From Serogroup to Genome: The Unfinished Transition in EU Food Safety Criteria for Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) remain a leading cause of severe foodborne illness in the European Union, including haemolytic uraemic syndrome and fatalities. EU food safety criteria for STEC, established by Commission Regulation (EC) No 2073/2005 as amended, require serogroup-based testing for six designations — and only in sprouts. Most high-risk food categories, including raw milk cheese and minced meat, lack any mandatory STEC-specific food safety criterion. This serogroup-centred approach persists despite the 2020 EFSA scientific opinion concluding that all STEC strains are pathogenic, that any stx subtype may be associated with severe illness, and that serogroup alone cannot predict clinical outcome. The recent adoption of Implementing Regulation (EU) 2025/179, mandating whole genome sequencing for any Escherichia coli associated with foodborne outbreaks — without serogroup restriction — further highlights the disconnect between reactive investigation tools and preventive criteria. With the new WGS mandate becoming applicable in August 2026, we argue that a parallel effort is urgently needed to update food safety criteria from serogroup-based testing towards virulence gene profiling, aligning prevention with the scientific evidence and the genomic paradigm already adopted for outbreak response.