Evolution ofChlamydia trachomatisdiversity occurs by widespread interstrain recombination involving hotspots

Abstract

Chlamydia trachomatis is an obligate intracellular bacterium of major public health significance, infecting over one-tenth of the world's population and causing blindness and infertility in millions. Mounting evidence supports recombination as a key source of genetic diversity among free-living bacteria. Previous research shows that intracellular bacteria such as Chlamydiaceae may also undergo recombination but whether this plays a significant evolutionary role has not been determined. Here, we examine multiple loci dispersed throughout the chromosome to determine the extent and significance of recombination among 19 laboratory reference strains and 10 present-day ocular and urogenital clinical isolates using phylogenetic reconstructions, compatibility matrices, and statistically based recombination programs. Recombination is widespread; all clinical isolates are recombinant at multiple loci with no two belonging to the same clonal lineage. Several reference strains show nonconcordant phylogenies across loci; one strain is unambiguously identified as recombinantly derived from other reference strain lineages. Frequent recombination contrasts with a low level of point substitution; novel substitutions relative to reference strains occur less than one per kilobase. Hotspots for recombination are identified downstream from ompA, which encodes the major outer membrane protein. This widespread recombination, unexpected for an intracellular bacterium, explains why strain-typing using one or two genes, such as ompA, does not correlate with clinical phenotypes. Our results do not point to specific events that are responsible for different pathogenicities but, instead, suggest a new approach to dissect the genetic basis for clinical strain pathology with implications for evolution, host cell adaptation, and emergence of new chlamydial diseases.

Interstrain Gene Transfer inChlamydia trachomatisIn Vitro: Mechanism and Significance

“…Since an exchange anywhere in the 143-kb region between the mutant sites would have conferred resistance to both Ofx and Rif to a recombinant, the nonrandomly high concentration of exchanges within the rpoB gene suggests that there is a mechanistic predisposition to recombination rather than selection for doubly resistant recombinants that have exchanges in rpoB. Below we show how this result obtained with our in vitro LGT methodology affects possible interpretations of nonrandomly high concentrations of crossovers ("hot spots") in clinical isolates (see Discussion) (10).…”

“…The reported recombination data indicate that LGT can involve widely separated loci distributed over much or all of the 1.04-Mb C. trachomatis chromosome (10). Sequences resembling insertion sequences (9) and other sequences that were interpreted as recombination "hot spots" (10) have been reported, but LGT mechanisms were not definitely identified. The life cycle impediment to direct experimental investigation of LGT mechanisms was partially removed by our recent use of in vitro methodology to discover…”

“…DNA sequencing of long-established strains (23) and clinical isolates (3,9,10,12) has detected numerous, diverse genetic recombinants possessing alleles of polymorphic loci that were derived from at least two different strains. Traditionally, C. trachomatis strains called "serovars" have been serologically defined by polymorphic variations in the MOMP.…”

A characteristic of polymorphic membrane protein F of Chlamydia trachomatis isolated from male urogenital tracts in Japan

“…As a homosexual male reference group, seven of the male strains obtained from rectums in the current study (Strain numbers: 70, 150, 2923, 6276, 9301, 9768, 11023, 11074, and 11222) that has been reported previously [18], were also used for the study. Furthermore, as female strain groups, eleven of the female strains used in the present study were previously isolated from Sapporo, Japan (Strain designations: nv266, nv283, nv287, nv307, nv381, nv399, nv441, nv417, nv437, nv443, and nv448), as previously reported [19] S-91, 537C-05, S-141, and CS-500-96) had also been previously reported [11,16] (Category: Ref-females). The origins and accession numbers of all of the strains are summarized in Table 1.…”

“…Thus, the surface exposure of the PmpF molecule indicates that it could be strongly subjected to host-selective pressures such as microbial flora [15]. In fact, phylogenetic studies of pmp genes found that among them pmpF exhibited the greatest genetic diversity, both at the nucleotide and amino acid level, among C. trachomatis genital strains [13,16].…”