Whole genome sequencing is a mature, reliable technology with significant potential for the food industry, but realizing its benefits requires organizations to strategically weigh risks, applications, and persistent legal and regulatory barriers to adoption.
An analysis of multinational WGS surveillance data suggests that a multidrug-resistant lineage of Campylobacter coli has circulated across human, animal, food, and environmental sources in Europe for years, highlighting the need for coordinated One Health genomic surveillance.
The researchers analyzed cost and sequencing-volume data from 23 FDA and FDA partner GenomeTrakr laboratories. Findings suggested that WGS-based genomic surveillance is a cost-effective public health investment.
Regulation (EU) 2025/179, which came into effect on August 23, requires EU Member States to conduct WGS on five key pathogens during foodborne illness outbreak investigations. An interview with EFSA’s Dr. Frank Verdonck unpacks the new rule and previews the upcoming Science Meets Policy conference.
Reoccurring, emerging, and persisting (REP) strains cause foodborne illnesses over extended periods of time, rather than through isolated outbreaks. The REP framework was jointly developed by CDC, FDA, and USDA-FSIS through the Interagency Foodborne Outbreak Response Collaboration.
In 2025, a genetically unique hybrid STEC/STEC strain was the cause of a foodborne illness outbreak that affected exclusively adults, with 90 percent of patients developing hemolytic uremic syndrome (HUS) and three deaths occurring.
Associated with freshwater fish consumption and handling, GBS ST283 causes invasive infections, including meningitis, septic arthritis, and bacteremia. WGS has played a central role in recognizing the pathogen as a foodborne hazard. FAO has identified GBS ST283 as a hazard requiring structured risk profiling.
The third Science Meets Policy conference will take place September 2–3 in Rome, Italy, focused on helping EU competent authorities and industry members effectively implement new WGS data-sharing requirements for foodborne pathogens.
The updated Microbiology Laboratory Guidebook chapter on whole genome sequencing (WGS) of bacterial isolates now includes protocols for using both the Illumina MiSeq and MiSeq i100 sequencing platforms.
A national study led by the UK Food Standards Agency (FSA) found concerning increases in antimicrobial resistance (AMR) among poultry-associated Campylobacter isolates. Source attribution modeling predicted that chicken meat is by far the most dominant source of human campylobacteriosis cases.
