Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages

Abstract

Chlamydia trachomatis causes sexually transmitted infections and the blinding disease trachoma. Current data on C. trachomatis phylogeny show that there is only a single trachoma-causing clade, which is distinct from the lineages causing urogenital tract (UGT) and lymphogranuloma venerum diseases. Here we report the whole-genome sequences of ocular C. trachomatis isolates obtained from young children with clinical signs of trachoma in a trachoma endemic region of northern Australia. The isolates form two lineages that fall outside the classical trachoma lineage, instead being placed within UGT clades of the C. trachomatis phylogenetic tree. The Australian trachoma isolates appear to be recombinants with UGT C. trachomatis genome backbones, in which loci that encode immunodominant surface proteins (ompA and pmpEFGH) have been replaced by those characteristic of classical ocular isolates. This suggests that ocular tropism and association with trachoma are functionally associated with some sequence variants of ompA and pmpEFGH.

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

“…S3). Importantly, some of these isolates, which have a urogenital backbone and ocular ompA genes, were associated both with urogenital infections and ocular disease in children up to 9 yr of age, a finding detailed by Andersson et al (2016). We find European isolates that are almost identical, including ompA type, showing that these strains are not geographically isolated.…”

“…Second, ocular disease is today mostly understood in the context of the ocular lineage, which has maintained genetic coherence potentially due to geographical factors. Recent results (Andersson et al 2016), included here, indicate that the trachoma lineage is not the only source for ocular disease and that this disease may be more ancient and genetically diverse than the ocular lineage alone. Finally, the expansion of genotype E, currently the most prevalent genotype, may be due to increased fitness at or around ompA, preventing recombinations being fixed in this region, being simply a stochastic increase, or being a combination of the two.…”

“…This limited range reflects the fact that most control programs do not routinely collect samples, so our sampling is largely limited to the areas that have active research projects; therefore, we are limited to analyzing small pockets of genetic variation for this disease. A recent study investigating trachoma in the Aboriginal population of Australia showed that isolates with genotypes B, Ba, and C were found outside the ocular lineage and were associated with ocular disease (Andersson et al 2016), as indicated in Supplemental Figure S3. Within this study, we find isolates with the same genomic backbone, including genotype, as those from Australia in urogenital samples from Europe (Supplemental Fig.…”

“…C. trachomatis comprises a ∼1-Mb chromosome and ∼7-kb plasmid (Stephens et al 1998). The species phylogeny consists of four deeply branching lineages that are strongly, but not exclusively, associated with site of infection (Joseph et al 2011;Borges et al 2012;Harris et al 2012;Andersson et al 2016).…”

Survey, Culture, and Genome Analysis of Ocular Chlamydia trachomatis in Tibetan Boarding Primary Schools in Qinghai Province, China

“…Several putative tropism loci relating with respect to ocular or UGT infections have been previously described, such as ompA (Andersson et al, 2016), the trp operon (Caldwell et al, 2003), tarp (Lutter et al, 2010), pmp (Carlson et al, 2005; Andersson et al, 2016), cytotoxin (Carlson et al, 2004), and the plasmid (Seth-Smith et al, 2009). The sequence of QH111L suggests that this isolate is a classical ocular strain with UGT-type features in pmpC , the plasmid, and the plasmid-regulated CT049 gene.…”