Molecular and environmental indicators of Listeria monocytogenes persistence in food processing facilities: a multi sector approach.

Listeria monocytogenes is a foodborne pathogen capable of persisting in food processing environments. This persistence results from interactions between strain-specific traits and environmental conditions. This study aimed to identify molecular and environmental indicators associated with L. monocytogenes persistence across high-risk food production sectors. Three environmental sampling events were conducted in nine facilities from seafood, vegetable, and pork (n = 3 each) sectors. In total 1097 samples were analysed for the presence of L. monocytogenes, the temperature, and surface characteristics, pH, humidity, temperature, and surface characteristics. L. monocytogenes was detected in 114 samples (≈10%), with the highest prevalence observed in the vegetable sector. Isolates were characterized by Whole Genome Sequencing and classified into persistent or transient clusters based on core genome multilocus sequence typing profiles. Persistent clusters were defined by ≤ 7 allelic differences and repeated detection across at least two sampling events, whereas transient isolates were detected only once. We identified 13 persistent clusters including 67 isolates, of which 42 were assigned to CC121, 9 to CC5, 5 to CC31, 4 to CC101, 4 to CC155, and 3 to CC412. Pangenome analysis identified several loci enriched among persistent isolates, including prophage-related loci, genes encoding transport systems such as TatA, TatC and EfeO, and genes involved in stress response mechanisms. Persistence was associated with higher total microbial counts and high humidity, with persistent isolates mainly detected under conditions exceeding 5-6 log CFU/mL of total microbial counts and 80% relative humidity. Overall, results highlight persistence arising from the interplay between bacterial genetic traits and environmental conditions, emphasizing the importance of integrated approaches for monitoring and control in food processing environments.