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

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Harris, Simon R 
Clarke, Ian N 
Seth-Smith, Helena MB 
Solomon, Anthony W 
Cutcliffe, Lesley T 

Abstract

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.

Description

Keywords

Bacterial Outer Membrane Proteins, Base Sequence, Chlamydia Infections, Chlamydia trachomatis, DNA, Bacterial, Gene Transfer, Horizontal, Genome, Bacterial, Humans, Lymphogranuloma Venereum, Molecular Sequence Data, Phylogeny, Plasmids, Polymorphism, Single Nucleotide, RNA, Ribosomal, 16S, Recombination, Genetic, Sequence Analysis, DNA, Trachoma

Journal Title

Nat Genet

Conference Name

Journal ISSN

1061-4036
1546-1718

Volume Title

44

Publisher

Springer Science and Business Media LLC

Rights

All rights reserved