Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution

Martina Jelocnik; Nathan Bachmann; Helena Seth-Smith; Nicholas R Thomson; Peter Timms; Adam Polkinghorne

doi:10.7717/peerj.1661

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Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution

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Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution

Martina Jelocnik, Nathan Bachmann, Helena Seth-Smith, Nicholas R Thomson, Peter Timms and Adam Polkinghorne

PeerJ, Vol.4, e1661

2016

DOI: https://doi.org/10.7717/peerj.1661

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Abstract

Chlamydia pecorum

molecular characterisation

comparative analyses

plasmid

phylogeny

koala

Background. Highly stable, evolutionarily conserved, small, non-integrative plasmids are commonly found in members of the Chlamydiaceae and, in some species, these plasmids have been strongly linked to virulence. To date, evidence for such a plasmid in Chlamydia pecorum has been ambiguous. In a recent comparative genomic study of porcine, ovine, bovine, and koala C. pecorum isolates, we identified plasmids (pCpec) in a pig and three koala strains, respectively. Screening of further porcine, ovine, bovine, and koala C. pecorum isolates for pCpec showed that pCpec is common, but not ubiquitous in C. pecorum from all of the infected hosts. Methods. We used a combination of (i) bioinformatic mining of previously sequenced C. pecorum genome data sets and (ii) pCpec PCR-amplicon sequencing to characterise a further 17 novel pCpecs in C. pecorum isolates obtained from livestock, including pigs, sheep, and cattle, as well as those from koala. Results and Discussion. This analysis revealed that pCpec is conserved with all eight coding domain sequences (CDSs) present in isolates from each of the hosts studied. Sequence alignments revealed that the 21 pCpecs show 99% nucleotide sequence identity, with 83 single nucleotide polymorphisms (SNPs) shown to differentiate all of the plasmids analysed in this study. SNPs were found to be mostly synonymous and were distributed evenly across all eight pCpec CDSs as well as in the intergenic regions. Although conserved, analyses of the 21 pCpec sequences resolved plasmids into 12 distinct genotypes, with five shared between pCpecs from different isolates, and the remaining seven genotypes being unique to a single pCpec. Phylogenetic analysis revealed congruency and co-evolution of pCpecs with their cognate chromosome, further supporting polyphyletic origin of the koala C. pecorum. This study provides further understanding of the complex epidemiology of this pathogen in livestock and koala hosts and paves the way for studies to evaluate the function of this putative C. pecorum virulence factor.

Details

Title: Molecular characterisation of the Chlamydia pecorum plasmid from porcine, ovine, bovine, and koala strains indicates plasmid-strain co-evolution
Authors: Martina Jelocnik (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Nathan Bachmann (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Helena Seth-Smith (Author) - University of Zurich, Switzerland
Nicholas R Thomson (Author) - The Wellcome Trust Snager Institute, United Kingdom
Peter Timms (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Adam Polkinghorne (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Publication details: PeerJ, Vol.4, e1661; 17
Publisher: PeerJ, Ltd.
Date published: 2016
DOI: 10.7717/peerj.1661
ISSN: 2167-8359
Copyright note: Copyright © 2016 Jelocnik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
Organisation Unit: University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99449181302621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Microbiology

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