Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity

Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naive trachoma-endemic population in Guinea Bissau, West Africa. All sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified twenty-one Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (OR=4.07, p*=0.001) and tarP (OR=0.34, p*=0.009). Eight SNPs associated with disease severity were found in yjfH (rlmB) (OR=0.13, p*=0.037), CTA0273 (OR=0.12, p*=0.027), trmD (OR=0.12, p*=0.032), CTA0744 (OR=0.12, p*=0.041), glgA (OR=0.10, p*=0.026), alaS (OR=0.10, p*=0.032), pmpE (OR=0.08, p*=0.001) and the intergenic region CTA0744-CTA0745 (OR=0.13, p*=0.043). This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct, and the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.