, Rojas E, Hao L et al.

    PloS one 2019;14;1;e0208356

  • Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.

    Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M et al.

    PloS one 2019;14;3;e0209395

  • Mutations in the MAB_2299c TetR Regulator Confer Cross-Resistance to Clofazimine and Bedaquiline in Mycobacterium abscessus.

    Richard M, Gutiérrez AV, Viljoen A, Rodriguez-Rincon D, Roquet-Baneres F et al.

    Antimicrobial agents and chemotherapy 2019;63;1

  • Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013.

    Toleman MS, Reuter S, Jamrozy D, Wilson HJ, Blane B et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2019;24;4

  • Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding.

    MacFadyen AC, Drigo I, Harrison EM, Parkhill J, Holmes MA and Paterson GK

    International journal of systematic and evolutionary microbiology 2019;69;1;82-86

  • A highly conserved mecC-encoding SCCmec type XI in a bovine isolate of methicillin-resistant Staphylococcus xylosus.

    MacFadyen AC, Harrison EM, Ellington MJ, Parkhill J, Holmes MA and Paterson GK

    The Journal of antimicrobial chemotherapy 2018;73;12;3516-3518

  • Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution.

    Atack JM, Weinert LA, Tucker AW, Husna AU, Wileman TM et al.

    Nucleic acids research 2018;46;21;11466-11476

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

    Dorman MJ, Feltwell T, Goulding DA, Parkhill J and Short FL

    mBio 2018;9;6

  • 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 et al.

    mBio 2018;9;6

  • A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa.

    Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ et al.

    Microbial genomics 2018;4;11

  • Comparative genomics of Czech vaccine strains of Bordetella pertussis.

    Dienstbier A, Pouchnik D, Wildung M, Amman F, Hofacker IL et al.

    Pathogens and disease 2018;76;7

  • Spatial structuring of a Legionella pneumophila population within the water system of a large occupational building.

    David S, Mentasti M, Lai S, Vaghji L, Ready D et al.

    Microbial genomics 2018;4;10

  • Arginine-deprivation-induced oxidative damage sterilizes Mycobacterium tuberculosis.

    Tiwari S, van Tonder AJ, Vilchèze C, Mendes V, Thomas SE et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;39;9779-9784

  • New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam.

    Mather AE, Phuong TLT, Gao Y, Clare S, Mukhopadhyay S et al.

    mBio 2018;9;5

  • Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.

    Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J et al.

    Microbiome 2018;6;1;151

  • Low genomic diversity of Legionella pneumophila within clinical specimens.

    David S, Mentasti M, Parkhill J and Chalker VJ

    Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2018;24;9;1020.e1-1020.e4

  • Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data.

    Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE et al.

    BMC genomics 2018;19;1;613

  • Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System.

    Liu MM, Boinett CJ, Chan ACK, Parkhill J, Murphy MEP and Gaynor EC

    mBio 2018;9;4

  • Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates.

    Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A et al.

    Scientific reports 2018;8;1;11597

  • Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck.

    Lamelas A, Hamid AM, Dangy JP, Hauser J, Jud M et al.

    Genome biology and evolution 2018;10;8;2102-2109

  • Recognizing the reagent microbiome.

    de Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A et al.

    Nature microbiology 2018;3;8;851-853

  • Reply to Dookie et al., "Whole-Genome Sequencing To Guide the Selection of Treatment for Drug-Resistant Tuberculosis".

    Köser CU, Heyckendorf J, Andres S, Olaru ID, Schön T et al.

    Antimicrobial agents and chemotherapy 2018;62;8

  • Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.

    Peacock SJ, Parkhill J and Brown NM

    Microbiology (Reading, England) 2018

  • Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches.

    Otchere ID, Coscollá M, Sánchez-Busó L, Asante-Poku A, Brites D et al.

    Scientific reports 2018;8;1;11269

  • Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157.

    Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ et al.

    mBio 2018;9;4

  • Gene exchange drives the ecological success of a multi-host bacterial pathogen.

    Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S et al.

    Nature ecology & evolution 2018;2;9;1468-1478

  • Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

    Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M et al.

    Scientific reports 2018;8;1;9868

  • The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from Atopic Dermatitis patients.

    Harkins CP, McAleer MA, Bennett D, McHugh M, Fleury OM et al.

    The British journal of dermatology 2018

  • Are commercial providers a viable option for clinical bacterial sequencing?

    Raven K, Blane B, Churcher C, Parkhill J and Peacock SJ

    Microbial genomics 2018;4;4

  • Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.

    Moradigaravand D, Gouliouris T, Ludden C, Reuter S, Jamrozy D et al.

    Microbial genomics 2018;4;3

  • Gut microbiota trajectory in early life may predict development of celiac disease.

    Olivares M, Walker AW, Capilla A, Benítez-Páez A, Palau F et al.

    Microbiome 2018;6;1;36

  • The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.

    Kennedy NA, Lamb CA, Berry SH, Walker AW, Mansfield J et al.

    Inflammatory bowel diseases 2018;24;3;583-592

  • The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare.

    Harkins CP, Pettigrew KA, Oravcová K, Gardner J, Hearn RMR et al.

    The Journal of investigative dermatology 2018;138;2;336-343

  • Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

    Coll F, Phelan J, Hill-Cawthorne GA, Nair MB, Mallard K et al.

    Nature genetics 2018;50;2;307-316

  • Limited Impact of Adolescent Meningococcal ACWY Vaccination on Neisseria meningitidis Serogroup W Carriage in University Students.

    Oldfield NJ, Green LR, Parkhill J, Bayliss CD and Turner DPJ

    The Journal of infectious diseases 2018;217;4;608-616

  • Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

    Lees JA, Kendall M, Parkhill J, Colijn C, Bentley SD and Harris SR

    Wellcome open research 2018;3;33

  • Global Scale Dissemination of ST93: A Divergent Staphylococcus aureus Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.

    van Hal SJ, Steinig EJ, Andersson P, Holden MTG, Harris SR et al.

    Frontiers in microbiology 2018;9;1453

  • Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis.

    de Vries SPW, Hadjirin NF, Lay EM, Zadoks RN, Peacock SJ et al.

    International journal of systematic and evolutionary microbiology 2018;68;1;21-27

  • Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action.

    Fukuda K, Limmathurotsakul D, Okeke IN, Shetty N, van Doorn R et al.

    Wellcome open research 2018;3;59

  • Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand.

    Price-Carter M, Brauning R, de Lisle GW, Livingstone P, Neill M et al.

    Frontiers in veterinary science 2018;5;272

  • Role of Alanine Racemase Mutations in Mycobacterium tuberculosis d-Cycloserine Resistance.

    Nakatani Y, Opel-Reading HK, Merker M, Machado D, Andres S et al.

    Antimicrobial agents and chemotherapy 2017;61;12

  • Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting.

    Toleman MS, Watkins ER, Williams T, Blane B, Sadler B et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;65;12;2069-2077

  • Genomic history of the seventh pandemic of cholera in Africa.

    Weill FX, Domman D, Njamkepo E, Tarr C, Rauzier J et al.

    Science (New York, N.Y.) 2017;358;6364;785-789

  • Integrated view of Vibrio cholerae in the Americas.

    Domman D, Quilici ML, Dorman MJ, Njamkepo E, Mutreja A et al.

    Science (New York, N.Y.) 2017;358;6364;789-793

  • 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 et al.

    Science translational medicine 2017;9;413

  • A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children.

    Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J et al.

    PLoS neglected tropical diseases 2017;11;10;e0005975

  • Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand.

    Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S et al.

    Genome medicine 2017;9;1;81

  • Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.

    Jamrozy D, Coll F, Mather AE, Harris SR, Harrison EM et al.

    BMC genomics 2017;18;1;684

  • Community outbreaks of group A Streptococcus revealed by genome sequencing.

    Turner CE, Bedford L, Brown NM, Judge K, Török ME et al.

    Scientific reports 2017;7;1;8554

  • Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England.

    Harrison EM, Coll F, Toleman MS, Blane B, Brown NM et al.

    Scientific reports 2017;7;1;7406

  • Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration.

    Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J et al.

    eLife 2017;6

  • Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.

    Brodrick HJ, Raven KE, Kallonen T, Jamrozy D, Blane B et al.

    Genome medicine 2017;9;1;70

  • Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice.

    Harkins CP, Pichon B, Doumith M, Parkhill J, Westh H et al.

    Genome biology 2017;18;1;130

  • Systematic longitudinal survey of invasiveEscherichia coliin England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

    Kallonen T, Brodrick HJ, Harris SR, Corander J, Brown NM et al.

    Genome research 2017

  • Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes.

    Moradigaravand D, Jamrozy D, Mostowy R, Anderson A, Nickerson EK et al.

    mBio 2017;8;4

  • The Influence of HIV on the Evolution of Mycobacterium tuberculosis.

    Koch AS, Brites D, Stucki D, Evans JC, Seldon R et al.

    Molecular biology and evolution 2017;34;7;1654-1668

  • Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns.

    Donker T, Reuter S, Scriberras J, Reynolds R, Brown NM et al.

    Microbial genomics 2017;3;7;e000113

  • Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex.

    Loveridge EJ, Jones C, Bull MJ, Moody SC, Kahl MW et al.

    Journal of bacteriology 2017;199;13

  • Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.

    Ludden C, Reuter S, Judge K, Gouliouris T, Blane B et al.

    Microbial genomics 2017;3;7;e000114

  • Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.

    David S, Sánchez-Busó L, Harris SR, Marttinen P, Rusniok C et al.

    PLoS genetics 2017;13;6;e1006855

  • 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;64;9;1251-1259

  • Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.

    Raven KE, Gouliouris T, Brodrick H, Coll F, Brown NM et al.

    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2017;64;7;886-893

  • 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

  • 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-ResistantKlebsiella pneumoniaein the United Kingdom and Ireland.

    Moradigaravand D, Martin V, Peacock SJ and Parkhill J

    mBio 2017;8;1

  • 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

  • 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

  • Global and regional dissemination and evolution of Burkholderia pseudomallei.

    Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z et al.

    Nature microbiology 2017;2;16263

  • A non-endoscopic device to sample the oesophageal microbiota: a case-control study.

    Elliott DRF, Walker AW, O'Donovan M, Parkhill J and Fitzgerald RC

    The lancet. Gastroenterology & hepatology 2017;2;1;32-42

  • Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

    Yahara K, Méric G, Taylor AJ, de Vries SP, Murray S et al.

    Environmental microbiology 2017;19;1;361-380

  • Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis.

    Lees JA, Kremer PHC, Manso AS, Croucher NJ, Ferwerda B et al.

    Microbial genomics 2017;3;1;e000103

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

    Power RA, Parkhill J and de Oliveira T

    Nature reviews. Genetics 2017;18;1;41-50

  • 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;23;4;264.e1-264.e9

  • 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

  • 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;26;10;1388-1396

  • 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;48;10;1211-1217

  • 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

  • Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.

    Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M et al.

    mBio 2016;7;5

  • The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland.

    Moradigaravand D, Reuter S, Martin V, Peacock SJ and Parkhill J

    Nature microbiology 2016;1;16173

  • Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.

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

    Genome announcements 2016;4;5

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

    Lees JA, Vehkala M, Välimäki N, Harris SR, Chewapreecha C et al.

    Nature communications 2016;7;12797

  • 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

  • Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii.

    Hassan KA, Cain AK, Huang T, Liu Q, Elbourne LD et al.

    mBio 2016;7;5

  • 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;71;9;795-803

  • Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.

    Judge K, Hunt M, Reuter S, Tracey A, Quail MA et al.

    Microbial genomics 2016;2;9;e000085

  • 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

  • Wild-Type and Non-Wild-Type Mycobacterium tuberculosis MIC Distributions for the Novel Fluoroquinolone Antofloxacin Compared with Those for Ofloxacin, Levofloxacin, and Moxifloxacin.

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

    Antimicrobial agents and chemotherapy 2016;60;9;5232-7

  • Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.

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

    Genome announcements 2016;4;4

  • What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B.

    Connor TR, Owen SV, Langridge G, Connell S, Nair S et al.

    mBio 2016;7;4

  • 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

  • Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

    Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J et al.

    Microbial genomics 2016;2;8;e000083

  • 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;214;3;447-53

  • 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

  • Genomic Analysis and Comparison of Two Gonorrhea Outbreaks.

    Didelot X, Dordel J, Whittles LK, Collins C, Bilek N et al.

    mBio 2016;7;3

  • Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

    Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR et al.

    BMC genomics 2016;17;440

  • 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 for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

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    mBio 2016;7;3

  • Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic.

    Jamrozy DM, Harris SR, Mohamed N, Peacock SJ, Tan CY et al.

    Microbial genomics 2016;2;5;e000058

  • 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

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

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    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

  • Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

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    Nature microbiology 2016;1;16027

  • Genomes on ice.

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    Nature reviews. Microbiology 2016;14;3;134

  • 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;15033

  • 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

  • Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

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    BMC genomics 2016;17;79

  • 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;15023

  • Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network.

    Brodrick HJ, Raven KE, Harrison EM, Blane B, Reuter S et al.

    Genome medicine 2016;8;1;4

  • Modulation of the human gut microbiota by dietary fibres occurs at the species level.

    Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J et al.

    BMC biology 2016;14;3

  • The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water.

    Karkey A, Jombart T, Walker AW, Thompson CN, Torres A et al.

    PLoS neglected tropical diseases 2016;10;1;e0004346

  • 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 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

  • 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

  • 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

  • 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

  • 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;1193-1202

  • 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

  • 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

  • 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

  • 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

  • Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015.

    Hadjirin NF, Lay EM, Paterson GK, Harrison EM, Peacock SJ et al.

    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2015;20;24

  • 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

  • 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

  • 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

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

    Baker KS, Parkhill J and Thomson NR

    Genome announcements 2015;3;3

  • Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus.

    Steinig EJ, Andersson P, Harris SR, Sarovich DS, Manoharan A et al.

    BMC genomics 2015;16;388

  • 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

  • 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

  • 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 GGR, 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

  • Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

    Nandi T, Holden MT, Holden MT, Didelot X, Mehershahi K et al.

    Genome research 2015;25;1;129-41

  • 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

  • Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov.

    Tong SY, Schaumburg F, Ellington MJ, Corander J, Pichon B et al.

    International journal of systematic and evolutionary microbiology 2015;65;Pt 1;15-22

  • 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

  • A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.

    Bratcher HB, Corton C, Jolley KA, Parkhill J and Maiden MC

    BMC genomics 2014;15;1138

  • 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

  • The extant World War 1 dysentery bacillus NCTC1: a genomic analysis.

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

    Lancet (London, England) 2014;384;9955;1691-7

  • 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

  • Comparative genome analysis of Wolbachia strain wAu.

    Sutton ER, Harris SR, Parkhill J and Sinkins SP

    BMC genomics 2014;15;928

  • 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.

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    PLoS biology 2014;12;8;e1001920

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    Genome research 2007;17;7;1082-92

  • Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.

    Holt KE, Thomson NR, Wain J, Phan MD, Nair S et al.

    Journal of bacteriology 2007;189;11;4257-64

  • Genome plasticity of BCG and impact on vaccine efficacy.

    Brosch R, Gordon SV, Garnier T, Eiglmeier K, Frigui W et al.

    Proceedings of the National Academy of Sciences of the United States of America 2007;104;13;5596-601

  • Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

    Bentley SD, Vernikos GS, Snyder LA, Churcher C, Arrowsmith C et al.

    PLoS genetics 2007;3;2;e23

  • Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.

    Holden MT, Scott A, Cherevach I, Chillingworth T, Churcher C et al.

    Journal of bacteriology 2007;189;4;1473-7

  • The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

    Thomson NR, Howard S, Wren BW, Holden MT, Crossman L et al.

    PLoS genetics 2006;2;12;e206

  • Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction.

    Sebaihia M, Preston A, Maskell DJ, Kuzmiak H, Connell TD et al.

    Journal of bacteriology 2006;188;16;6002-15

  • Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.

    Vernikos GS and Parkhill J

    Bioinformatics (Oxford, England) 2006;22;18;2196-203

  • The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.

    Sebaihia M, Wren BW, Mullany P, Fairweather NF, Minton N et al.

    Nature genetics 2006;38;7;779-86

  • Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes.

    Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E et al.

    PLoS genetics 2006;2;3;e31

  • The genome of Rhizobium leguminosarum has recognizable core and accessory components.

    Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF et al.

    Genome biology 2006;7;4;R34

  • Complete genome sequence and lytic phase transcription profile of a Coccolithovirus.

    Wilson WH, Schroeder DC, Allen MJ, Holden MT, Parkhill J et al.

    Science (New York, N.Y.) 2005;309;5737;1090-2

  • Wolbachia variability and host effects on crossing type in Culex mosquitoes.

    Sinkins SP, Walker T, Lynd AR, Steven AR, Makepeace BL et al.

    Nature 2005;436;7048;257-60

  • ACT: the Artemis Comparison Tool.

    Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J

    Bioinformatics (Oxford, England) 2005;21;16;3422-3

  • Comparative apicomplexan genomics.

    Pain A, Crossman L and Parkhill J

    Nature reviews. Microbiology 2005;3;6;454-5

  • The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.

    Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD et al.

    Genome research 2005;15;5;629-40

  • Livelihood hazards.

    Sebaihia M, Thomson NR, Crossman L and Parkhill J

    Nature reviews. Microbiology 2005;3;4;278-9

  • Extensive DNA inversions in the B. fragilis genome control variable gene expression.

    Cerdeño-Tárraga AM, Patrick S, Crossman LC, Blakely G, Abratt V et al.

    Science (New York, N.Y.) 2005;307;5714;1463-5

  • Diversity at every level.

    Crossman L, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2005;3;3;196-7

  • Brothers in arms.

    Thomson N, Holden M and Parkhill J

    Nature reviews. Microbiology 2005;3;2;100-1

  • Genomic pot pourri.

    Bentley S, Crossman L, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;12;928-9

  • Eukaryotes: not beyond compare.

    Pain A, Bentley S and Parkhill J

    Nature reviews. Microbiology 2004;2;11;856-7

  • The use of genome annotation data and its impact on biological conclusions.

    Tettelin H and Parkhill J

    Nature genetics 2004;36;10;1028-9

  • Pathogens in decay.

    Cerdeño-Tárraga A, Thomson N and Parkhill J

    Nature reviews. Microbiology 2004;2;10;774-5

  • Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.

    Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;39;14240-5

  • Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.

    Bell KS, Sebaihia M, Pritchard L, Holden MT, Hyman LJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;30;11105-10

  • Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance.

    Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP et al.

    Proceedings of the National Academy of Sciences of the United States of America 2004;101;26;9786-91

  • New environments, versatile genomes.

    Cerdeño-Tárraga A, Crossman L and Parkhill J

    Nature reviews. Microbiology 2004;2;6;446-7

  • The bordetellae: lessons from genomics.

    Preston A, Parkhill J and Maskell DJ

    Nature reviews. Microbiology 2004;2;5;379-90

  • Strength in diversity.

    Pain A, Crossman L, Sebaihia M, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;5;358-9

  • Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes.

    Liu M, Gingery M, Doulatov SR, Liu Y, Hodes A et al.

    Journal of bacteriology 2004;186;5;1503-17

  • Sequencing the environment.

    Crossman L, Sebaihia M, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;3;184-5

  • Pathogenomics of non-pathogens.

    Holden M, Crossman L, Cerdeño-Tárraga A and Parkhill J

    Nature reviews. Microbiology 2004;2;2;91

  • Shrinking genomics.

    Thomson NR, Sebaihia M, Cerdeño-Tárraga AM, Holden MT and Parkhill J

    Nature reviews. Microbiology 2004;2;1;11

  • Pathogenomics.

    Crossman L, Cerdeño-Tárraga A, Bentley S and Parkhill J

    Nature reviews. Microbiology 2003;1;3;176-7

  • The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.

    Cerdeño-Tárraga AM, Efstratiou A, Dover LG, Holden MT, Pallen M et al.

    Nucleic acids research 2003;31;22;6516-23

  • Fitting the niche by genomic adaptation.

    Thomson N, Bentley S, Holden M and Parkhill J

    Nature reviews. Microbiology 2003;1;2;92-3

  • The value of comparison.

    Thomson N, Sebaihia M, Cerdeño-Tárraga A, Bentley S, Crossman L and Parkhill J

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

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

    Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N et al.

    Nature genetics 2003;35;1;32-40

  • The complete genome sequence of Mycobacterium bovis.

    Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H et al.

    Proceedings of the National Academy of Sciences of the United States of America 2003;100;13;7877-82

  • Genomics: Relative pathogenic values.

    Parkhill J and Berry C

    Nature 2003;423;6935;23-5

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

    Bentley SD, Maiwald M, Murphy LD, Pallen MJ, Yeats CA et al.

    Lancet (London, England) 2003;361;9358;637-44

  • Restricting genome data won't stop bioterrorism.

    Read TD and Parkhill J

    Nature 2002;417;6887;379

  • 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.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D et al.

    Nature 2001;413;6858;848-52

  • 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.

    Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al.

    Bioinformatics (Oxford, England) 2000;16;10;944-5

  • In defense of complete genomes.

    Parkhill J

    Nature biotechnology 2000;18;5;493-4

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

    Parkhill J, Achtman M, James KD, Bentley SD, Churcher C et al.

    Nature 2000;404;6777;502-6

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

    Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C et al.

    Nature 2000;403;6770;665-8