Genomic Characterization of Resident Bacteria from Selected Swine Feed Mills in the Midwest Region of the United States

Knowledge of resident bacteria present within animal food manufacturing facilities, as well as the understanding of antimicrobial resistance genes (ARGs), can help inform cleaning and sanitation practices to reduce microbial risks for the animal and human food chains. The goal of this study was to characterize resident bacteria previously isolated in selected swine feed mills within the Midwest region of the United States at multiple seasonal timepoints. About 121 resident bacterial isolates were identified and classified into six genera, consisting of 68 Enterobacter, 34 Citrobacter, four Cronobacter, eight Klebsiella, three Proteus, and four Pseudomonas, in addition to 30 Escherichia coli and 33 Salmonella characterized previously. Among the 121 isolates discussed within the current work, the majority (48; 39.7%) came from environmental samples taken from either non-feed contact surfaces such as floors and feed contact surfaces (38; 31.4%) or transient surfaces such as brooms and workers' shoes (20; 16.5%), and only 12 samples (9.9%) came directly from finished feed. A range of ARGs and metal tolerance genes (MTGs) were identified. This research provides an initial framework to understand the diversity of resident flora in feed mill facilities in the Midwest region and identify areas to focus on for housekeeping and sanitization within mills. This information is critical to developing feed safety strategies and preventing antimicrobial resistance spread in the farm-to-table continuum.