Food safety in animal protein processing remains an ongoing concern. However, rapid advances have been made in the detection of foodborne pathogens as well as in control measures. Detection methods that are faster and more sensitive are constantly being developed and implemented in commercial processing-plant operations. Equally important, prevention measures such as vaccines, probiotics, and prebiotics have been examined for use in live animal production to support optimal gut health and limit the establishment of foodborne pathogens in the gut. A battery of antimicrobials have been introduced to decrease foodborne pathogen loads in meat processing and extend the shelf life of various meat products. While significant progress has been made, much of the research on the food safety of meat has been conducted somewhat piecemeal. Outcomes of studies have relied on the capabilities of individual research facilities. Ideally, to get an accurate picture of tracking pathogens and preharvest and postharvest control measures, integrated longitudinal studies that allow the introduction of marker foodborne strains throughout the production chain are needed. The ability to track foodborne pathogens and quantitate pathogen responses throughout the meat production chain can provide baseline data for evaluating the efficacy of intervention measures. However, research facilities are often limited by possessing only certain components of the meat production chain, such as live animal housing but minimal or no processing capacity or, conversely, processing facilities but minimal live animal capabilities.