Validating Pathogen Nucleic Acid Extraction from Animal Feed and Feed Ingredients

The risk of feed serving as a vehicle for pathogen introduction into swine farms and production systems became evident after the porcine epidemic diarrhea virus (PEDV) outbreak in the US in 2013. Recent studies in feed biosecurity have shown that the protective environment provided by different feed matrices promotes the survival of viral pathogens of swine for prolonged periods of time, thus potentially providing an opportunity for transmission, should contaminated feed be introduced into the farm. Most importantly, follow up studies have shown that consumption of contaminated feed leads to successful infection of pigs by porcine epidemic diarrhea virus (PEDV), African swine fever virus (ASFV), Senecavirus A (SVA) and foot and mouth disease virus (FMDV). The potential risk of pathogen transmission through feed could be reduced through testing of feed ingredients and feed prior to their introduction into farms. For this to be successfully implemented, sampling procedures and validated nucleic acid extraction procedures and diagnostic tests are required. In the present study, we evaluated the performance and validated the use of a commercially available nucleic extraction kit (MagMax Core) for pathogen nucleic extraction from feed and feed ingredients. To determine the efficiency of the nucleic acid extraction method selected we tested each feed ingredient for an RNA (SVA) and a DNA (ASFV) virus using commercially available and validated PCR assays. Overall, our results demonstrate that the MagMax core kit efficiently extracts pathogen nucleic acid from diverse feed ingredients, resulting in good performance of validated diagnostic assays for SVA and ASFV. To complete the assessment of the protocols and procedures established in this study, we conducted a follow up project (Funded by SHIC, https://www.swinehealth.org/wp-content/uploads/2021/10/10-21-Diel-feed-…) in which we compared the extraction procedures developed, optimized and validated here with the extraction efficacy of two other commercial nucleic acid extraction kits. Together these studies showed that extraction of pathogen nucleic acid from feed ingredients using the core procedure presents a higher sensitivity and diagnostic performance, thus representing a good alternative for pathogen detection in feed. Additional challenges that still need to be addressed for full implementation of routine feed testing include representative sampling of feed for testing and validation of additional PCR assays for other swine pathogens in nucleic acid extracted from feed ingredients.