Identifying the reservoirs of pathogenic bacteria in Illinois

Each year, foodborne pathogens cause hundreds of millions of illnesses and hundreds of thousands of deaths globally. These numbers in the U. S. alone amounts to 48,000,000 and 3,000 per year, respec�vely. The U. S. Food and Drug Administra�on (FDA) through its successful ini�a�ve, GenomeTrakr, has taken considerable steps towards modernizing our food safety system by implemen�ng and using whole-genome sequencing (WGS) in its inves�ga�ve and regulatory workflow. Establishment of an interna�onal laboratory network and the crea�on of the GenomeTrakr database are but two impressive accomplishments of this ini�a�ve. The GenomeTrakr laboratory network and its database are the products of a scien�fic vision that incorporates a global and data driven approach to the problem of foodborne illnesses. However, despite significant accomplishments of this ini�a�ve, a cri�cal gap remains in our knowledge about the environmental reservoirs where pathogens like E. coli, Salmonella, and Listeria reside and persist before contamina�ng the food supply. This in turn hampers our preven�ve efforts. Our proposed project directly addresses this gap and supports the FDA's Laboratory Flexible Funding Model (LFFM) Program by establishing and employing a dedicated capability for high-throughput sequencing (HTS) of the microbial communi�es and WGS of foodborne pathogens isolated from the posi�ve environmental samples (Track A5). The core scien�fic work, detailed in the A5 Microbiology Component, involves systema�c environmental surveillance across diverse agricultural and ecological landscapes in Illinois. Our proposal is designed to meet this condi�on and will generate three main types of data: a) the sequence data from microbial communi�es in the environmental samples; b) geographic, topographic, meteorological and anthropogenic metadata; and c) WGS data from the pathogens isolated from the posi�ve samples. To ensure consistency and replicability, we will adhere to current protocols issued by the FDA's GenomeTrakr Program Coordinators in all our laboratory work and in data dissemina�on and submission to the Na�onal Center for Biotechnology Informa�on (NCBI). By characterizing pathogen reservoirs and contribu�ng genomic data from underrepresented environmental sources, this project will improve our understanding of pathogen ecology, strengthen na�onal surveillance infrastructure, and ul�mately support the development of more effec�ve strategies to prevent foodborne disease and protect public health. The project leverages the unique resources and exper�se at the Ins�tute for Food Safety and Health (IFSH) at Illinois Ins�tute of Technology.