Intensive environmental sampling and whole genome sequence-based characterization of Listeria in small and medium sized dairy plants reveal opportunities for simplified and size-appropriate environmental monitoring strategies

Small and medium sized dairy processing plants (SMDPs) may face unique challenges with respect to controlling Listeria in their processing environments, e.g., due to limited resources. The aim of this study was to implement and evaluate environmental monitoring programs (EMPs) for Listeria control in eight SMDPs in a [~]1-year longitudinal study; this included a comparison of pre-operation (i.e., after cleaning and sanitation and prior to production) and mid-operation (i.e., at least 4 h into production) sampling strategies. Among 2,072 environmental sponge samples collected across all plants, 272 (13%) were positive for Listeria. Listeria prevalence among pre- and mid-operation samples (15 and 17%, respectively), was not significantly different. Whole genome sequencing (WGS) performed on select isolates to characterize Listeria persistence patterns revealed repeated isolation of closely related Listeria isolates (i.e., [≤]20 high quality single nucleotide polymorphism [hqSNP] differences) in 5/8 plants over >6 months, suggesting Listeria persistence and/or re-introduction was relatively common among the SMDPs evaluated here. WGS furthermore showed that for 41 sites where samples collected pre- and mid- operation were positive for Listeria, Listeria isolates obtained were highly related (i.e., [≤]10 hqSNP differences), suggesting that pre-operation sampling alone may be sufficient and more effective for detecting sites of Listeria persistence. Importantly, our data also showed that only 1/8 plants showed a significant decrease in Listeria prevalence over 1 year, indicating continued challenges with Listeria control in at least some SMDPs. We conclude that options for simplified Listeria EMP programs (e.g., with a focus on pre-operation sampling, which allows for more rapid identification of likely persistence sites) may be valuable for improved Listeria control in SMDPs.