BACKGROUND: @entity1047 pecorum is a globally recognised pathogen of livestock and @entity34075 . To date, comparative genomics of @entity11292 strains from @entity742 , @entity291 and @entity34075 has revealed that only single nucleotide polymorphisms (SNPs) and a limited number of pseudogenes appear to contribute to the genetic diversity of this pathogen. No chlamydial plasmid has been detected in these strains despite its ubiquitous presence in almost all other chlamydial species. Genomic analyses have not previously included @entity11292 from porcine hosts. We sequenced the genome of three @entity11292 isolates from @entity1707 with differing pathologies in order to re-evaluate the genetic differences and to update the phylogenetic relationships between @entity11292 from each of the hosts. METHODS: Whole genome sequences for the three porcine @entity11292 isolates (L1, L17 and L71) were acquired using @entity11292 -specific sequence capture probes with culture-independent methods, and assembled in CLC Genomics Workbench. The pairwise comparative genomic analyses of 16 @entity1707 , @entity742 , @entity291 and @entity34075 @entity11292 genomes were performed using several bioinformatics platforms, while the phylogenetic analyses of the core @entity11292 genomes were performed with predicted recombination regions removed. Following the detection of a @entity11292 plasmid, a newly developed @entity11292 -specific plasmid PCR screening assay was used to evaluate the plasmid distribution in 227 @entity11292 samples from @entity1707 , @entity742 , @entity291 and @entity34075 hosts. RESULTS: Three porcine @entity11292 genomes were sequenced using @entity11292 -specific sequence capture probes with culture-independent methods. Comparative genomics of the newly sequenced porcine @entity11292 genomes revealed an increased average number of SNP differences (~11 500) between porcine and @entity742 , @entity291 , and @entity34075 @entity11292 strains, compared to previous @entity11292 genome analyses. We also identified a third copy of the chlamydial cytotoxin gene, found only in porcine @entity11292 isolates. Phylogenetic analyses clustered porcine isolates into a distinct clade, highlighting the polyphyletic origin of @entity11292 in livestock. Most surprising, we also discovered a plasmid in the porcine @entity11292 genome. Using this novel @entity11292 plasmid (pCpec) sequence, a) we developed a pCpec screening assay to evaluate the plasmid distribution in @entity11292 from different hosts; and b) to characterise the pCpec sequences from available previously sequenced @entity11292 genome data. pCpec screening showed that the pCpec is common in all hosts of @entity11292 , however not all @entity11292 strains carry pCpec. CONCLUSIONS: This study provides further insight into the complexity of @entity11292 epidemiology and novel genomic regions that may be linked to host specificity. @entity11292 plasmid characterisation may aid in improving our understanding of @entity11292 pathogenesis across the variety of host species this animal pathogen infects.

Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates XXXX pecorum strains from @entity1707 , @entity742 , @entity291 , and @entity34075 .

@entity1707 :: ('9823', 'Species') :: ['pigs', 'pig'] @entity291 :: ('9913', 'Species') :: ['cattle'] @entity742 :: ('9940', 'Species') :: ['sheep'] @entity11292 :: ('85991', 'Species') :: ['C. pecorum'] @entity34075 :: ('38626', 'Species') :: ['koalas', 'koala'] @entity1047 :: ('MESH:D002690', 'Disease') :: ['Chlamydia']
@entity1047 :: (MESH:D002690,Disease) :: ['Chlamydia']
