A screen of Salmonella enterica mutants interacting with fresh onions and alfalfa sprouts

Salmonella enterica is a zoonotic pathogen that primarily causes disease through the contamination of food products. Foodborne salmonellosis outbreaks have frequently been associated with the consumption of contaminated ready-to-eat foods, including sprouts and fresh diced onions. To better control Salmonella throughout the food chain and enhance food safety, it is crucial to understand the interaction mechanisms of S. enterica with relevant food matrices. To identify the genetic determinants underlying the persistence of Salmonella on sprouts and onions, we analyzed barcoded transposon mutant libraries in two relevant S. enterica serovars, Typhimurium and Enteritidis, on these two food matrices for five days under refrigerated storage conditions. Key fitness determinants of S. enterica were observed to be under selection, including virulence factors, two-component systems, flagellar assembly, cell wall integrity, RNA degradation, and mismatch repair systems. The phenotype of selected S. Typhimurium mutants was subsequently verified in competition assays. Our study showed that disruption of tolC, encoding a multidrug efflux pump, resulted in a greater fitness reduction on onions than on sprouts and in nutrient-rich media. Furthermore, the fitness disadvantage of mutants in oxyR, a key regulator of the oxidative stress response, was much reduced on sprouts, compared to onions or standard growth conditions. This study provides a comprehensive overview of the genetic determinants that influence the interaction of S. enterica with these fresh produce items under real-world conditions.