Genome Detectives

In the increasingly global food system, ensuring food safety is no small feat. Today's foods are complex, produced with ingredients sourced from around the world, and the challenges of safeguarding public health have grown in tandem.

Over the past decade, whole-genome sequencing has transformed food safety by enabling precise surveillance of foodborne pathogens through networks of public health and university labs, such as GenomeTrakr. By leveraging this technology and centralized data repositories, foodborne disease clusters are detected more rapidly, contamination sources are identified sooner, and public exposures are reduced significantly. The investment yielded an annual health benefit of approximately $500 million, representing a positive return on a $22 million investment, according to research published in the journal PLOS One.

Penn State's College of Agricultural Sciences, particularly the Department of Food Science, has been pivotal in advancing these efforts. In 2017, Penn State partnered with the Pennsylvania Department of Health to establish the Pennsylvania GenomeTrakr network lab. This lab has contributed to national pathogen surveillance and international food safety research in Ethiopia and Cambodia. Beyond research, it has supported training programs such as the U.S. Department of Agriculture-funded Research and Extension Experiences for Undergraduates and the Food and Agricultural Sciences National Needs Graduate Fellowship program, increasing access to research and graduate education for diverse groups of students, fostering a more inclusive and skilled workforce.

During the COVID-19 pandemic, Penn State's sequencing infrastructure proved invaluable for tracking and forecasting novel SARS-CoV-2 variants through wastewater monitoring in rural Pennsylvania. These resources also were used to pilot wastewater as an early warning system for foodborne outbreaks.

Traditional surveillance often misses cases due to underreporting. Wastewater analysis, for example, detected a Salmonella strain tied to a national outbreak involving contaminated peanut butter even though clinical cases have not been reported in Pennsylvania. This and similar studies demonstrated how wastewater monitoring can help uncover hidden cases, providing critical data for investigations.

Beyond outbreak investigations, Penn State faculty have collaborated with industry to address food safety risks proactively. Identifying persistent pathogen strains in production facilities and analyzing their genomic and antimicrobial profiles have helped processors develop more effective pathogen control strategies.

The One Health Microbiome Center has further supported innovative research using microbiome data in food systems. In food science, researchers analyzed environmental microbiomes in production settings using explainable machine learning to detect microbial community shifts signaling increased pathogen risks, such as elevated biofilm-forming microorganisms. This knowledge enabled proactive interventions to mitigate contamination risks. Similarly, in animal science, faculty analyzed milk microbiome data with explainable AI and successfully detected anomalies such as milk from antibiotic-treated animals or different food sources.

Looking ahead, genomic tools will become even more integral to food safety as the food system grows in complexity. Advances in sequencing and AI-driven analytics will enable faster detection, more precise traceback and predictive risk assessments. Combining data from multifaceted sources (e.g., wastewater, production environments and food) with microbiome insights will continue shifting food safety from reactive to predictive and preventive.

Through its leadership in genomic and microbiome research and education, our college stands at the forefront of these innovations. By fostering partnerships across academia, industry and government, and by training a multifaceted and skilled workforce, we are paving the way for a future when food safety is achieved with unprecedented precision and sustainability.

Jasna Kovac is associate professor of food science and Lester Earl and Veronica Casida Career Development Professor of Food Safety in the College of Agricultural Sciences.