1. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
- Author
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Bertille de Barbeyrac, Cécile Bébéar, David A. Lewis, Kenneth Persson, Carina Bjartling, Ian N. Clarke, Nicholas R. Thomson, Maïté Clerc, Martin J. Holland, Rosanna W. Peeling, Robert C. Brunham, Anthony W. Solomon, Henry J. C. de Vries, Peter Marsh, Magnus Unemo, Rachel J. Skilton, Helena M. B. Seth-Smith, David Mabey, Arjen G. C. L. Speksnijder, Simon R. Harris, Lesley T. Cutcliffe, Brian G. Spratt, Julian Parkhill, Servaas A. Morré, RS: CAPHRI School for Public Health and Primary Care, RS: GROW - School for Oncology and Reproduction, Institute for Public Health Genomics, AII - Amsterdam institute for Infection and Immunity, APH - Amsterdam Public Health, Dermatology, The Wellcome Trust Sanger Institute [Cambridge], Molecular Microbiology Group (COMB), University of the Ruykyus, Southampton General Hospital, London School of Hygiene and Tropical Medicine (LSHTM), National Health Laboratory Service, University of the Witwatersrand [Johannesburg] (WITS), Imperial College London, Örebro University Hospital [Örebro, Sweden], Malmö University Hospital, British Columbia Centre for Disease Control [Vancouver] (BCCDC), Vrije universiteit = Free university of Amsterdam [Amsterdam] (VU), Public Health Service of Amsterdam, Maastricht University [Maastricht], Institut National de la Recherche Agronomique (INRA), Université Sciences et Technologies - Bordeaux 1, Wellcome Trust grant numbers 098051 and 080348, Parkhill, Julian [0000-0002-7069-5958], Apollo - University of Cambridge Repository, Medical Microbiology and Infection Prevention, CCA - Immuno-pathogenesis, and VU University Amsterdam
- Subjects
DNA, Bacterial ,Gene Transfer, Horizontal ,[SDV]Life Sciences [q-bio] ,Population ,Molecular Sequence Data ,Chlamydia trachomatis ,Biology ,medicine.disease_cause ,urologic and male genital diseases ,Polymorphism, Single Nucleotide ,Article ,03 medical and health sciences ,Phylogenetics ,RNA, Ribosomal, 16S ,Genetics ,medicine ,Humans ,education ,Phylogeny ,030304 developmental biology ,Genetics & Heredity ,Recombination, Genetic ,Trachoma ,0303 health sciences ,education.field_of_study ,Medical And Health Sciences ,Chlamydia ,Science & Technology ,Phylogenetic tree ,Base Sequence ,030306 microbiology ,Human evolutionary genetics ,Lymphogranuloma venereum ,Sequence Analysis, DNA ,Biological Sciences ,Chlamydia Infections ,medicine.disease ,bacterial infections and mycoses ,female genital diseases and pregnancy complications ,3. Good health ,Lymphogranuloma Venereum ,Life Sciences & Biomedicine ,Genome, Bacterial ,Developmental Biology ,Bacterial Outer Membrane Proteins ,Plasmids - Abstract
International audience; Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections, causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed phylogeny based on whole-genome sequencing of representative strains of C. trachomatis from both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis shows that predicting phylogenetic structure using ompA, which is traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks any true relationships present. We show that in many instances, ompA is a chimera that can be exchanged in part or as a whole both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, which is another key diagnostic target. 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.
- Published
- 2011