Tetracycline-resistant and -susceptible Chlamydia suis remain viable during manure processing.

Chlamydia suis is commonly found in pigs and the only known chlamydial species to have acquired a tetracycline resistance gene, the tetA(C) gene. It has been established that both tetA(C)-positive and -negative C. suis strains can be isolated from rectal swabs of pigs, implying fecal shedding and fecal-oral transmission. However, little is known about the occurrence, viability and tetA(C) positivity of C. suis during manure processing. In this study, fresh feces and manure from slurry channels (storage up to two weeks), and manure silos (storage for several months until field application) from 30 pig farms across Switzerland were investigated regarding these parameters. Moreover, given the complex nature of feces and manure as matrices for molecular applications, three DNA extraction methods (Maxwell, MagPurix and DNeasy PowerSoil Pro Kit) were compared. Among these tested protocols, the DNeasy PowerSoil Pro Kit yielded the highest DNA quality and most consistent qPCR results. C. suis was detected and successfully isolated in cell culture from all investigated pig farms and sample types, demonstrating its ability to survive throughout the manure production process, with an isolation success rate of 100% (fecal samples), 96% (slurry channel) and 79% (silo). The viability of C. suis was further confirmed using viability PCR, which correlated well with cell culture isolation. Furthermore, the majority of isolated C. suis (66%) carried the tetA(C) gene, confirming the high prevalence of tetracycline resistance. The risk of spreading viable, tetracycline-resistant C. suis on the field is not eliminated by current manure management practices.