Shotgun Sequencing-Based Assessment of Foodborne Pathogens in Retail Chicken Meat

Chicken serves as a primary reservoir for numerous zoonotic pathogens, including Salmonella, Campylobacter, Clostridium, and Escherichia coli. Foodborne illnesses linked to these pathogens are a growing public health concern across all age groups in the United States. Furthermore, the rise in antibiotic resistance among major bacterial pathogens of concern is a global challenge. To mitigate the chicken-related foodborne illnesses, it is essential to study foodborne pathogens such as bacteria, viruses, fungi, and protozoa, as well as the associated virulence properties of these pathogens in chicken microbiome. This study aimed to evaluate the pathogenic microbiota present in retail chicken meat and the effectiveness of sample processing methods (i.e. whole carcass enrichment and rinse methods) using shotgun sequencing.