J Parkhill

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences
    S M Townsend
    Department of Medical Microbiology and Immunology, College of Medicine, Texas A and M University, College Station, Texas 77843, USA
    Infect Immun 69:2894-901. 2001
  2. pmc Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen
    Paul W O'Toole
    Department of Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
    BMC Genomics 11:164. 2010
  3. pmc Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study
    Josephine M Bryant
    Wellcome Trust Sanger Institute, Hinxton, UK
    Lancet 381:1551-60. 2013
  4. pmc Bacterial epidemiology and biology--lessons from genome sequencing
    Julian Parkhill
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 12:230. 2011
  5. pmc Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants
    Peter M Power
    University of Oxford Department of Paediatrics, Medical Sciences Division, John Radcliffe Hospital, Headington, Oxford, UK
    BMC Microbiol 12:273. 2012
  6. pmc Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica
    Umesh Ahuja
    Department of Microbiology, Immunology and Molecular Genetics, University of California, BSRB 254, 615 Charles E, Young Drive East, Los Angeles, CA 90095 1747, USA
    BMC Microbiol 12:167. 2012
  7. pmc Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974
    Kelly L Wyres
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    BMC Genomics 14:500. 2013
  8. pmc Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity
    Luke J Mappley
    Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Reading University, Addlestone, Surrey, UK
    BMC Genomics 13:454. 2012
  9. pmc Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens
    Jihye Park
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
    BMC Genomics 13:545. 2012
  10. pmc The genome of Rhizobium leguminosarum has recognizable core and accessory components
    J Peter W Young
    Department of Biology, University of York, York, UK
    Genome Biol 7:R34. 2006

Collaborators

Detail Information

Publications45

  1. pmc Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences
    S M Townsend
    Department of Medical Microbiology and Immunology, College of Medicine, Texas A and M University, College Station, Texas 77843, USA
    Infect Immun 69:2894-901. 2001
    ..However, the serotype Typhi genome differed from that of all other Salmonella serotypes investigated in that it contained a unique combination of putative fimbrial operons...
  2. pmc Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen
    Paul W O'Toole
    Department of Microbiology, and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
    BMC Genomics 11:164. 2010
    ..mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome...
  3. pmc Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study
    Josephine M Bryant
    Wellcome Trust Sanger Institute, Hinxton, UK
    Lancet 381:1551-60. 2013
    ..How this organism is acquired is not currently known, but there is growing concern that person-to-person transmission could occur. We aimed to define the mechanisms of acquisition of M abscessus in individuals with cystic fibrosis...
  4. pmc Bacterial epidemiology and biology--lessons from genome sequencing
    Julian Parkhill
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 12:230. 2011
    ..Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution...
  5. pmc Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants
    Peter M Power
    University of Oxford Department of Paediatrics, Medical Sciences Division, John Radcliffe Hospital, Headington, Oxford, UK
    BMC Microbiol 12:273. 2012
    ..Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species...
  6. pmc Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica
    Umesh Ahuja
    Department of Microbiology, Immunology and Molecular Genetics, University of California, BSRB 254, 615 Charles E, Young Drive East, Los Angeles, CA 90095 1747, USA
    BMC Microbiol 12:167. 2012
    ..bronchiseptica subpopulations, designated complexes I and IV. Complex IV isolates appear to have a bias for infecting humans; however, little is known regarding their epidemiology, virulence properties, or comparative genomics...
  7. pmc Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974
    Kelly L Wyres
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    BMC Genomics 14:500. 2013
    ..In this study the genomes of 38 pneumococci isolated prior to 1974 were probed for the presence of tet(M), cat, erm(B), mef(A/E) and int (integrase) to indicate the presence of Tn916/Tn5252-like elements...
  8. pmc Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity
    Luke J Mappley
    Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Reading University, Addlestone, Surrey, UK
    BMC Genomics 13:454. 2012
    ..Finally we report the first application of the high-throughput Biolog phenotype screening tool on the B. pilosicoli strains for detailed comparisons between genotype and phenotype...
  9. pmc Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens
    Jihye Park
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
    BMC Genomics 13:545. 2012
    ..The compelling picture from previous comparisons of the three sequenced genomes was of genome degradation, with substantial loss of genome content (up to 24%) associated with adaptation to humans...
  10. pmc The genome of Rhizobium leguminosarum has recognizable core and accessory components
    J Peter W Young
    Department of Biology, University of York, York, UK
    Genome Biol 7:R34. 2006
    ..We have sequenced the genome of R. leguminosarum biovar viciae strain 3841...
  11. pmc The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants
    Lisa C Crossman
    Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 9:R74. 2008
    ..Whilst relatively distant phylogenetically, the closest sequenced relatives of S. maltophilia are the plant pathogenic xanthomonads...
  12. pmc Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
    Mark W Silby
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA
    Genome Biol 10:R51. 2009
    ..A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species...
  13. pmc Genetic flux over time in the Salmonella lineage
    Georgios S Vernikos
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 8:R100. 2007
    ..Over time, the composition of those sequences tends to become more similar to the compositional signature of their host (amelioration)...
  14. pmc Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium
    Richard A Stabler
    London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
    Genome Biol 10:R102. 2009
    ..difficile (CD196), a recent epidemic and hypervirulent 027 (R20291) and a previously sequenced PCR-ribotype 012 strain (630)...
  15. pmc High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease
    Alan W Walker
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Microbiol 11:7. 2011
    ..We therefore specifically sought to compare the mucosa-associated microbiota from both inflamed and non-inflamed sites of the colon in CD and UC patients to that from non-IBD controls and to detect disease-specific profiles...
  16. pmc High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    BMC Infect Dis 10:144. 2010
    ..Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection...
  17. pmc Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06
    Julia S Bennett
    Department of Zoology, University of Oxford, UK
    BMC Genomics 11:652. 2010
    ..Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally...
  18. pmc Identification, variation and transcription of pneumococcal repeat sequences
    Nicholas J Croucher
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Genomics 12:120. 2011
    ..However, little is known about the role they play in pneumococcal genetics...
  19. pmc Comparative genomics of prevaccination and modern Bordetella pertussis strains
    Marieke J Bart
    Laboratory for Infectious Diseases and Screening, Netherlands Centre for Infectious Diseases Control, RIVM, Bilthoven, Netherlands
    BMC Genomics 11:627. 2010
    ..To elucidate how B. pertussis has adapted to vaccination, we compared genome sequences of two ptxP3 strains with four strains isolated before and after the introduction vaccination...
  20. pmc Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Genomics 10:36. 2009
    ..The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi...
  21. pmc The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay
    Erik Hjerde
    Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N 9037 Tromsø, Norway
    BMC Genomics 9:616. 2008
    ..The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo...
  22. pmc Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens
    Paul Wilkinson
    School of Biosciences, University of Exeter in Cornwall, Penryn TR10 9EZ, UK
    BMC Genomics 10:302. 2009
    ..Here we compare the complete genome of Pa ATCC43949 with that of the previously sequenced insect pathogen P. luminescens strain TT01 which was isolated from its entomopathogenic nematode vector collected from soil in Trinidad and Tobago...
  23. pmc Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
    Helena M B Seth-Smith
    Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, UK
    BMC Genomics 10:239. 2009
    ..This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis...
  24. pmc Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
    Ozan Gundogdu
    Pathogen Molecular Department, London School of Hygiene and Tropical Medicine, UK
    BMC Genomics 8:162. 2007
    ..We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation...
  25. pmc Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement
    Andrew P Jackson
    The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    BMC Genomics 10:584. 2009
    ..coli. By comparing rhs repertoires across the Enterobacteriaceae, this study provides a robust explanation of rhs diversification and evolution, and a mechanistic model of how rhs diversity is gained and lost...
  26. pmc Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis
    Philip N Ward
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Genomics 10:54. 2009
    ..Comparative analysis of the complete genome sequence of S. uberis strain 0140J was undertaken to help elucidate the biology of this effective bovine pathogen...
  27. pmc Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group
    Thomas Walker
    Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    BMC Biol 5:39. 2007
    ..Species in the Culex pipiens complex display an unusually high number of Wolbachia-induced crossing types, and based on present data, only the wPip strain is present...
  28. ncbi request reprint Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491
    J Parkhill
    The Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 404:502-6. 2000
    ..Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen...
  29. ncbi request reprint Genome sequence of Yersinia pestis, the causative agent of plague
    J Parkhill
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 413:523-7. 2001
    ..The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve...
  30. ncbi request reprint Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
    J Parkhill
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nature 413:848-52. 2001
    ..typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis...
  31. ncbi request reprint Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
    Julian Parkhill
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nat Genet 35:32-40. 2003
    ....
  32. pmc The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129
    A M Cerdeño-Tárraga
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 31:6516-23. 2003
    ..The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus...
  33. ncbi request reprint SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2)
    S D Bentley
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Mol Microbiol 51:1615-28. 2004
    ..This may be related to atypical features of its end sequences...
  34. pmc Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946
    M Sebaihia
    The Sanger Institute, Hinxton, Cambridge, United Kingdom
    J Bacteriol 192:2020-1. 2010
    ..The analysis of the sequence and its comparison with sequenced genomes of closely related enterobacteria revealed signs of pathoadaptation to rosaceous hosts...
  35. ncbi request reprint Evolutionary strategies of human pathogens
    J Parkhill
    The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
    Cold Spring Harb Symp Quant Biol 68:151-8. 2003
  36. ncbi request reprint Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
    S D Bentley
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 417:141-7. 2002
    ..The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering...
  37. ncbi request reprint Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
    S T Cole
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, UK
    Nature 393:537-44. 1998
    ....
  38. pmc Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors
    K S Bell
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 101:11105-10. 2004
    ....
  39. ncbi request reprint Artemis: sequence visualization and annotation
    K Rutherford
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Bioinformatics 16:944-5. 2000
    ..Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format. AVAILABITLTY: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis..
  40. pmc Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity
    N Dorrell
    Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
    Genome Res 11:1706-15. 2001
    ..These studies reveal extensive genetic diversity among C. jejuni strains and pave the way toward identifying correlates of pathogenicity and developing improved epidemiological tools for this problematic pathogen...
  41. ncbi request reprint Homology between a human apoptosis specific protein and the product of APG5, a gene involved in autophagy in yeast
    E M Hammond
    CRC Institute for Cancer Studies, The University of Birmingham, Edgbaston, UK
    FEBS Lett 425:391-5. 1998
    ..These data indicate a possible relationship between apoptosis and autophagy and suggest evolutionary conservation in mammalian apoptosis of a degradative process present in yeast...
  42. pmc Genetic basis for lipopolysaccharide O-antigen biosynthesis in bordetellae
    A Preston
    Centre for Veterinary Science, Department of Clinical Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, Cambridge CB10 1SA, United Kingdom
    Infect Immun 67:3763-7. 1999
    ..Mutations in the locus in B. bronchiseptica and B. parapertussis prevent O-antigen biosynthesis and provide tools for the study of the role of O antigen in infections caused by these bacteria...
  43. pmc Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid
    M B Prentice
    Department of Medical Microbiology, St Bartholomew s and the Royal London School of Medicine and Dentistry, London, United Kingdom
    J Bacteriol 183:2586-94. 2001
    ..pestis strains which distinguish Y. pestis bv. Orientalis strains from other biovars. We also present evidence for plasmid-associated DNA exchange between Y. pestis and the exclusively human pathogen Salmonella enterica serovar Typhi...
  44. ncbi request reprint Mutations revealed by sequencing the 5' half of the gene for ataxia telangiectasia
    P J Byrd
    Institute for Cancer Studies, University of Birmingham, Edgbaston, UK
    Hum Mol Genet 5:145-9. 1996
    ....
  45. ncbi request reprint The decaying genome of Mycobacterium leprae
    K Eiglmeier
    , Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris, France
    Lepr Rev 72:387-98. 2001
    ..This may explain the unusually long generation time and account for our inability to culture the leprosy bacillus...