Adaptation factors of Salmonella Typhimurium, 1,4,[5],12:i:-and Dublin serovars to disinfection in the pig/pork and dairy industries : characterization of strain diversity and mechanisms of persistence

Biocides are routinely used in food processing industries to control microbial contamination. Despite their proven effectiveness, some Salmonella spp. strains exhibit environmental persistence, surviving and reappearing even after stringent sanitation measures. Various tolerance mechanisms and adaptative pathways have been described for Enterobacteriaceae, particularly in foodborne pathogens. However, the specific mechanisms of Salmonella adaptation to these environments and the genetic determinants associated with its persistence despite cleaning and disinfection remain unclear. The current study aims 1/to decipher the increased potential of Salmonella strains for biocides tolerance and biofilm formation, and 2/develop a fast molecular tool to identify the strains with high survival potential. The genomic and phenotypical diversity of three distinct serovars of Salmonella (Typhimurium, its monophasic variant and Dublin) will be examined using a collection of 935 strains isolated in France between 2017 and 2024 from both the pig/pork and dairy production chains. Genes known as involved in biocides tolerance and biofilm production will be identified and characterized. Building on these results, a representative panel of 300 strains will be selected to investigate their phenotypic response to biocides in biofilm models, close to conditions undergone by bacteria on food processing chains. Finally, Association Studies will be conducted to identify possible new genetic markers involved in strain adaptation in food processing plants. The results will shed light on the potential presence of persistent Salmonella strains (Typhimurium, 1,4,[5],12:i:-, and Dublin) which are prevalent in the French pig/pork and dairy product sectors. This study will identify and describe genes implicated in persistence within the Salmonella populations of both sectors. The genetic markers identified will then be used to develop a molecular tool detecting strains capable of surviving in food processing plants. This test will assist the food industry in decision-making to improve sanitation measures and control Salmonella in the pig/pork and dairy product industries.