Optimization of PathogenDx Microarray for the Detection of E. coli O157:H7 and Salmonella in Ground Beef

In the United States, from 1998 to 2008, meat and poultry product contamination has led to 2.1 million illnesses, 12,200 hospitalizations, and 418 deaths per year. Ground beef is responsible for 45% of all meat related outbreaks. Ground beef has the capacity to harbor harmful bacteria, most importantly pathogenic E. coli and Salmonella sp., especially when raw, undercooked, or mishandled. The gastrointestinal tract of cattle is a common reservoir to these pathogens, making fecal matter a very common contamination vehicle for foods. The rapid detection of foodborne pathogens in beef matrices plays an important role in the prevention of foodborne outbreaks. Conventional microbiological techniques used for detection and identification of these pathogens are often time consuming and laborious. As these methods have been evolving, there has been a shift towards molecular testing approaches as a solution to decrease testing time, cost of labor, and culture media. This thesis covers a literature review about food safety associated with ground beef, common safety practices of pre- and post-harvest intervention, government regulations, associated pathogens, and testing technologies used for microbial verification in the beef industry, including a discussion of conventional microbiological methods and the shift to rapid methods focusing on the use of PCR and multiplex PCR and its use in the food industry. The second part looks at evaluating parameters of the novel PathogenDx detection system to be used as an alternative to conventional methods for pathogen detection in ground beef. The objectives of this study aim to 1) establish the parameters of detection for E. coli O157:H7 and Salmonella sp. in raw ground beef, including detection thresholds and optimal enrichment times, and 2) evaluate the specificity and sensitivity of the microarray at various contamination levels.