Whole genome sequencing becomes mandatory in foodborne outbreak investigations
From 23 August 2026 EU countries must sequence the genomes of isolates of five foodborne pathogens. For microbiology the default method becomes sequencing, not serotyping.
- From 23 August 2026 whole genome sequencing stops being a supplement to serotyping and becomes an obligation.
- It covers five pathogens: Salmonella, Listeria monocytogenes, Escherichia coli and Campylobacter jejuni and coli.
- Isolates from humans and from food, feed and animals are reported, and the reads go to the joint EFSA and ECDC system.
- A genome settles whether the strain from a sample and the strain from a patient are the same clone; a serotype only points to a large group.
- A laboratory needs access to a sequencer, people able to judge read quality and procedures ready for the accreditation scope. Strains have to be kept in case of re-reading.
- Production plants feel the change indirectly: comparing a strain from the production environment with a patient isolate becomes routine.
Source: EFSA