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Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

Harris, Simon R., Clarke, I., Seth-Smith, Helena M.B., Solomon, Anthony W., Cutcliffe, Lesley T., Marsh, Peter, Skilton, Rachel J., Holland, Martin J., Mabey, David., Peeling, Rosanna W., Lewis, David A., Spratt, Brian G., Unemo, Magnus, Persson, Kenneth, Bjartling, Carina, Brunham, Robert, de Vries, Henry J.C., Morré, Servaas A., Speksnijder, Arjen, Bébéar, Cécile M., Clerc, Maïté, de Barbeyrac, Bertille, Parkhill, Julian and Thomson, Nicholas R. (2012) Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing Nature Genetics, 44, (4), pp. 413-419. (doi:10.1038/ng.2214). (PMID:22406642).

Record type: Article


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.

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Published date: 11 March 2012
Organisations: Clinical & Experimental Sciences


Local EPrints ID: 337341
ISSN: 1061-4036
PURE UUID: 32e88466-612b-4716-92ae-56118270d04e
ORCID for I. Clarke: ORCID iD

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Date deposited: 23 Apr 2012 15:46
Last modified: 18 Jul 2017 06:03

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Author: Simon R. Harris
Author: I. Clarke ORCID iD
Author: Helena M.B. Seth-Smith
Author: Anthony W. Solomon
Author: Lesley T. Cutcliffe
Author: Peter Marsh
Author: Rachel J. Skilton
Author: Martin J. Holland
Author: David. Mabey
Author: Rosanna W. Peeling
Author: David A. Lewis
Author: Brian G. Spratt
Author: Magnus Unemo
Author: Kenneth Persson
Author: Carina Bjartling
Author: Robert Brunham
Author: Henry J.C. de Vries
Author: Servaas A. Morré
Author: Arjen Speksnijder
Author: Cécile M. Bébéar
Author: Maïté Clerc
Author: Bertille de Barbeyrac
Author: Julian Parkhill
Author: Nicholas R. Thomson

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