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

Abstract

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.

Isolation of Tetracycline-Resistant Chlamydia suis from a Pig Herd Affected by Reproductive Disorders and Conjunctivitis

“…We detected genetically diverse C. suis isolates in the herd described in this case report. Genetic diversity is consistent with previous studies [38][39][40], depicting the unprecedented diversity of the C. suis genome compared to other chlamydial species, which is strongly influenced by recombination and plasmid exchange. A broad diversity of isolates circulates within Europe, even within individual farms or within the same animal [39].…”

“…Genetic diversity is consistent with previous studies [38][39][40], depicting the unprecedented diversity of the C. suis genome compared to other chlamydial species, which is strongly influenced by recombination and plasmid exchange. A broad diversity of isolates circulates within Europe, even within individual farms or within the same animal [39]. Together with studies from the USA, Switzerland, Japan, and China, this present case report on Austrian fattening pigs further illustrates a consistent diversity on a global level rather than regional clustering, even though C. suis is genetically quite diverse.…”

“…Together with studies from the USA, Switzerland, Japan, and China, this present case report on Austrian fattening pigs further illustrates a consistent diversity on a global level rather than regional clustering, even though C. suis is genetically quite diverse. This diversity has also been observed for other veterinary chlamydial species such as C. pecorum and C. psittaci [30,39,40].…”

Development of aChlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C

“…At the moment we performed this study, the genome of MD56 was the only available draft genome sequence. More recently, sequenced C. suis genomes are, as far as we know, not yet publicly available (Joseph et al., ) or were only very recently (March 2017) submitted to GenBank (Seth‐Smith et al., ). Now that more genomes will become publicly available, it would be interesting to study the level of conservation of PmpC proteins within C. suis .…”

“…The Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis and vaccination (Becker & Hegemann, 2014;Cevenini, Donati, Brocchi, Desimone, & Laplaca, 1991;Desclozeaux et al, 2017;Grimwood & Stephens, 1999;Liu et al, 2016;M€ uller Becker et al, 2017;Niessner et al, 2003;Tan et al, 2009;Van Lent, De Vos, et al, 2016;Wehrl, Brinkmann, Jungblut, Meyer, & Szczepek, 2004 (Joseph et al, 2016) or were only very recently (March 2017) submitted to GenBank (Seth-Smith et al, 2017). Now that more genomes will become publicly available, it would be interesting to study the level of conservation of PmpC proteins within C. suis.…”