Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States

Abstract

Chlamydia trachomatis is a major cause of ocular and sexually transmitted diseases worldwide. While much of our knowledge about its genetic diversity comes from serotyping or ompA genotyping, no quantitative assessment of genetic diversity within serotypes has been performed. To accomplish this, 507 urogenital samples from a multicenter U.S. study were analyzed by phylogenetic and statistical modeling. No B, Da, or I serotypes were represented. Based on our analyses, all but one previous urogenital B serotype was identified as Ba. This, coupled with the lack of B serotypes in our population, suggests that B has specific tropism for ocular mucosa. We identified a Ba/D recombinant (putative crossover nucleotide 477; P < 0.0001) similar to a B/D mosaic we described previously from an African trachoma patient. Computational analyses of the Ba/D recombinant indicated that upstream changes were less important for tissue tropism than downstream incorporation of the D sequence. Since most serotypes had nonsynonymous/synonymous ratios of <1.0, the major outer membrane protein, encoded by ompA, has many functional constraints and is under purifying selection. Surprisingly, all serotype groups except for J had a unimodal population structure indicating rapid clonal expansion. Of the groups with a unimodal structure, E and Ia and, to a lesser extent, G and K were prevalent, had infrequent incorporation of mutations, and, compared to other groups, had a relatively greater degree of diversifying selection, consistent with a selective sweep of mutations within these groups. Collectively, these data suggest a diverse evolutionary strategy for different serogroups of the organism.

FIG. 1.

Phylogenetic reconstructions for the unique ompA gene sequences in the B seroclass (A), the intermediate seroclass (B), and the C seroclass (C) using the neighbor-joining method. The values at the nodes are the bootstrap confidence levels (BCL) for the interior branch. The BCL represents the percentage of 500 bootstrap resamplings for which the strain to the right was separated from the other strains.

FIG. 2.

Mean Hamming distance within each serotype group based on average Hamming distance between all possible pairs of sequences of similar serotypes. Minimum and maximum values represent lower and upper limits of the 95% CI of the estimate, while the value plotted at the horizontal bar level represents the mean estimate.

FIG. 3.

Mean synonymous (top panel) and nonsynonymous (middle panel) mutation rates, respectively, for serotype groups based on the method of Nei and Gojobori. Minimum and maximum values represent lower and upper limits of the 95% CI of the estimate, while a value plotted at horizontal bar level represents the mean estimate. The bottom panel shows the nonsynonymous/synonymous mutation rate ratio for serotype groups based on the mean estimates shown in the prior two graphs.

FIG. 4.

Population structure of serotype groups in this study based on histogram of Hamming distances between all possible pairs of sequences of similar serotypes. (A) Unimodal structure with shoulder was seen for serotype D, with the main group and shoulder group roughly 99.7% similar. (B) The only serotype group to have a bimodal structure was serotype J, with the two main groups roughly 98.5% similar. (C) Unimodal structure was typical of most serotypes exemplified by serotype E.

FIG. 5.

Phylogenetic reconstructions with a starburst superimposed at the end of the branch corresponding to the appropriate serotype group. Starbursts represent the relative frequency of shared mutations within a serotype group pool as described in Materials and Methods. The radial spoke length is inversely proportional to the frequency of mutations, so that longer spoke lengths correspond to less frequent incorporation of mutations among similar serotype group strains. The location of the radial spoke within a 360° circle was determined by the nucleotide location of the mutation as described in Materials and Methods. The starbursts were each magnified to ×250 in order to discern the radial spoke length and star-like quality of the radial wheel for each serotype group.