Transcriptomic Adaptation and Small RNA-Mediated Regulation in Salmonella enterica Serovar Typhimurium During Survival on Food Matrices

Abstract

Salmonella enterica serovar Typhimurium remains a leading cause of global foodborne gastroenteritis, yet its physiological adaptation to post-harvest food environments, which differ from the host infection cycle, remains poorly understood. This thesis characterizes the survival strategies of S. Typhimurium (strain ST4/74) across different food matrices, specifically chicken meat and pasteurized bovine milk, using integrated transcriptomic, physiological, and molecular approaches. Initial RNA-sequencing across lag, log/exponential, and stationary growth phases on chicken meat revealed extensive transcriptional remodeling. Classical virulence factors, including Salmonella Pathogenicity Islands 1 and 2 (SPI-1, SPI-2), were largely down-regulated, whereas SPI-9 (biofilm-associated) and various stress-response genes were induced. This indicates a fundamental shift from an invasive profile to a stress-adaptive, persistence-driven physiological state. The management of a pro-oxidant environment was critical to this adaptation. S. Typhimurium significantly up-regulated reactive oxygen species (ROS) detoxification systems (sodA, katE, ahpC) and the glyoxylate shunt (aceAB). Simultaneously, manganese acquisition (sitABCD, mntH) was prioritized over iron to maintain redox balance and DNA synthesis through the Class Ib ribonucleotide reductase system (nrdHIEF). Furthermore, this research identifies the small regulatory RNA (sRNA) STnc3080 as a novel post-transcriptional regulator of the nrdH gene. Using a two-plasmid reporter system, STnc3080 was validated as an antisense repressor of nrdH, acting in parallel with Fur-dependent transcriptional control and independently of the ProQ chaperone. These findings reveal an additional regulatory layer coordinating nucleotide metabolism with environmental stress responses. Comparative transcriptomic analysis with pasteurized bovine milk showed that, while certain stress responses (iron/redox homeostasis) are conserved, S. Typhimurium exhibits significant metabolic plasticity, particularly in carbon and formate utilization, depending on the matrix composition. Collectively, these findings demonstrate that Salmonella persistence on food is an active, highly regulated physiological process. By defining the food-associated transcriptome and identifying sRNA-mediated regulatory mechanisms, this study highlights manganese homeostasis and redox-conservative metabolic pathways as promising targets for future food safety interventions.