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Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.ORCID iD: 0000-0003-1512-6194
Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, United Kingdom.ORCID iD: 0000-0002-4938-1620
Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.ORCID iD: 0000-0001-7101-6649
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2012 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 44, no 4, 413-419 p.Article 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, 413-419 p.
National Category
Infectious Medicine Medical Genetics
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URN: urn:nbn:se:oru:diva-58676DOI: 10.1038/ng.2214ISI: 000302130600015PubMedID: 22406642Scopus ID: 2-s2.0-84859326308OAI: oai:DiVA.org:oru-58676DiVA: diva2:1121661
Funder
Wellcome trust, 098051 080348
Available from: 2017-07-12 Created: 2017-07-12 Last updated: 2017-09-13Bibliographically approved

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Unemo, Magnus

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Harris, Simon R.Clarke, Ian N.Solomon, Anthony W.Mabey, DavidUnemo, Magnusde Vries, Henry J. C.Bébéar, Cecile M.Parkhill, Julian
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