Stephen D Bentley

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18
    Stephen D Bentley
    Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    PLoS Genet 3:e23. 2007
  2. 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
  3. 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
  4. 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
  5. pmc Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
    Claudio Donati
    Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100 Siena, Italy
    Genome Biol 11:R107. 2010
  6. 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
  7. pmc Sequence and functional analyses of Haemophilus spp. genomic islands
    Mario Juhas
    Clinical Microbiology and Infectious Diseases, NDCLS, University of Oxford, Headley Way, Oxford OX3 9DU, UK
    Genome Biol 8:R237. 2007
  8. pmc New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor
    Corin Yeats
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    BMC Microbiol 3:3. 2003
  9. pmc Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    BMC Genomics 11:449. 2010
  10. 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

Detail Information

Publications49

  1. pmc Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18
    Stephen D Bentley
    Wellcome Trust Sanger Institute, Hinxton, United Kingdom
    PLoS Genet 3:e23. 2007
    ....
  2. 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...
  3. 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...
  4. 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...
  5. pmc Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
    Claudio Donati
    Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100 Siena, Italy
    Genome Biol 11:R107. 2010
    ..Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group...
  6. 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...
  7. pmc Sequence and functional analyses of Haemophilus spp. genomic islands
    Mario Juhas
    Clinical Microbiology and Infectious Diseases, NDCLS, University of Oxford, Headley Way, Oxford OX3 9DU, UK
    Genome Biol 8:R237. 2007
    ..More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily...
  8. pmc New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor
    Corin Yeats
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
    BMC Microbiol 3:3. 2003
    ..We sought to expand our understanding of this organism at the molecular level through identification and annotation of novel protein domains. Protein domains are the evolutionary conserved units from which proteins are formed...
  9. pmc Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the secondary endosymbiont of tsetse flies
    Eugeni Belda
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
    BMC Genomics 11:449. 2010
    ....
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. ncbi request reprint Comparative genomic structure of prokaryotes
    Stephen D Bentley
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Annu Rev Genet 38:771-92. 2004
    ..We also describe examples where mechanisms of genome evolution have acted in the adaptation of bacterial species to particular niches...
  15. pmc Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes
    Stephen D Bentley
    Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Genet 2:e31. 2006
    ..Remarkably, the total size of alternative coding DNA at this one locus exceeds 1.8 Mbp, almost equivalent to the entire S. pneumoniae chromosomal complement...
  16. ncbi request reprint The devil is in the detail
    Stephen D Bentley
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Trends Microbiol 11:256-8. 2003
  17. pmc The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients
    Matthew T G Holden
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
    J Bacteriol 191:261-77. 2009
    ..The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen...
  18. 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...
  19. pmc Evolutionary dynamics of Clostridium difficile over short and long time scales
    Miao He
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 107:7527-32. 2010
    ..1-85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages...
  20. pmc Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation
    Stephen D Bentley
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
    J Bacteriol 190:2150-60. 2008
    ....
  21. pmc The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 15:629-40. 2005
    ....
  22. pmc Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
    Simon R Harris
    Wellcome Trust Sanger Institute, Cambridge, UK
    Lancet Infect Dis 13:130-6. 2013
    ..We assessed the use of whole-genome sequencing to enhance detection of MRSA transmission between these settings...
  23. pmc Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei
    Matthew T G Holden
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 101:14240-5. 2004
    ..mallei. We propose that variable horizontal gene acquisition by B. pseudomallei is an important feature of recent genetic evolution and that this has resulted in a genetically diverse pathogenic species...
  24. pmc Evolution of MRSA during hospital transmission and intercontinental spread
    Simon R Harris
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 15A, UK
    Science 327:469-74. 2010
    ..The ability to interrogate and resolve bacterial populations is applicable to a range of infectious diseases, as well as microbial ecology...
  25. pmc Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak
    M Estee Torok
    Department of Medicine, University of Cambridge, Cambridge, United Kingdom
    J Clin Microbiol 51:611-4. 2013
    ..Whole-genome sequencing of the isolates found them to be genetically identical, suggesting a missed transmission event...
  26. pmc Rapid pneumococcal evolution in response to clinical interventions
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Science 331:430-4. 2011
    ..This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales...
  27. pmc Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes
    Mohammed Sebaihia
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
    Genome Res 17:1082-92. 2007
    ..This pathogen relies on its toxin to rapidly kill a wide range of prey species, and to gain access to nutrient sources, it releases a large number of extracellular enzymes to soften and destroy rotting or decayed tissues...
  28. pmc Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81
    Nicholas J Croucher
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, United Kingdom
    J Bacteriol 191:1480-9. 2009
    ..However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success...
  29. pmc Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak
    Claudio U Köser
    University of Cambridge, Cambridge, United Kingdom
    N Engl J Med 366:2267-75. 2012
    ..Whole-genome sequencing may provide improved resolution to define transmission pathways and characterize outbreaks...
  30. pmc Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW)
    Matthew T G Holden
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
    J Bacteriol 192:888-92. 2010
    ..The strain is resistant to a wide range of antibiotics, antiseptics, and heavy metals due to resistance genes encoded on mobile genetic elements and also mutations in housekeeping genes...
  31. 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...
  32. pmc Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor
    David J Studholme
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
    BMC Microbiol 4:14. 2004
    ..We wished to apply a recently published bioinformatic method for identifying novel regulatory sequence signals to gain new insights into regulation in S. coelicolor...
  33. pmc Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens
    Matthew T G Holden
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 5:e1000346. 2009
    ..We conclude that the complex interplay of functional loss, pathogenic specialization, and genetic exchange between S. equi, S. zooepidemicus, and S. pyogenes continues to influence the evolution of these important streptococci...
  34. 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
    ....
  35. pmc Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance
    Matthew T G Holden
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 101:9786-91. 2004
    ....
  36. pmc A simple method for directional transcriptome sequencing using Illumina technology
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SA, UK
    Nucleic Acids Res 37:e148. 2009
    ..Hence, this simple method should prove a useful tool in aiding genome annotation and gene expression studies in both prokaryotes and eukaryotes...
  37. pmc A high-resolution view of genome-wide pneumococcal transformation
    Nicholas J Croucher
    Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 8:e1002745. 2012
    ....
  38. doi request reprint Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences
    Josephine Bryant
    Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Future Microbiol 7:1283-96. 2012
    ..In this review, we focus on recent work that has applied this powerful new approach and summarize some of the advances that this has brought in our understanding of the details of how bacterial pathogens evolve...
  39. pmc The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex
    Stephen D Bentley
    Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, UK
    PLoS Negl Trop Dis 6:e1552. 2012
    ..M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis...
  40. 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...
  41. ncbi request reprint The good, the bad and the ugly?
    Mohammed Sebaihia
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Trends Microbiol 11:204-5. 2003
  42. pmc Population genomics of post-vaccine changes in pneumococcal epidemiology
    Nicholas J Croucher
    Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Genet 45:656-63. 2013
    ..These alterations resulted in little overall effect on accessory genome composition at the population level, contrasting with the decrease in pneumococcal disease rates after the vaccine's introduction...
  43. pmc A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic
    Matthew T G Holden
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB19 1SA, United Kingdom
    Genome Res 23:653-64. 2013
    ..We document the genetic changes associated with adaptation to the hospital environment and with increasing drug resistance over time, and how MRSA evolution likely has been influenced by country-specific drug use regimens...
  44. ncbi request reprint Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei
    Stephen D Bentley
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Lancet 361:637-44. 2003
    ..The causative agent, Tropheryma whipplei, is a Gram-positive bacterium about which little is known. Our aim was to investigate the biology of this organism by generating and analysing the complete DNA sequence of its genome...
  45. pmc Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome
    N Luisa Hiller
    Allegheny General Hospital, Allegheny Singer Research Institute, Center for Genomic Sciences, Pittsburgh, PA 15212, USA
    J Bacteriol 189:8186-95. 2007
    ....
  46. pmc Genetic relatedness of the Streptococcus pneumoniae capsular biosynthetic loci
    Angeliki Mavroidi
    Department of Infectious Disease Epidemiology, Imperial College London, Room G22, Old Medical School Building, St Mary s Hospital, Norfolk Place, London W2 1PG, United Kingdom
    J Bacteriol 189:7841-55. 2007
    ....
  47. pmc Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci
    David M Aanensen
    Department of Infectious Disease Epidemiology, Imperial College London, Room G22, Old Medical School Building, St Mary s Hospital, Norfolk Place, London W2 1PG, United Kingdom
    J Bacteriol 189:7856-76. 2007
    ..These assignments should provide a stimulus for biochemical studies to evaluate the reactions that are proposed...
  48. ncbi request reprint WebACT: an online genome comparison suite
    James C Abbott
    Centre for Bioinformatics, Imperial College London, UK
    Methods Mol Biol 395:57-74. 2007
    ..The use of ACT to view the selected comparison is then explored using examples from bacterial genomes...
  49. ncbi request reprint Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species
    Richard A Stabler
    Bacterial Microarray Group, St George s Hospital Medical School, London SW7 0RE, UK
    Microbiology 151:2907-22. 2005
    ..The subset of pathogen-specific genes identified represents potential drug or vaccine targets that would not eliminate commensal neisseriae and the associated naturally acquired immunity...