Predicting phenotype and emerging strains among Chlamydia trachomatis infections

Abstract

Chlamydia trachomatis is a global cause of blinding trachoma and sexually transmitted infections (STIs). We used comparative genomics of the family Chlamydiaceae to select conserved housekeeping genes for C. trachomatis multilocus sequencing, characterizing 19 reference and 68 clinical isolates from 6 continental/subcontinental regions. There were 44 sequence types (ST). Identical STs for STI isolates were recovered from different regions, whereas STs for trachoma isolates were restricted by continent. Twenty-nine of 52 alleles had nonuniform distributions of frequencies across regions (p<0.001). Phylogenetic analysis showed 3 disease clusters: invasive lymphogranuloma venereum strains, globally prevalent noninvasive STI strains (ompA genotypes D/Da, E, and F), and nonprevalent STI strains with a trachoma subcluster. Recombinant strains were observed among STI clusters. Single nucleotide polymorphisms (SNPs) were predictive of disease specificity. Multilocus and SNP typing can now be used to detect diverse and emerging C. trachomatis strains for epidemiologic and evolutionary studies of trachoma and STI populations worldwide.

Figure 1

Comparison of 14 housekeeping genes among genome sequences of 4 Chlamydiaceae species and 7 strains. Circle 1, genes on forward Chlamydia trachomatis strand, color coded by role category; Circle 2, genes on reverse C. trachomatis strand; Circle 3, multilocus sequence typing (MLST) candidates, C. trachomatis; Circle 4, MLST candidates, C. pneumoniae AR39; Circle 5, MLST candidates, C. caviae (GPIC); Circle 6, MLST candidates, C. muridarum (MoPn). Colors in circles 3, 4, 5 and 6 are consistent for each gene across genomes i.e., “blue” gene in each circle is ortholog in that genome for “blue” gene in C. trachomatis. Blue, glyA, serine hydroxymethyl-transferase; red, tryptophanyl-tRNA synthetase; yellow, mdhC, malate dehydrogenase; green, V-type ATPase, subunit A; cyan, pdhA, pyruvate dehydrogenase; black, GTP-binding protein lepa; magenta, transcription termination factor rho; brown, yhbG, probable ABC transporter ATP-binding protein; orange, pykF, pyruvate kinase; olive green, conserved hypothetical protein; gray, acetyl-CoA carboxylase beta subunit; pink, threonyl-tRNA synthetase; violet, lysS, lysyl-tRNA synthetase; light green, leuS, leucyl-tRNA synthetase. Those denoted in boldface above were used for C. trachomatis MLST. ompA gene location is shown for C. trachomatis (dark green).

Figure 2

eBURST population snapshot for Chlamydia trachomatis isolates. Sequence types (STs) that are linked differ at single multilocus sequence typing locus and represent clonal complexes. Strains in the same clonal complexes are likely descended from the same recent ancestor. Each circle represents a ST. An ST in blue is most likely the primary founder of the clonal complex; STs in red are subgroup founders. The number of isolates of each ST is represented by the area of the circle. Clonal complex A (CC-A) for trachoma strains; CC-B, noninvasive, nonprevalent urogenital strains; and CC-C, noninvasive, globally prevalent urogenital strains. The eBURST report is shown in the Technical Appendix.

Figure 3

Minimum evolution tree. The tree was constructed using the matrix of pairwise differences between the 87 concatenated sequences for the 7 loci using maximum composite likelihood method for estimating genetic distances. Numbers are bootstrap values (1,000 replicates) >70%. Lavender, invasive lymphogranuloma venereum (LGV); gold, noninvasive, nonprevalent sexually transmitted infection (STI) strains; red, trachoma strains; blue, noninvasive, highly prevalent STI strains; green, putative recombinant stains. Scale bar indicates number of substitutions per site.

Figure 4

Minimum evolution tree for ompA. The tree was constructed using the matrix of pairwise differences between the 87 sequences by using the maximum composite likelihood method for estimating genetic distances. Numbers are bootstrap values (1,000 replicates) >70%. Lavender, invasive lymphogranuloma venereum (LGV); gold, noninvasive, nonprevalent sexually transmitted infection (STI) strains; red, trachoma strains; blue, noninvasive, highly prevalent STI strains; green, putative recombinant stains. Scale bar indicates number of substitutions per site.

Figure 5

SplitsTree obtained by using concatenated sequences of the 7 loci for the 87 isolates. Cluster I, noninvasive, nonprevalent Chlamydia trachomatis strains (gold) with trachoma Subcluster I (red); cluster II, invasive lymphogranuloma venereum (LGV) isolates (purple); and cluster III, noninvasive globally prevalent sexually transmitted infection (STI) strains (blue). Isolates colored green represent putative recombinant strains. Scale bar indicates number of substitutions per site.