Keith A Jolley

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. pmc Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods
    Keith A Jolley
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    J Clin Microbiol 50:3046-53. 2012
  2. pmc Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
    Keith A Jolley
    Department of Zoology, University of Oxford, Oxford, UK
    Microbiology 158:1005-15. 2012
  3. pmc BIGSdb: Scalable analysis of bacterial genome variation at the population level
    Keith A Jolley
    Department of Zoology, University of Oxford, UK
    BMC Bioinformatics 11:595. 2010
  4. pmc Long-term evolution of antigen repertoires among carried meningococci
    Caroline O Buckee
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Proc Biol Sci 277:1635-41. 2010
  5. pmc Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing
    Alison J Cody
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    J Clin Microbiol 51:2526-34. 2013
  6. pmc Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
    Samuel K Sheppard
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 110:11923-7. 2013
  7. pmc Description and nomenclature of Neisseria meningitidis capsule locus
    Odile B Harrison
    Department of Zoology, University of Oxford, Oxford, UK
    Emerg Infect Dis 19:566-73. 2013
  8. pmc Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing
    Julia S Bennett
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
    BMC Biol 5:35. 2007
  9. ncbi request reprint Molecular typing of meningococci: recommendations for target choice and nomenclature
    Keith A Jolley
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, UK
    FEMS Microbiol Rev 31:89-96. 2007
  10. pmc A common gene pool for the Neisseria FetA antigen
    Julia S Bennett
    Department of Zoology, The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
    Int J Med Microbiol 299:133-9. 2009

Detail Information

Publications34

  1. pmc Resolution of a meningococcal disease outbreak from whole-genome sequence data with rapid Web-based analysis methods
    Keith A Jolley
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    J Clin Microbiol 50:3046-53. 2012
    ....
  2. pmc Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
    Keith A Jolley
    Department of Zoology, University of Oxford, Oxford, UK
    Microbiology 158:1005-15. 2012
    ..This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism...
  3. pmc BIGSdb: Scalable analysis of bacterial genome variation at the population level
    Keith A Jolley
    Department of Zoology, University of Oxford, UK
    BMC Bioinformatics 11:595. 2010
    ..These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner...
  4. pmc Long-term evolution of antigen repertoires among carried meningococci
    Caroline O Buckee
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Proc Biol Sci 277:1635-41. 2010
    ..We contrast this antigenic structure with the overlapping but relatively stable combinations of the housekeeping genes observed among the same isolates, and use a novel network approach to visualize these relationships...
  5. pmc Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing
    Alison J Cody
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    J Clin Microbiol 51:2526-34. 2013
    ..The approach is widely applicable to analyses of human bacterial pathogens in real time in clinical laboratories, with little specialist training required. ..
  6. pmc Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter
    Samuel K Sheppard
    Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 110:11923-7. 2013
    ..Three of the seven genes encoded vitamin B5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B5-depleted media and propose that this difference may be an adaptation to host diet. ..
  7. pmc Description and nomenclature of Neisseria meningitidis capsule locus
    Odile B Harrison
    Department of Zoology, University of Oxford, Oxford, UK
    Emerg Infect Dis 19:566-73. 2013
    ..In this report, a comprehensive description of all N. meningitidis serogroups is provided, along with a proposed nomenclature, which was presented at the 2012 XVIIIth International Pathogenic Neisseria Conference...
  8. pmc Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing
    Julia S Bennett
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
    BMC Biol 5:35. 2007
    ..Here, the same seven locus Neisseria scheme was used to characterize a diverse collection of N. gonorrhoeae isolates to investigate whether this method would allow differentiation among isolates, and to distinguish these three species...
  9. ncbi request reprint Molecular typing of meningococci: recommendations for target choice and nomenclature
    Keith A Jolley
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, UK
    FEMS Microbiol Rev 31:89-96. 2007
    ..It is further recommended that a modified nomenclature be adopted of the form: serogroup: PorA type: FetA type: sequence type (clonal complex), thus: B: P1.19,15: F5-1: ST-33 (cc32)...
  10. pmc A common gene pool for the Neisseria FetA antigen
    Julia S Bennett
    Department of Zoology, The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
    Int J Med Microbiol 299:133-9. 2009
    ..Carriage of commensal Neisseria species, such as N. lactamica, that express FetA may be involved in the development of natural immunity to meningococcal disease...
  11. pmc Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis
    Caroline O Buckee
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Proc Natl Acad Sci U S A 105:15082-7. 2008
    ..These findings have general implications for the emergence of lineage structure and virulence in recombining bacterial populations...
  12. ncbi request reprint Cryptic ecology among host generalist Campylobacter jejuni in domestic animals
    Samuel K Sheppard
    Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford, OX1 3PS, UK Institute of Life Science, College of Medicine, Swansea University, Swansea, SA2 8PP, UK
    Mol Ecol 23:2442-51. 2014
    ..This suggests ecological rather than essential barriers to recombination, caused by a cryptic niche structure within the hosts...
  13. pmc MLST revisited: the gene-by-gene approach to bacterial genomics
    Martin C J Maiden
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nat Rev Microbiol 11:728-36. 2013
    ..Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data. ..
  14. pmc Opa protein repertoires of disease-causing and carried meningococci
    Martin J Callaghan
    Dept of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Churchill Hospital, Headington, Oxford OX3 9DU, United Kingdom
    J Clin Microbiol 46:3033-41. 2008
    ..Meningococcal Opa repertoire is strongly linked to MLST genotype irrespective of epidemiological sampling and therefore correlates with invasiveness. It is not, however, strongly associated with severity of meningococcal disease...
  15. doi request reprint Internet-based sequence-typing databases for bacterial molecular epidemiology
    Keith A Jolley
    Department of Zoology and Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford, UK
    Methods Mol Biol 551:305-12. 2009
    ..BLAST searching of antigen sequence databases is also described...
  16. pmc The effect of immune selection on the structure of the meningococcal opa protein repertoire
    Martin J Callaghan
    Department of Paediatrics, University of Oxford, Centre for Clinical Vaccinology and Tropical Medicine CCVTM, Churchill Hospital, Oxford, United Kingdom
    PLoS Pathog 4:e1000020. 2008
    ..These data are consistent with the predictions of a mathematical model of strong immune selection upon a system where identical alleles may occupy different loci...
  17. pmc Introgression in the genus Campylobacter: generation and spread of mosaic alleles
    Samuel K Sheppard
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Microbiology 157:1066-74. 2011
    ..coli sequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species...
  18. ncbi request reprint Multilocus sequence typing for global surveillance of meningococcal disease
    Carina Brehony
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, Oxford, UK
    FEMS Microbiol Rev 31:15-26. 2007
    ..The project demonstrates how molecular typing can be combined with epidemiological data via the Internet for global disease surveillance...
  19. pmc Progressive genome-wide introgression in agricultural Campylobacter coli
    Samuel K Sheppard
    Department of Zoology, The Tinbergen Building, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Mol Ecol 22:1051-64. 2013
    ..jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution...
  20. pmc AgdbNet - antigen sequence database software for bacterial typing
    Keith A Jolley
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
    BMC Bioinformatics 7:314. 2006
    ..Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences...
  21. pmc Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland
    Samuel K Sheppard
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS ONE 5:e15708. 2010
    ..coli infection. Taken together these analyses are consistent with an evolutionary scenario describing the emergence of agriculture-associated C. coli lineage that is an important human pathogen...
  22. pmc A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria
    Julia S Bennett
    Department of Zoology, University of Oxford, Oxford, UK
    Microbiology 158:1570-80. 2012
    ....
  23. pmc Genome sequence analyses show that Neisseria oralis is the same species as 'Neisseria mucosa var. heidelbergensis'
    Julia S Bennett
    Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
    Int J Syst Evol Microbiol 63:3920-6. 2013
    ..oralis is most closely related to N. mucosa. ..
  24. pmc Changes in serogroup and genotype prevalence among carried meningococci in the United Kingdom during vaccine implementation
    Ana Belén Ibarz-Pavón
    Department of Zoology, University of Oxford, United Kingdom
    J Infect Dis 204:1046-53. 2011
    ..A large multicenter study investigated the effect of meningococcal serogroup C conjugate vaccine introduction on the meningococcal population...
  25. pmc Opacity-associated adhesin repertoire in hyperinvasive Neisseria meningitidis
    Martin J Callaghan
    Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, South Parks Road, Oxford OX1 3SY, United Kingdom
    Infect Immun 74:5085-94. 2006
    ....
  26. pmc Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene
    Julia S Bennett
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    J Clin Microbiol 52:1375-81. 2014
    ..This approach provides an alternative to 16S rRNA gene sequencing, which can be readily replicated for other organisms for which more resolution is required, and it has potential applications in high-resolution metagenomic studies. ..
  27. pmc Dam inactivation in Neisseria meningitidis: prevalence among diverse hyperinvasive lineages
    Keith A Jolley
    Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
    BMC Microbiol 4:34. 2004
    ..Here, we report the results of a survey to assess the prevalence of drg in a globally representative panel of disease-associated meningococci...
  28. pmc mlstdbNet - distributed multi-locus sequence typing (MLST) databases
    Keith A Jolley
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, OX1 3SY, UK
    BMC Bioinformatics 5:86. 2004
    ..The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet...
  29. pmc Sequence, distribution and chromosomal context of class I and class II pilin genes of Neisseria meningitidis identified in whole genome sequences
    Mirka E Wörmann
    Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
    BMC Genomics 15:253. 2014
    ..The purpose of this work was to use whole genome sequences to further investigate the frequency and variability of the class II pilE genes in meningococcal isolate collections...
  30. pmc Clinical Clostridium difficile: clonality and pathogenicity locus diversity
    Kate E Dingle
    Nuffield Department of Clinical Laboratory Sciences, Oxford University, John Radcliffe Hospital, Oxford, United Kingdom
    PLoS ONE 6:e19993. 2011
    ....
  31. pmc Genetic diversity and carriage dynamics of Neisseria lactamica in infants
    Julia S Bennett
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
    Infect Immun 73:2424-32. 2005
    ..Some participants shared identical isolates with siblings, but none shared identical isolates with their parents. These findings have implications for the design of vaccines based on this organism...
  32. ncbi request reprint Using MLST to study bacterial variation: prospects in the genomic era
    Keith A Jolley
    Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
    Future Microbiol 9:623-30. 2014
    ....
  33. pmc Implications of differential age distribution of disease-associated meningococcal lineages for vaccine development
    Carina Brehony
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Clin Vaccine Immunol 21:847-53. 2014
    ..The nonrandom age distribution of hyperinvasive lineages has consequences for the design and implementation of vaccines, as different variants, or perhaps targets, may be required for different age groups. ..
  34. pmc PorA variable regions of Neisseria meningitidis
    Joanne E Russell
    University of Oxford, Oxford, United Kingdom
    Emerg Infect Dis 10:674-8. 2004
    ..A Web-accessible database describing this nomenclature and its relationship to previous schemes was established (available from: http://neisseria.org/nm/typing/pora)...