Research is performed to generate knowledge and practical solutions to implement environmental monitoring programs (EMPs) in fresh produce production and processing facilities and establish the relatedness of organisms involved in a single contamination event. The high-throughput capability and the increased speed of next-generation sequencing (NGS), together with the development of new bioinformatics tools to process the data, has allowed the application to identify the origin of contamination accurately. The use of whole genome sequencing (WGS) in food processing environments represents a powerful tool to enhance the understanding of the origin, cross-contamination, reservoir, and possible persistence of specific subpopulations along the food chain.