** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** APPROXIMATELY 1 IN 6 AMERICANS ARE AFFECTED BY FOOD CONTAMINATED WITH DANGEROUS MICROORGANISMS EVERY YEAR. RECURRING, EMERGING, AND PERSISTENT (REP) MICROORGANISMS SUCH AS ESCHERICHIA COLI, SALMONELLA ENTERICA AND LISTERIA MONOCYTOGENES CAN RE-EMERGE PERIODICALLY IN FOOD SYSTEMS, CAUSING REPEATED ACUTE OUTBREAKS, OR PERSIST AND CAUSE ILLNESSES OVER LONG PERIODS OF TIME. THUS, THERE IS AN URGENT NEED TO DEVELOP STRATEGIES TO PREDICT THE SPREAD AND SUBSEQUENTLY CONTROL THESE MICROBIAL CONTAMINANTS IN OUR FOOD SUPPLY. TRADITIONALLY, MICROBIAL BEHAVIOR IS MODELED USING SIMPLE MATHEMATICAL AND STATISTICAL MODELS. HOWEVER, IN RECENT YEARS, GENOMIC AND OTHER 'OMICS'-BASED METHODS ARE INCREASINGLY BEING USED TO MONITOR, IDENTIFY, AND CHARACTERIZE PATHOGENIC MICROORGANISMS, INTRODUCING NOVEL DIMENSIONS TO MICROBIAL DATA. IT IS CRITICAL TO DEVELOP ANALYTICAL TOOLKITS OR RISK MITIGATION STRATEGIES TO ANALYZE AND IDENTIFY USEFUL PATTERNS FROM THIS GENOMIC DATA IN ORDER TO EFFECTIVELY PREDICT AND MANAGE FOOD SAFETY RISK OF REP PATHOGENS TO IMPROVE PUBLIC HEALTH. THIS PROPOSAL AIMS TO DEVELOP NOVEL TOOLS AND PIPELINES TO ANALYZE AND PREDICT THE PRESENCE AND BEHAVIOR OF REP PATHOGENS UNDER THE VARIOUS CONDITIONS OBSERVED IN THE AGRICULTURAL AND FOOD ECOSYSTEM. WE WILL LEVERAGE PUBLICLY AVAILABLE GENOMIC AND PHENOTYPIC DATA FOR REP PATHOGENS FROM FOOD PRODUCTION AND PROCESSING ENVIRONMENTS, METAGENOMICS DATA FROM SAMPLING ACTIVITIES, AND PUBLICLY AVAILABLE ENVIRONMENTAL DATA TO DELINEATE MOLECULAR MARKERS ASSOCIATED WITH THE PERSISTENCE AND EVOLUTION OF REP PATHOGENS. WE WILL EMPLOY A COMBINATION OF MACHINE LEARNING, BIOINFORMATICS ANALYSIS AND ADVANCED COMPUTATIONAL MODELS TO ACHIEVE OUR OBJECTIVES. OUR DEVELOPED MODELS AND TOOLS WILL BE UTILIZED TO DEVELOP A REPRODUCIBLE PIPELINE TO IDENTIFY GENETIC DETERMINANTS OF PATHOGEN PERSISTENCE AND RECURRENCE IN THE FOOD AND AGRICULTURAL DOMAIN. THIS IN TURN WILL ASSIST IN MAKING BETTER RISK MANAGEMENT DECISIONS TO IMPROVE FOOD SAFETY AND PROTECT PUBLIC HEALTH FROM REP PATHOGENS.