Nicholas R Thomson

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. doi request reprint Chlamydia trachomatis: small genome, big challenges
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Cambridge, UK
    Future Microbiol 5:555-61. 2010
  2. 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
  3. 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
  4. 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
  5. ncbi request reprint Comparative genome analyses of the pathogenic Yersiniae based on the genome sequence of Yersinia enterocolitica strain 8081
    Nicholas R Thomson
    The Pathogen Sequencing Unit, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Cambridge, UK
    Adv Exp Med Biol 603:2-16. 2007
  6. pmc Studying bacterial transcriptomes using RNA-seq
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
    Curr Opin Microbiol 13:619-24. 2010
  7. 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
  8. pmc Salmonella bongori provides insights into the evolution of the Salmonellae
    Maria Fookes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 7:e1002191. 2011
  9. pmc Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux
    Nicola K Petty
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 7:e1002018. 2011
  10. pmc Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi
    Christina Bronowski
    Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
    PLoS Negl Trop Dis 7:e2557. 2013

Detail Information

Publications72

  1. doi request reprint Chlamydia trachomatis: small genome, big challenges
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Cambridge, UK
    Future Microbiol 5:555-61. 2010
    ..Here we present a review of what is currently known about the genomics of C. trachomatis and discuss the usefulness of molecular typing systems and the prospects of developing a pan-chlamydial genome resource...
  2. 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...
  3. 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
    ....
  4. 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)...
  5. ncbi request reprint Comparative genome analyses of the pathogenic Yersiniae based on the genome sequence of Yersinia enterocolitica strain 8081
    Nicholas R Thomson
    The Pathogen Sequencing Unit, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Cambridge, UK
    Adv Exp Med Biol 603:2-16. 2007
    ..enterocolitica gene functions and important insights into the intra-species differences between the high, low and non-pathogenic Y. enterocolitica biotypes...
  6. pmc Studying bacterial transcriptomes using RNA-seq
    Nicholas J Croucher
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
    Curr Opin Microbiol 13:619-24. 2010
    ....
  7. 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...
  8. pmc Salmonella bongori provides insights into the evolution of the Salmonellae
    Maria Fookes
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 7:e1002191. 2011
    ..This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC...
  9. pmc Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux
    Nicola K Petty
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 7:e1002018. 2011
    ..We draw parallels with the evolution of other bacterial pathogens and conclude that C. rodentium is a recently evolved pathogen that may have emerged alongside the development of inbred mice as a model for human disease...
  10. pmc Genomic characterisation of invasive non-typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans isolates from Malawi
    Christina Bronowski
    Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
    PLoS Negl Trop Dis 7:e2557. 2013
    ..Salmonella enterica serovar Bovismorbificans was a common serovar in Malawi between 1997 and 2004...
  11. pmc Comparative genomics of Shiga toxin encoding bacteriophages
    Darren L Smith
    Microbiology Research Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
    BMC Genomics 13:311. 2012
    ....
  12. pmc Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids
    Bruce Humphrey
    Bristol Centre for Antimicrobial Research, Department of Cellular and Molecular Medicine, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
    BMC Microbiol 12:53. 2012
    ....
  13. 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...
  14. 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...
  15. pmc Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates
    Laura Betancor
    Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Universidad de la Republica, Montevideo, Uruguay
    BMC Microbiol 9:237. 2009
    ..In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay...
  16. pmc Analysis of the role of 13 major fimbrial subunits in colonisation of the chicken intestines by Salmonella enterica serovar Enteritidis reveals a role for a novel locus
    Debra J Clayton
    Division of Microbiology, Institute for Animal Health, Compton, Berkshire, UK
    BMC Microbiol 8:228. 2008
    ..Here we report the first systematic analysis of each chromosomally-encoded major fimbrial subunit of S. Enteritidis in intestinal colonisation of chickens...
  17. 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...
  18. 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...
  19. pmc Evidence for a lineage of virulent bacteriophages that target Campylobacter
    Andrew R Timms
    Division of Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
    BMC Genomics 11:214. 2010
    ..Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism...
  20. 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...
  21. 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...
  22. pmc Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 18:1624-37. 2008
    ..Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica...
  23. pmc The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Genet 2:e206. 2006
    ..Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens...
  24. ncbi request reprint The role of prophage-like elements in the diversity of Salmonella enterica serovars
    Nicholas Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    J Mol Biol 339:279-300. 2004
    ..Lysogenic bacteriophages therefore play a crucial role in the generation of genetic diversity within S.enterica...
  25. pmc Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates
    Nicholas R Thomson
    The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 18:161-71. 2008
    ..We have used new sequencing technologies to show that the recent clinical LGV isolate causing proctitis is unlikely to be a newly emerged strain but is most probably an old strain with relatively new clinical manifestations...
  26. 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...
  27. pmc Characterization of the genomes of a diverse collection of Salmonella enterica serovar Typhimurium definitive phage type 104
    Fiona J Cooke
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    J Bacteriol 190:8155-62. 2008
    ..Thus, here the nature of variation in different Salmonella serovar Typhimurium DT104 isolates is further defined at the gene and whole-genome levels, illustrating how this phage type evolves over time...
  28. 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...
  29. 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...
  30. 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...
  31. pmc A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
    Timothy T Perkins
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    PLoS Genet 5:e1000569. 2009
    ..Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome...
  32. pmc A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407
    Lisa C Crossman
    The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
    J Bacteriol 192:5822-31. 2010
    ..This study provides a genetic context for the vast amount of experimental and epidemiological data that have been published...
  33. pmc The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli
    Nicola K Petty
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    J Bacteriol 192:525-38. 2010
    ..rodentium and EPEC/EHEC have converged on a common host infection strategy through access to a common pool of mobile DNA and that C. rodentium has lost gene functions associated with a previous pathogenic niche...
  34. pmc Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
    Robert A Kingsley
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Cambridge, United Kingdom
    Genome Res 19:2279-87. 2009
    ..Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field...
  35. ncbi request reprint The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
    Mohammed Sebaihia
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Nat Genet 38:779-86. 2006
    ..The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism...
  36. 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...
  37. pmc Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar
    Robert A Kingsley
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    MBio 4:e00565-13. 2013
    ..Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage...
  38. pmc Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    J Bacteriol 189:4257-64. 2007
    ..Our data show that these serovar Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and have acquired similar mobile elements encoding antibiotic resistance genes in past decades...
  39. pmc Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa
    Craig Winstanley
    Division of Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool L69 3GA, United Kingdom
    Genome Res 19:12-23. 2009
    ..This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes...
  40. pmc Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever
    Minh Duy Phan
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    Antimicrob Agents Chemother 53:716-27. 2009
    ..We propose that antibiotic selection acts to maintain resistance genes on the plasmid, but there is also competition between plasmids encoding the same resistance phenotype...
  41. pmc Molecular characterization of the Salmonella enterica serovar Typhi Vi-typing bacteriophage E1
    Derek Pickard
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    J Bacteriol 190:2580-7. 2008
    ..The genome of the Vi phage E1 is significantly related to other bacteriophages belonging to the same serovar Typhi phage-typing set, and we demonstrate a role for phage DNA modification in determining host specificity...
  42. 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...
  43. 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
    ....
  44. ncbi request reprint Shrinking genomics
    Nicholas R Thomson
    Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Rev Microbiol 2:11. 2004
    ..N. equitans seems to be the coelacanth of the microbial world--it has been assigned to a new phylum and represents a primitive form of prokaroytic life...
  45. 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
  46. 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...
  47. 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...
  48. ncbi request reprint All walks of life
    Nicholas R Thomson
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Trends Microbiol 11:159-60. 2003
  49. pmc Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042
    Roy R Chaudhuri
    Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
    PLoS ONE 5:e8801. 2010
    ..as a cause of bacterial-mediated diarrhea. Furthermore, enteroaggregative E. coli are a predominant cause of persistent diarrhea in the developing world where infection has been associated with malnourishment and growth retardation...
  50. pmc 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
    Mohammed Sebaihia
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
    J Bacteriol 188:6002-15. 2006
    ..A number of putative iron-regulated outer membrane proteins were predicted from the sequence, and this regulation was confirmed experimentally for five of these...
  51. 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...
  52. ncbi request reprint Chalk and cheese
    Lisa Crossman
    Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Rev Microbiol 2:528-9. 2004
  53. pmc Antagonistic coevolution accelerates molecular evolution
    Steve Paterson
    School of Biological Sciences, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
    Nature 464:275-8. 2010
    ..These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species...
  54. 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...
  55. ncbi request reprint The building blocks of pathogenicity
    Nicholas R Thomson
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Trends Microbiol 11:66-7. 2003
  56. doi request reprint Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians
    Helena M B Seth-Smith
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Curr Opin Infect Dis 26:90-8. 2013
    ..Although genome analysis of bacterial sexually transmitted infections (STIs) lags far behind that of many other bacterial pathogens, genomics can reveal previously inaccessible aspects of pathogen biology...
  57. pmc Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids
    Carlos Revilla
    Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria CSIC IDICAN, C Herrera Oria s n, 39011 Santander, Spain
    Antimicrob Agents Chemother 52:1472-80. 2008
    ....
  58. pmc Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility
    Melanie M Pearson
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Bacteriol 190:4027-37. 2008
    ....
  59. pmc The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number
    Nicola E Collins
    Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
    Proc Natl Acad Sci U S A 102:838-43. 2005
    ..Rather then being the result of the reductive evolution seen in other intracellular bacteria, these pseudogenes appear to be the product of ongoing sequence duplication events...
  60. pmc The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates
    David A Rasko
    Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201, USA
    J Bacteriol 190:6881-93. 2008
    ..This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens...
  61. doi request reprint Vive la différence
    Nicholas R Thomson
    Nat Rev Microbiol 6:502-3. 2008
  62. ncbi request reprint The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics
    Matthew W Gilmour
    Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alta, Canada T6G 2R3
    Plasmid 52:182-202. 2004
    ..The similarity to a diverse set of bacterial sequences highlights the ability of horizontally transferable DNA elements to acquire and disseminate genetic traits through the bacterial gene pool...
  63. pmc A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?
    Xavier Didelot
    Department of Statistics, University of Oxford, Oxford OX1 3SY, United Kingdom
    Genome Res 17:61-8. 2007
    ..We propose that recombination between Typhi and Paratyphi A has allowed the exchange of gene variants that are important for their adaptation to their common ecological niche, the human host...
  64. ncbi request reprint Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli
    Edward G Dudley
    Center for Vaccine Development, University of Maryland School of Medicine, 685 W Baltimore St, Baltimore, MD 21201, USA
    Mol Microbiol 61:1267-82. 2006
    ..These data support the hypothesis that AggR is a global regulator of EAEC virulence determinants, and builds on the hypothesis that T6SS is an importance mediator of pathogenesis...
  65. ncbi request reprint Livelihood hazards
    Mohammed Sebaihia
    Nat Rev Microbiol 3:278-9. 2005
  66. ncbi request reprint Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate
    Vinayak Kapatral
    Integrated Genomics, Inc, 2201 West Campbell Park Dr, Chicago, IL 60612, USA
    Microbiology 150:2289-300. 2004
    ..These data are consistent with the hypothesis that temperature regulation of flagella genes might be mediated by the flagella-specific sigma factor FliA and not the flagella master regulator FlhD/FlhC...
  67. pmc Microevolution and history of the plague bacillus, Yersinia pestis
    Mark Achtman
    Department of Molecular Biology, Max Planck Institut für Infektionsbiologie, D 10117 Berlin, Germany
    Proc Natl Acad Sci U S A 101:17837-42. 2004
    ..pestis inferred here is compatible with the dates of historical pandemic plague. However, it is premature to infer an association between any modern molecular grouping and a particular pandemic wave that occurred before the 20th century...
  68. ncbi request reprint Microbial genomics: spot the difference. .
    Nicholas R Thomson
    Trends Microbiol 10:489-90. 2002
  69. pmc Escherichia coli K-12: a cooperatively developed annotation snapshot--2005
    Monica Riley
    Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
    Nucleic Acids Res 34:1-9. 2006
    ..Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles...
  70. ncbi request reprint Carbapenem antibiotic biosynthesis in Erwinia carotovora is regulated by physiological and genetic factors modulating the quorum sensing-dependent control pathway
    Simon J McGowan
    Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
    Mol Microbiol 55:526-45. 2005
    ..The nature of the carbon source and the temperature of growth influence carbapenem production by modulating the level of the OHHL signalling molecule, and thereby physiologically fine-tune the quorum sensing regulatory system...
  71. pmc The neglected role of antibody in protection against bacteremia caused by nontyphoidal strains of Salmonella in African children
    Calman A MacLennan
    Malawi Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
    J Clin Invest 118:1553-62. 2008
    ..This finding and the age-incidence of NTS bacteremia suggest that antibody protects against NTS bacteremia and support the development of vaccines against NTS that induce protective antibody...