Submitted to: Ensuring safety and quality in the production of beef
Publication Type: Book / Chapter
Publication Acceptance Date: 7/30/2016
Publication Date: 3/31/2017
Citation: Fratamico, P.M., Bosilevac, J.M., Schmidt, J.W. 2017. Methods for detecting pathogens in the beef food chain: an overview. In: Acuff, G., Dickson, J. Ensuring safety and quality in the production of beef. Volume 1: Safety. Cambridge, UK: Burleigh Dobbs Science. p.35-51.
Technical Abstract: The main food-borne pathogens of concern in the beef chain are Shiga toxin-producing Escherichia coli (STEC) and Salmonella. Other pathogens, including Listeria monocytogenes and Campylobacter spp. may also be present and pose contamination concerns in both the cattle production environment and beef products. Furthermore, the occurrence and development of antimicrobial resistant (AMR) pathogens in the beef chain is a concern, and accurate methods for testing for resistance to antibiotics are of importance in human medicine and are of high priority in animal agriculture. Food safety regulations and the food industry have relied on microbiological testing for ensuring the safety of meat and other foods; however, traditional culture-based methods are laborious and time consuming. Rapid methods, including nucleic acid-, immunologic-, and biosensor-based techniques can be very sensitive and specific and provide more timely information regarding the presence of pathogens in the beef chain. Research is being directed toward development of techniques for sample processing to recover and concentrate target pathogens from food samples in efforts to shorten or eliminate the enrichment step to achieve real-time of near real-time detection during food processing. Recent advances in next generation sequencing technologies are allowing the development of culture-independent methods for pathogen detection and characterization. Whole genome sequencing (WGS) is currently being employed for epidemiological investigations, and in conjunction with robust bioinformatic pipelines, the usefulness of WGS for distinguishing and tracking pathogens, including STEC and Salmonella, to the source level, including specific farms, facilities, and foods is being revealed.