The European Commission has published a document to answer frequently asked questions (FAQs) about the requirements of new EU legislation that mandates whole genome sequencing (WGS) testing and data reporting for important foodborne pathogens.

Commission Implementing Regulation (EU) 2025/179 aims to facilitate the swift identification of causes of a foodborne illness outbreak and the related batches, lots, or consignments of potentially unsafe food by requiring WGS analysis and reporting to the European Food Safety Authority (EFSA) for isolates of Salmonella enterica, Campylobacter jejuni and Campylobacter coli, Listeria monocytogenes, and Escherichia coli. When one of these pathogens are suspected to be associated with a foodborne illness outbreak, at least one isolate obtained from animals, feed, food, or the feed/food production environment must be analyzed and data must be submitted to EFSA.

According to the FAQ document, pathogens that are “suspected to be associated with a foodborne illness outbreak” means pathogens that have been detected in at least one of two or more human cases, and when an epidemiological link has been established between at least two of the human cases and a food where the same pathogen was found.

In the case of a multinational outbreak, the competent authority of each Member State where an isolate was detected from food, animals, feed, or the related environment, and where the isolate is associated or suspected to be associated with an outbreak, are responsible for carrying out WGS. The regulation does not impose mandatory WGS on food businesses, but food businesses must submit isolates to competent authorities for WGS upon request.

Certain data is required to be submitted to EFSA along with WGS sequences, including reference numbers, pathogen species, and date and Member State of samplings, as well as the description of the food, animal species, feed, or environment from which the isolate was derived. WGS results should be transmitted to EFSA as soon as they are available. Laboratories conducting WGS analyses should be ISO 17025-accredited.

Although it is not required by the regulation, Member States are encouraged to share any WGS results collected from routine sampling or other activities in which the isolates are not necessarily associated with a foodborne illness outbreak.

Regulation (EU) 2025/179 comes into force on August 23, 2026.