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.
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 are 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 United States 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.
Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.
Helena M B
HM
Seth-Smith
Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.
Sabrina
S
Wanninger
Centre for Animal Health Innovation, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia.
Nathan
N
Bachmann
Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.
Hanna
H
Marti
Functional Genomics Centre Zurich, University of Zurich, Switzerland.
Weihong
W
Qi
DIMES, Microbiology, Policlinico S. Orsola, University of Bologna, Italy.
Manuela
M
Donati
Department of Veterinary Medical Sciences, University of Bologna, Ozzano Emilia, Bologna, Italy.
Antonietta
A
di Francesco
Centre for Animal Health Innovation, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia.
Adam
A
Polkinghorne
Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.
Nicole
N
Borel
D000818:Animals; D002689:Chlamydia / Q000235:genetics* / Q000472:pathogenicity; D002690:Chlamydia Infections / Q000235:genetics* / Q000382:microbiology / Q000662:veterinary; D023281:Genomics; D058751:Livestock / Q000235:genetics / Q000382:microbiology; D008826:Microbial Sensitivity Tests; D010957:Plasmids / Q000235:genetics; D013552:Swine / Q000235:genetics / Q000382:microbiology; D013752:Tetracycline / Q000627:therapeutic use; D013753:Tetracycline Resistance / Q000235:genetics*
D013752:Tetracycline
farming; phylogenetics; recombination; tetracycline resistance; whole genome sequencing