| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Chlamydia pecorum </it>is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. <it>C. pecorum </it>strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the <it>omp</it>A gene remains the most widely-used target in <it>C. pecorum </it>typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the <it>omp</it>A gene locus is not congruent with the phylogeny of the <it>C. pecorum </it>genome. Using the recently sequenced <it>C. pecorum </it>genome sequence (E58), we analysed 10 genes, including <it>omp</it>A, to evaluate the use of <it>omp</it>A as a molecular marker in the study of koala <it>C. pecorum </it>genetic diversity.</p> <p>Results</p> <p>Three genes (<it>inc</it>A, ORF663, <it>tar</it>P) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with <it>omp</it>A, to genotype 24 <it>C. pecorum </it>PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. <it>Omp</it>A and <it>inc</it>A were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the <it>tar</it>P and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala <it>C. pecorum</it>. Furthermore, the concatenation of <it>omp</it>A, <it>inc</it>A and ORF663 sequences highlighted the monophyletic nature of koala <it>C. pecorum </it>infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts.</p> <p>Conclusions</p> <p>While the continued use of <it>omp</it>A as a fine-detailed molecular marker for epidemiological analysis appears justified, the <it>tar</it>P and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the <it>C. pecorum </it>intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of <it>C. pecorum </it>infections in the koala and other animal species.</p>
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