Foodborne illness caused by shiga toxin-producing escherichia coli (STEC) is a major public health concern that severely impacts the livestock, produce, and food processing industries

The Department of Agriculture National Institute of Food and Agriculture awarded Florida State University $779,438 under the Agriculture and Food Research Initiative (AFRI) program on September 1, 2026, to develop and validate a partition-based digital PCR testing method for detecting Shiga toxin-producing Escherichia coli (STEC) in food products. Current STEC testing methods produce high rates of false-positive results, triggering unnecessary product recalls, testing delays, and millions of dollars in annual losses for food processors. The digital PCR approach is resistant to interference from proteins, fats, and phenolic compounds present in food matrices and eliminates the need for time-consuming DNA isolation, enabling genetic analysis directly from bacterial cells in enrichment broth. Researchers will standardize an instrument-independent testing workflow, validate assay performance across laboratory-inoculated food samples including beef and fresh produce, and complete official performance certification through the AOAC Research Institute to enable commercial adoption by food testing laboratories. Performance extends from September 1, 2026, through August 31, 2030, with work performed in Tallahassee, Florida. Florida State University's Sponsored Research Administration Division serves as the recipient. Upon successful adoption, the technology is intended to reduce food waste, lower industry costs, and prevent contaminated food from reaching consumers while helping producers meet regulatory requirements.

Currently available testing methods frequently produce high rates of false-positive results. These false alarms mistakenly identify harmless bacteria as dangerous STEC strains, leading to massive product waste, testing delays, and millions of dollars in financial losses for food processors each year. To address this urgent priority highlighted by USDA-afri and key industry stakeholders, there is a critical need for a reliable testing approach that eliminates false positives and speeds up sample screening without sacrificing accuracy. This project uses partition-based digital PCR (DPCR), an advanced diagnostic technology that is highly resistant to interference caused by proteins, fats, and phenolic compounds found in food products. The DPCR technology enables performing genetic analysis directly from the bacterial cells collected from enrichment broth and eliminates the need for time-consuming DNA isolation. Using this technology, researchers will standardize an instrument-independent testing workflow directly from food enrichments. The team will then validate the assay's performance across laboratory-inoculated food samples, such as beef and fresh produce, before completing official performance certification through the aoac research institute to enable widespread adoption by commercial food testing laboratories.ultimately, this project aims to deliver a robust, highly specific, aoac-certified STEC testing method to the food safety sector. Once adopted, this technology will save the food industry millions of dollars annually, reduce unnecessary food waste, and protect public health by preventing contaminated food from reaching consumers. Furthermore, IT will help food producers meet increasingly stringent regulatory requirements, making the domestic agricultural industry more competitive both nationally and internationally.