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.

Figure 1. Maximum likelihood reconstruction of the phylogeny of C. trachomatis with recombinations removed

(a) C. trachomatis species phylogeny using the chromosomal sequences of 52 genomes after predicted recombinations have been removed using the method described in Croucher et al.. Bootstrap support for nodes on the tree are shown in Supplementary Figure 1. (b) Phylogenetic reconstruction of the C. trachomatis plasmid after predicted recombinations have been removed. Strain names are colored by serotype, see key. Scale bar represents number of SNPs. Plasmid sequences were not available for all strains in a. For comparison, trees without recombination removal are shown in Supplementary Figure 2.

Figure 2. Reconstruction of recombination events on the species phylogeny of C. trachomatis

The top line represents the full chromosome structure of C. trachomatis based on L2/434/BU, with CDSs represented as blue boxes on the relevant coding strand. Numbers indicate position in the genome alignment, beginning at CTL0001 (L2/434/BU accession number AM884176). Each horizontal track represents the chromosome of a strain in the species phylogeny on the left. Blocks shown on the tracks represent the location of received homologous replacements, with their color corresponding to the color of the donor branch on the tree. Tree branches and taxon names are colored by phylogenetic distance, with more similar colors representing more closely related branches. Regions of interest along the genome are highlighted immediately below the recombination tracks. Below this are plots of the density of non-homoplasic SNP sites, homoplasic SNP sites and recombination events, based on a moving window analysis. Window size = 2000bp.

Figure 3. Distribution of SNPs in the ompA gene of C. trachomatis

The top line represents the structure of the ompA gene, showing the location of variable regions (VS1-4, red blocks) and cysteine residues (conserved in blue, non-conserved in orange). On the left is the species phylogeny of C. trachomatis, with strain names colored by serotype, see key. Adjacent to each strain name is a track with a background color based on the serotype of the corresponding strain. Colored vertical lines along the tracks represent bases that differ from the ancestral sequence: grey=non-homoplasic change; colored lines represent homoplasic bases: red=A, blue=T, green=C, orange=G. The pattern of lines provide a barcode of ompA similarity between strains.