Ecology of Salmonella and antimicrobial resistance in a pig slaughterhouse

Arnaud Bridier et al., Food Micro, 3-6 septembre 2018, Berlin, Allemagne et I3S, 24-26 septembre 2018, Saint-Malo, France

Salmonella is a bacterial pathogen responsible for a large number of food associated infections. In order to guarantee food safety, a better understanding of Salmonella ecology and adaptation strategies on the food production chain constitutes a prerequisite. In a One Health perspective, data on Salmonella antibiotic resistance in food environments are also crucial to decipher transmission routes of resistant foodborne pathogens as well as resistance genetic determinants involved, and the role of process and selection pressures underwent in food industries (as cleaning and disinfection) in bacterial adaptation and antimicrobial resistance emergence.
Using a pig slaughterhouse as a model food environment, occurrence of Salmonella was investigated at six different areas along the slaughter chain and through 4 sampling campaign, each time before and after cleaning and disinfection procedures (a total of 48 surface samples). Characterization of isolated Salmonella strains using serotyping and pulsotyping enabled to identify and trace persistent strains in the slaughterhouse. Minimal inhibiting concentrations (MIC) were also determined for various relevant antibiotics and for biocides used in the slaughterhouse. In addition, associated indigenous bacterial communities were characterized using 16S rRNA amplicon sequencing. 
Results revealed the presence of Salmonella at all sampling area. Five serotypes were identified: S.4,5,12:i:- (50%), Rissen (16%), Typhimurium (16%), Infantis (10%) and Derby (8%). Strains were found at different dates and potentially at the same sampling area suggesting they persist in the slaughterhouse despite of the cleaning and disinfection procedures. Approximately 70% of isolated Salmonella strains exhibit resistance to ampicillin and sulfamethoxazole, 80% to tetracycline and 10% to chloramphenicol. There was no evolution of CMI comparing strains before and after cleaning and disinfection procedures concerning both biocides and antibiotics. Bacterial diversity analyses showed that populations in slaughterhouse were highly dominated by &a1;-proteobacteria and especially by the Moraxellaceae family (genus Psychrobacter, Moraxella, Enhydrobacter and Acinetobacter) at the different sampling areas. Population compositions were overall stable in time at a given sampling area suggesting that the surface populations are resident populations within the slaughterhouse, rather than populations introduced each week by the new swine bands. Cleaning and disinfection procedures tend to reduce bacterial diversity by eliminating the minority species but did not greatly impact the composition of bacterial communities with regards to the dominant species.
Together, such data participate to the construction of a comprehensive view of Salmonella ecology in food environments integrating associated resident microbial flora and the distribution of antimicrobial resistance in relation to processing conditions.