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UGT C. trachomatis genome backbones, in which loci that encode immunodominant surface proteins (ompA and pmpEFGH) have been replaced by those characteristic of classical ocular isolates.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.
Highlights
Chlamydia trachomatis causes sexually transmitted infections and the blinding disease trachoma
OmpA genotypes A, B, Ba and C are associated with trachoma, genotypes D-K associated with non-invasive urogenital tract (UGT) infections, and genotypes L1-L3 and L2b associated with invasive infections and lymphogranuloma venerum (LGV)
Recent wholegenome sequence-based studies have shown that recombination events mean that ompA sequence is not a reliable phylogenetic marker across the species, isolates with ompA sequences that define the trachoma ompA genotypes all fall within a single clade of the C. trachomatis phylogenetic tree that shares a distant common ancestor with one of the two UGT lineages[8,9,10]
Summary
Chlamydia trachomatis causes sexually transmitted infections and the blinding disease trachoma. Recent wholegenome sequence-based studies have shown that recombination events mean that ompA sequence is not a reliable phylogenetic marker across the species, isolates with ompA sequences that define the trachoma ompA genotypes all fall within a single clade of the C. trachomatis phylogenetic tree that shares a distant common ancestor with one of the two UGT lineages[8,9,10]. On the basis of genome-wide orthologous single-nucleotide polymorphisms (SNPs), the Australian isolates are not descended from the most common ancestor of the classical ocular clade, but rather are close relatives of urogenital isolates This impacts current models regarding C. trachomatis evolutionary history and determinants of anatomical tropism as well as having implication for our attempts to eradicate trachoma
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