Whole-genome sequencing and phylogenetic analysis of Salmonella isolated from pullets through final raw product in the processing plant of a conventional broiler complex: a longitudinal study.

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Salmonella continues to be the leading human bacterial foodborne pathogen, a serious food safety concern. The major challenges are to reduce the risk of introduction or spread of such bacteria in flocks, to minimize the persistence of such bacteria within the broiler complex, and to achieve USDA FSIS final product standards at the processing plants. Not well understood are the possible entry points and movement patterns of Salmonella along different stages of an integrated broiler complex. For this study, environmental sampling was considered from parent pullets through the final raw product at the processing plant, and SNP-based analysis of Salmonella isolates was conducted to determine the genetic relatedness and movement patterns. Interestingly, the samples from facilities (hatchery, transport, and processing plant) were more likely to be contaminated with Salmonella as compared to production farms (parent pullets, breeders, and broilers). Similarly, the phylogenetic analysis showed strong genetic relationship among strains isolated from different locations within the same stage and between different stages. The results show complex diversity of Salmonella serotypes along the chain and the possibility of multiple critical points for the entry of pathogen into the broiler complex and contaminate the final raw product at the processing plant. Furthermore, improper cooking or handling of contaminated raw chicken meat and meat products with Salmonella and other zoonotic pathogens can potentially cause foodborne illness in humans.