A genotypic evaluation of environmental Listeria isolates from a dairy plant

Listeria species are ubiquitous in nature. Despite improvements in hygiene protocols, some strains of Listeria can persist for long periods in dairy plant environment and pose a risk of product cross-contamination. A genotypic evaluation of environmental Listeria isolates can thus pro- vide an insight into their significance from a product cross-contamination and safety perspective. In this study, whole-genome sequencing was conducted to determine the genotypic variations and associated pheno- typic expressions of 6 Listeria isolates (Listeria innocua 634–2; Listeria innocua 634–34-S-5; Listeria innocua 634–34-S-6; Listeria welshimeri 634–3; Listeria welshimeri 634–253-S-5, and Listeria monocytogenes 315-S-1) obtained from the processing environment of a commercial dairy plant. Genomic DNA was extracted using the Wizard Genomic DNA extraction kit and run through whole-genome sequencing on the Illumina MiSeq platform using V2 chemistry with 2 × 250 paired-end chemistry. The genome was fed into the RAST database to develop the annotations. The results revealed at least 13 types of phenotypic responses related to the genotypic variants of the Listeria isolates. Overall, the genotypic variants differed with the species and within the strains. Some of the common variants and features identified in the isolates were virulence (DNase, phage terminase, tRNA-Arg-ACG), cell signaling (NAG-IIA, NAG-IIB), phage immunity (CRISPR pro- teins), osmotic stress (CadA), oxidative stress (YRKL), and antibiotic resistance (BaiE, Lde). While L. monocytogenes was positive for all these phenotypic characteristics, L. innocua and L. welshimeri isolates lacked variants for motility (ActA), biofilm formation (AgD), and acid tolerance (AdiA), making them less resilient to environmental stress. Such information about the genes and their role in expressing phenotypic attributes can help create more robust interventions for the control of Listeria in a dairy plant environment