Abstract
Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted diseases worldwide. The Ct Multi Locus Sequence Typing (MLST) scheme is effective in differentiating strain types (ST), deciphering transmission patterns and treatment failure, and identifying recombinant strains. Here, we analyzed 323 reference and clinical samples, including 58 samples from Russia, an area that has not previously been represented in Ct typing schemes, to expand our knowledge of the global diversification of Ct STs. The 323 samples resolved into 84 unique STs, a 3.23 higher typing resolution compared to the gold standard single locus ompA genotyping. Our MLST scheme showed a high discriminatory index, D, of 0.98 (95% CI 0.97–0.99) confirming the validity of this method for typing. Phylogenetic analyses revealed distinct branches for the phenotypic diseases of lymphogranuloma venereum, urethritis and cervicitis, and a sub-branch for ocular trachoma. Consistent with these findings, single nucleotide polymorphisms were identified that significantly correlated with each phenotype. While the overall number of unique STs per region was comparable across geographies, the number of STs was greater for Russia with a significantly higher ST/sample ratio of 0.45 (95% CI: 0.35–0.53) compared to Europe or the Americas (p < 0.009), which may reflect a higher level of sexual mixing with the introduction of STs from other regions and/or reassortment of alleles. Four STs were found to be significantly associated with a particular geographic region. ST23 [p = 0.032 (95% CI: 1–23)], ST34 [p = 0.019 (95% CI: 1.1–25)]; and ST19 [p = 0.001 (95% CI: 1.7–34.7)] were significantly associated with Netherlands compared to Russia or the Americas, while ST 30 [p = 0.031 (95% CI: 1.1–17.8)] was significantly associated with the Americas. ST19 was significantly associated with Netherlands and Russia compared with the Americans [p = 0.001 (95% CI: 1.7–34.7) and p = 0.006 (95% CI: 1.5–34.6), respectively]. Additionally, recombinant strains were ubiquitous in the data set [106 (32.8%)], although Europe had a significantly higher number than Russia or the Americas (p < 0.04), the majority of which were from Amsterdam [43 (87.8%) of 49)]. The higher number of recombinants in Europe indicates selective pressure and/or adaptive diversification that will require additional studies to elucidate.
Highlights
The modern pathogenic Chlamydiaceae family has a rich evolutionary history, diverging from environmental Chlamydiales approximately seven million years ago (Horn et al, 2004)
The characteristics of the alleles for each gene locus are shown in Supplementary Table 2
The phylogenetic relationships were initially evaluated by eBURST, which revealed clonal clusters (CC) similar to what we reported previously (Figure 1) (Dean et al, 2009; Batteiger et al, 2014) but with the addition of an LGV cluster
Summary
The modern pathogenic Chlamydiaceae family has a rich evolutionary history, diverging from environmental Chlamydiales approximately seven million years ago (Horn et al, 2004). The serovars are designated A through K, Ba, Da, Ia, Ja, and L1−3, and L2a while the ompA genotypes or strains are denoted by the same or by a number or letter after the conventional serovar name (e.g., D1; Ga) for new genotypes (Batteiger et al, 2014) These strains are responsible for ocular, urogenital and rectal infections. Our MLST scheme employs seven highly conserved housekeeping genes and successfully resolves reference and clinical Ct samples into LGV, trachoma, non-prevalent non-invasive urogenital, and prevalent non-invasive urogenital clonal complexes representing the respective diseases in addition to revealing evidence for recombination (Dean et al, 2009; Batteiger et al, 2014). Petersburg, Russia, a region that had not previously been evaluated by MLST
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
