The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes

Helena M B Seth-Smith; Sabrina Wanninger; Nathan Bachmann; Hanna Marti; Weihong Qi; Manuela Donati; Antonietta di Francesco; Adam Polkinghorne; Nicole Borel

doi:10.1093/gbe/evx043

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The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes

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The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes

Helena M B Seth-Smith, Sabrina Wanninger, Nathan Bachmann, Hanna Marti, Weihong Qi, Manuela Donati, Antonietta di Francesco, Adam Polkinghorne and Nicole Borel

Genome Biology and Evolution, Vol.9(3), pp.750-760

2017

DOI: https://doi.org/10.1093/gbe/evx043

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Abstract

phylogenetics

farming

whole genome sequencing

tetracycline resistance

recombination

Chlamydia suis is an endemic pig pathogen, belonging to a fascinating genus of obligate intracellular pathogens. Of particular interest, this is the only chlamydial species to have naturally acquired genes encoding for tetracycline resistance. To date, the distribution and mobility of the Tet-island is not well understood. Our study focused on whole genome sequencing of 29 C. suis isolates from a recent porcine cohort within Switzerland, combined with data from USA tetracycline-resistant isolates. Our findings show that the genome of C. suis is very plastic, with unprecedented diversity, highly affected by recombination and plasmid exchange. A large diversity of isolates circulates within Europe, even within individual Swiss farms, suggesting that C. suis originated around Europe. New World isolates have more restricted diversity and appear to derive from European isolates, indicating that historical strain transfers to the USA have occurred. The architecture of the Tet-island is variable, but the tetA(C) gene is always intact, and recombination has been a major factor in its transmission within C. suis. Selective pressure from tetracycline use within pigs leads to a higher number of Tet-island carrying isolates, which appear to be lost in the absence of such pressure, whereas the loss or gain of the Tet-island from individual strains is not observed. The Tet-island appears to be a recent import into the genome of C. suis, with a possible American origin.

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Title: The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes
Authors: Helena M B Seth-Smith (Author) - University of Zurich, Switzerland
Sabrina Wanninger (Author) - University of Zurich, Switzerland
Nathan Bachmann (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Hanna Marti (Author) - University of Zurich, Switzerland
Weihong Qi (Author) - University of Zurich, Switzerland
Manuela Donati (Author) - University of Bologna, Italy
Antonietta di Francesco (Author) - University of Bologna, Italy
Adam Polkinghorne (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Nicole Borel (Author) - University of Zurich, Switzerland
Publication details: Genome Biology and Evolution, Vol.9(3), pp.750-760
Publisher: Oxford University Press
Date published: 2017
DOI: 10.1093/gbe/evx043
ISSN: 1759-6653
Copyright note: Copyright © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Organisation Unit: University of the Sunshine Coast, Queensland
Language: English
Record Identifier: 99450340302621
Output Type: Journal article

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