Chlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics of C. pecorum strains from sheep, cattle and koalas has revealed that only single nucleotide polymorphisms (SNPs) and a limited number of pseudogenes found only in koala strains appear to contribute to the genetic diversity and virulence of this pathogen [1, 2, 3]. Almost ubiquitous in chlamydial species , no plasmids were detected in these C. pecorum strains.
Using culture independent methods , we sequenced genomes of three pig C. pecorum strains in order to re-evaluate the genetic differences and to update the phylogenetic relationships between C. pecorum from each of the hosts. Comparative genomics revealed increased SNPs between strains from pigs and other hosts, and an additional full length copy of chlamydial toxin gene  in the pig polyarthritis isolate. Phylogenetic analyses clustered pig isolates into a distinct clade, highlighting the polyphyletic origin of C. pecorum in different livestock hosts.
Most surprising, we also discovered a full length plasmid in the pig C. pecorum genome. Using this novel C. pecorum plasmid (pCpec) sequence, primer pairs were designed to a) develop a pCpec screening assay to evaluate the plasmid distribution in C. pecorum from different hosts ; and b) to characterise the sequences of pCpec from other hosts. pCpec screening showed that not all C. pecorum strains carry this plasmid, and if present, is more prevalent in the koala (80%) than livestock strains (33%). Phylogenies of an additional 16 pCpec from pigs, cattle, sheep and koala C. pecorum strains indicated similar levels of diversity and congruency with whole genome phylogenies.
This study provides further insight into the complexity of C. pecorum epidemiology and may open new opportunities for vaccine development since chlamydial plasmid proteins in other species are immunogenic and potentially important virulence factors .