Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas. (December 2015)

• Record Type: Journal Article
• Authors: Jelocnik, Martina; Bachmann, Nathan; Kaltenboeck, Bernhard; Waugh, Courtney; Woolford, Lucy; Speight, K.; Gillett, Amber; Higgins, Damien; Flanagan, Cheyne; Myers, Garry; Timms, Peter; Polkinghorne, Adam
• Is Part Of: BMC genomics. Volume 16:Number 1(2015)
• Page Start: 1
• Page End: 14
• Publication Date: 2015-12
• Subjects: C. pecorum plasmid -- Porcine hosts -- C. pecorum comparative genomics -- Cytotoxin gene -- Phylogenetic relationships; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-015-2053-8
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Chlamydia pecorum is a globally recognised pathogen of livestock and koalas. To date, comparative genomics ofC. pecorum strains from sheep, cattle and koalas 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 includedC. pecorum from porcine hosts. We sequenced the genome of threeC. pecorum isolates from pigs with differing pathologies in order to re-evaluate the genetic differences and to update the phylogenetic relationships betweenC. pecorum from each of the hosts. Methods Whole genome sequences for the three porcineC. pecorum isolates (L1, L17 and L71) were acquired usingC. pecorum -specific sequence capture probes with culture-independent methods, and assembled in CLC Genomics Workbench. The pairwise comparative genomic analyses of 16 pig, sheep, cattle and koalaC. pecorum genomes were performed using several bioinformatics platforms, while the phylogenetic analyses of the coreC. pecorum genomes were performed with predicted recombination regions removed. Following the detection of aC. pecorum plasmid, a newly developedC. pecorum -specific plasmid PCR screening assay was used to evaluate the plasmid distribution in 227C. pecorum samples from pig, sheep, cattle and koala hosts. Results Three porcineC. pecorum genomes were sequenced usingC. pecorum -specific sequence capture probes with culture-independent methods. Comparative genomics of the newly sequenced porcineC. pecorum genomes revealed an increased average number of SNP differences (~11 500) between porcine and sheep, cattle, and koalaC. pecorum strains, compared to previousC. pecorum genome analyses. We also identified a third copy of the chlamydial cytotoxin gene, found only in porcineC. pecorum isolates. Phylogenetic analyses clustered porcine isolates into a distinct clade, highlighting the polyphyletic origin ofC. pecorum in livestock. Most surprising, we also discovered a plasmid in the porcineC. pecorum genome. Using this novelC. pecorum plasmid (pCpec ) sequence, a) we developed a pCpec screening assay to evaluate the plasmid distribution inC. pecorum from different hosts; and b) to characterise the pCpec sequences from available previously sequencedC. pecorum genome data. pCpec screening showed that the pCpec is common in all hosts ofC. pecorum, however not allC. pecorum strains carry pCpec . Conclusions This study provides further insight into the complexity ofC. pecorum epidemiology and novel genomic regions that may be linked to host specificity.C. pecorum plasmid characterisation may aid in improving our understanding ofC. pecorum pathogenesis across the variety of host species this animal pathogen infects.