Temporality and Genetic Relatedness of Salmonella in a Pork Processing Facility

The goal of this study was to investigate the prevalence and genetic relatedness of Salmonella enterica in meat and contact surfaces from two processing lines at a pork processing plant over a commercial production schedule. Across 192 samples, there was no significant difference in Salmonella prevalence between Bootjack Trim (BJ) and Boston Butt Trim (BBT) meat (11.5% vs. 11.5%, P = 1.0), though prevalence was higher in meat than on contact surfaces for both the BJ (11.5% vs. 0%, P = 0.01) and BBT (11.5% vs. 3.1%, P = 0.08) processing lines. Both Salmonella prevalence and identified serotypes clustered within four distinct processing windows that spanned multiple dates and processing lines. Phylogenetic analysis using core single nucleotide polymorphisms (SNPs) identified a highly related Salmonella I4,[5],12:i:- strain (N = 33, 0–2 SNPs difference across all isolates) in both the BJ and BBT lines, persisting over consecutive days within one processing window. Similarly, a highly related Salmonella London strain (N = 18, 0–1 SNPs) was found across both processing lines on three processing dates that spanned 28 days. Additional highly related strains of Salmonella Typhimurium (N = 8, 0–1 SNPs) and Salmonella Agona (N = 7, 0–3 SNPs) were also detected across multiple dates. Strains of S. I4,[5],12:i:- and S. London were genetically distinct (>30 SNPs) from publicly available genomes from isolates obtained from other pork processing plants located in the Upper Midwest. Overall, findings suggested that Salmonella prevalence varies across processing lines and production schedules. However, the high phylogenetic relatedness among the Salmonella serotypes suggests a common source may have been present prior to each primal cut being processed into subprimal cuts.