Occurrence and characterization of Salmonella in a substrate-based CEA system: Genomic, phenotypic, and survival profiles of two serotypes.

This study investigated the occurrence, genomic characteristics, and environmental behavior of Salmonella enterica in a substrate-based Controlled Environment Agriculture (CEA) system representative of soilless leafy greens production. A total of 178 samples were collected over 1.5 years during three environmental monitoring events (EM1-EM3), including food-contact surfaces (n = 117), substrate (n = 13), irrigation water sources (n = 18), and product before and after harvest (n = 30). S. enterica was detected at low prevalence (2.8%) and exclusively during EM1 in reservoir water (n = 3), nutrient solution (n = 1), and pre-harvest product (n = 1). Whole-genome sequencing identified two distinct lineages: S. enterica subsp. enterica serovar Mikawasima (ST1815), associated with water matrices, and S. enterica subsp. salamae serovar 41:z10:1,2 (ST3614), recovered from pre-harvest product. Despite this genetic divergence, both serotypes exhibited similar phenotypic behavior under CEA-relevant conditions. Neither strain showed growth in irrigation water, and both displayed limited persistence, with declining populations over time. On baby lettuce, survival followed comparable inactivation patterns under different environmental conditions. Chlorine efficacy was evaluated: both serotypes remained detectable at 1 mg·L-1, whereas 5 mg·L-1 led to a rapid reduction, with no culturable cells detected under the conditions tested. Overall, sporadic Salmonella detections in CEA systems appear to reflect independent contamination events rather than persistent colonization. The integration of genomic characterization with targeted environmental monitoring and optimized water management strategies is essential to strengthen risk-based food safety in CEA production systems.