title: Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.
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.
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. sh16@sanger.ac.uk
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.forename: Ian N
authors.initials: IN
authors.lastname: Clarke
authors.forename: Helena M B
authors.initials: HM
authors.lastname: Seth-Smith
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Solomon
authors.forename: Lesley T
authors.initials: LT
authors.lastname: Cutcliffe
authors.forename: Peter
authors.initials: P
authors.lastname: Marsh
authors.forename: Rachel J
authors.initials: RJ
authors.lastname: Skilton
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Holland
authors.forename: David
authors.initials: D
authors.lastname: Mabey
authors.forename: Rosanna W
authors.initials: RW
authors.lastname: Peeling
authors.forename: David A
authors.initials: DA
authors.lastname: Lewis
authors.forename: Brian G
authors.initials: BG
authors.lastname: Spratt
authors.forename: Magnus
authors.initials: M
authors.lastname: Unemo
authors.forename: Kenneth
authors.initials: K
authors.lastname: Persson
authors.forename: Carina
authors.initials: C
authors.lastname: Bjartling
authors.forename: Robert
authors.initials: R
authors.lastname: Brunham
authors.forename: Henry J C
authors.initials: HJ
authors.lastname: de Vries
authors.forename: Servaas A
authors.initials: SA
authors.lastname: Morré
authors.forename: Arjen
authors.initials: A
authors.lastname: Speksnijder
authors.forename: Cécile M
authors.initials: CM
authors.lastname: Bébéar
authors.forename: Maïté
authors.initials: M
authors.lastname: Clerc
authors.forename: Bertille
authors.initials: B
authors.lastname: de Barbeyrac
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D001483:Base Sequence; D002690:Chlamydia Infections / Q000235:genetics*; D002692:Chlamydia trachomatis / Q000145:classification* / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D006801:Humans; D008219:Lymphogranuloma Venereum / Q000235:genetics / Q000382:microbiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010957:Plasmids; D020641:Polymorphism, Single Nucleotide; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014141:Trachoma / Q000382:microbiology
chemical_list: D001425:Bacterial Outer Membrane Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; C078167:OMPA outer membrane proteins