The European Food Safety Authority (EFSA) has published guidelines for reporting whole genome sequencing (WGS) data to EFSA as required by Regulation (EU) 2025/179, defining acceptance criteria for WGS data quality, metadata standards, and procedures for voluntary and mandatory data submissions. 

In February 2025, the EU adopted a new regulation requiring Member States to conduct WGS on the isolates of five important pathogens during the investigations of foodborne illness outbreaks and share relevant data with EU public health agencies.

Specifically, Regulation (EU) 2025/179 states that, during official controls at food and feed businesses suspected of being implicated in a foodborne illness outbreak, competent authorities within Member States must collect isolates of Salmonella enterica, Listeria monocytogenes, Escherichia coli, Campylobacter jejuni, and Campylobacter coli derived from food, animal feed, and related environmental samples. Member States will be required to carry out WGS on those isolates. WGS results must be transmitted to EFSA, which developed a joint One Health system together with the European Center for Disease Prevention and Control (ECDC). Within the joint One Health system, EFSA will be able to compare WGS data for food-related isolates with WGS data from human isolates that are communicated to ECDC. Certain information about the genome sequence, isolate, pathogen, and sample are required to be sent with the WGS data.

The new guidelines published on December 12 focus on the critical requirements and submission procedures that reporting countries must follow to ensure compliance with regulatory obligations under Regulation (EU) 2025/179 and EFSA criteria when submitting WGS data to EFSA.

The guidelines describe the scope of the data collection, which includes raw sequencing reads, genome assemblies, and typing results, along with mandatory metadata such as epidemiological and outbreak investigation data for submissions linked to foodborne illness outbreaks.

Additionally, roles and responsibilities are clearly defined in the guidelines: country officers coordinate submissions at the national level, reporting countries manage data release, and submitters handle technical uploads. The document also addresses the data ownership, intellectual property, and the use of human-origin data in compliance with EU privacy regulations.

The full guidelines document can be read here.