Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typingMolecular Microbiology Group, Southampton General Hospital, University Medical School, Southampton, United Kingdom.
Health Protection Agency, Public Health Laboratory Southampton, Southampton General Hospital, Southampton, United Kingdom.
Molecular Microbiology Group, Southampton General Hospital, University Medical School, Southampton, United Kingdom.
Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Sexually Transmitted Infections Reference Centre, National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa; Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Department of Infectious Disease Epidemiology, St. Mary's Hospital Campus, Imperial College, London, United Kingdom.
Department of Laboratory Medicine, Clinical Microbiology, Malmö University Hospital, Malmö, Sweden.
Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Malmö University Hospital, Malmö, Sweden.
British Columbia Centre for Disease Control, Vancouver BC, Canada.
Department of Medical Microbiology of Infection Prevention, Laboratory of Immunogenetics, Vrije University Medical Center, Amsterdam, Netherlands; Department of Genetics and Cell Biology, Institute of Public Health Genomics, University of Maastricht, Maastricht, Netherlands.
Geneeskundige en Gezondheidsdienst (GGD), Amsterdam, The Netherlands.
Unité Sous Contrat (USC) Mycoplasmal and Chlamydial Infections in Humans, French National Reference Center for Chlamydial Infections, Université de Bordeaux, Bordeaux, France; USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Center for Chlamydial Infections, Institut National de la Recherche Agronomique, Bordeaux, France.
Unité Sous Contrat (USC) Mycoplasmal and Chlamydial Infections in Humans, French National Reference Center for Chlamydial Infections, Université de Bordeaux, Bordeaux, France; USC Mycoplasmal and Chlamydial Infections in Humans, French National Reference Center for Chlamydial Infections, Institut National de la Recherche Agronomique, Bordeaux, France.
Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
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2012 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 44, no 4, p. 413-419Article in journal (Refereed) Published
Abstract [en]
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.
Place, publisher, year, edition, pages
Nature Publishing Group, 2012. Vol. 44, no 4, p. 413-419
National Category
Infectious Medicine Medical Genetics
Identifiers
URN: urn:nbn:se:oru:diva-58676DOI: 10.1038/ng.2214ISI: 000302130600015PubMedID: 22406642Scopus ID: 2-s2.0-84859326308OAI: oai:DiVA.org:oru-58676DiVA, id: diva2:1121661
Funder
Wellcome trust, 098051 0803482017-07-122017-07-122020-12-01Bibliographically approved