Simon R Harris

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Comparative genome analysis of Wolbachia strain wAu
    Elizabeth R Sutton
    Department of Zoology and Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
    BMC Genomics 15:928. 2014
  2. pmc Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression
    Paul Golby
    Animal Health and Veterinary Laboratories Agency, Woodham Lane, New Haw Addlestone, Surrey KT15 3NB, UK
    BMC Genomics 14:710. 2013
  3. pmc Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
    Simon R Harris
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:413-9, S1. 2012
  4. 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
  5. 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
  6. pmc Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone
    Nicholas J Croucher
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Biol 12:49. 2014
  7. pmc Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes
    Claire Chewapreecha
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Genet 10:e1004547. 2014
  8. doi request reprint Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
    Vanessa K Wong
    1 Wellcome Trust Sanger Institute, Hinxton, UK 2 Department of Microbiology, Addenbrooke s Hospital, Cambridge University Hospitals National Health Service NHS Foundation Trust, Cambridge, UK
    Nat Genet 47:632-9. 2015
  9. doi request reprint Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA
    Helena M B Seth-Smith
    1 Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK 2
    Nat Protoc 8:2404-12. 2013
  10. pmc BamView: visualizing and interpretation of next-generation sequencing read alignments
    Tim Carver
    Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Brief Bioinform 14:203-12. 2013

Detail Information

Publications31

  1. pmc Comparative genome analysis of Wolbachia strain wAu
    Elizabeth R Sutton
    Department of Zoology and Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
    BMC Genomics 15:928. 2014
    ..Genome sequencing and comparison with CI-inducing related strain wMel was undertaken in order to better understand the molecular basis of the phenotype...
  2. pmc Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression
    Paul Golby
    Animal Health and Veterinary Laboratories Agency, Woodham Lane, New Haw Addlestone, Surrey KT15 3NB, UK
    BMC Genomics 14:710. 2013
    ..To understand the underlying genetic changes that may be responsible for this evolution, we performed a comprehensive genome-level analyses of 4 M. bovis strains that encompass the main molecular types of the pathogen circulating in GB...
  3. pmc Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
    Simon R Harris
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:413-9, S1. 2012
    ..We used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b...
  4. 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...
  5. 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...
  6. pmc Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone
    Nicholas J Croucher
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    BMC Biol 12:49. 2014
    ....
  7. pmc Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes
    Claire Chewapreecha
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Genet 10:e1004547. 2014
    ..Identification of single nucleotide polymorphisms underlying resistance will be essential for future use of genome sequencing to predict antibiotic sensitivity in clinical microbiology. ..
  8. doi request reprint Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
    Vanessa K Wong
    1 Wellcome Trust Sanger Institute, Hinxton, UK 2 Department of Microbiology, Addenbrooke s Hospital, Cambridge University Hospitals National Health Service NHS Foundation Trust, Cambridge, UK
    Nat Genet 47:632-9. 2015
    ..This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species. ..
  9. doi request reprint Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA
    Helena M B Seth-Smith
    1 Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK 2
    Nat Protoc 8:2404-12. 2013
    ....
  10. pmc BamView: visualizing and interpretation of next-generation sequencing read alignments
    Tim Carver
    Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Brief Bioinform 14:203-12. 2013
    ..The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user...
  11. pmc Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
    Helena M B Seth-Smith
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 23:855-66. 2013
    ..This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern...
  12. pmc Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
    Nicholas J Croucher
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK Center for Communicable Disease Dynamics, Harvard School of Public Health, 677 Longwood Avenue, Boston, MA 02115, USA Department of Infectious Disease Epidemiology, Imperial College London, St Mary s Campus, Norfolk Place, London W2 1PG, UK
    Nucleic Acids Res 43:e15. 2015
    ..The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X. ..
  13. pmc Emergent and evolving antimicrobial resistance cassettes in community-associated fusidic acid and meticillin-resistant Staphylococcus aureus
    Matthew J Ellington
    Public Health England, Microbiology Services Division, Addenbrooke s Hospital, Hills Road, Cambridge CB2 0QW, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK Electronic address
    Int J Antimicrob Agents 45:477-84. 2015
    ..The development of chimeric cassettes that confer dual resistance to β-lactams and fusidic acid demonstrates that the genetics underpinning resistance in community-associated MRSA are evolving. ..
  14. pmc Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?
    M Estee Torok
    Department of Medicine, University of Cambridge, Cambridge, UK Department of Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK
    J Antimicrob Chemother 69:2238-45. 2014
    ..This may not be the case for healthcare-associated infections such as methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia...
  15. pmc Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection
    Nicholas J Croucher
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
    PLoS Genet 9:e1003868. 2013
    ..This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype. ..
  16. 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...
  17. pmc Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa
    Chinyere K Okoro
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 9:e0003611. 2015
    ..These data define phenotypes that distinguish ST313 isolates from other S. Typhimurium and may represent adaptation to a distinct pathogenesis and lifestyle linked to an-immuno-compromised human population. ..
  18. pmc Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape
    Nicholas J Croucher
    Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MassachusettsPathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Genome Biol Evol 6:1589-602. 2014
    ..The subsequent competition between these mutants makes this phenomenon difficult to detect without deep sampling of individual lineages. ..
  19. pmc Dense genomic sampling identifies highways of pneumococcal recombination
    Claire Chewapreecha
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 46:305-9. 2014
    ..These findings advance understanding of pneumococcal population dynamics and provide information for the design of future intervention strategies. ..
  20. pmc Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC
    Ewan M Harrison
    Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
    EMBO Mol Med 5:509-15. 2013
    ..This study demonstrates that mecC-MRSA ST130 isolates are capable of transmission between animals and humans, and underscores the potential of WGS in epidemiological investigations and source tracking of bacterial infections...
  21. pmc Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa
    Chinyere K Okoro
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:1215-21. 2012
    ....
  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 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
    Araceli Lamelas
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    MBio 5:e01974-14. 2014
    ..These results have major implications for the design of next-generation protein-based subunit vaccines...
  24. pmc A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    Michael A Quail
    Wellcome Trust Sanger Institute, Hinxton, UK
    BMC Genomics 13:341. 2012
    ..3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy...
  25. pmc Emergence and global spread of epidemic healthcare-associated Clostridium difficile
    Miao He
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 45:109-13. 2013
    ..Our analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system...
  26. 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
    ....
  27. pmc Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae
    Helena M B Seth-Smith
    Pathogen Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Bacteriol 194:1494-504. 2012
    ..We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae...
  28. pmc Genome sequence of the zoonotic pathogen Chlamydophila psittaci
    Helena M B Seth-Smith
    Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Bacteriol 193:1282-3. 2011
    ..A comparison with previously sequenced Chlamydophila genomes shows that, as in other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The C. psittaci plasmid was also sequenced...
  29. pmc Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study
    Josephine M Bryant
    Wellcome Trust Sanger Institute, Hinxton, UK
    Lancet Respir Med 1:786-92. 2013
    ..We used whole-genome sequencing-which is more accurate than conventional typing used to date-to assess the frequency of recurrence and to gain insight into the biological basis of re-infection...
  30. pmc Evidence for several waves of global transmission in the seventh cholera pandemic
    Ankur Mutreja
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 477:462-5. 2011
    ..Additionally, we show how the acquisition of the SXT family of antibiotic resistance elements has shaped pandemic spread, and show that this family was first acquired at least ten years before its discovery in V. cholerae...
  31. pmc Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
    Tim Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 28:464-9. 2012
    ....