Joint ECDC‐EFSA Rapid Outbreak Assessment
Whole genome sequencing in foodborne outbreaks
The European Union (EU) has a robust food safety system in place. However, food contamination by microorganisms can still occur. In our globalised world, contaminated foods can be traded across EU countries or imported from outside the Union. When people consume these contaminated foods, they may experience mild to severe symptoms of infection. By combining data from human cases and the food sector, EU agencies can determine if local and national incidents might evolve into larger, multi-country outbreaks.
Molecular typing A way of identifying specific strains of organisms by looking at their genetic material. Often used to characterise bacteria or viruses of microbes, also known as microbial fingerprinting, is a technique used to identify specific strains of microorganisms by analysing their genetic material. This method is essential for various applications, including tracking the spread of infectious diseases, identifying sources of outbreaks, and understanding the genetic diversity Genetic variation between and within species of microbial populations.
One of the most advanced molecular typing methods is whole genome sequencing Visualisation of the entire genetic makeup of a particular organism (WGS). This approach allows the detailed characterisation of microbial genomes, helping to identify genes that can cause diseases and that can lead to antibiotic resistance. It also helps track where pathogens come from and how they spread by reconstructing their phylogeny the evolutionary history and relationships among organisms or genes, typically represented in a tree-like structure. In whole genome sequencing, phylogenies help trace the origin, spread, and genetic evolution of pathogens.
WGS has significantly enhanced our ability to detect clusters of infections, confirm the food sources responsible for infections, and understand the genetic makeup of pathogens. By analysing and comparing the genomic profiles of bacteria from contaminated food and infected individuals, scientists can identify correlations between the sources of infection and human cases, providing the basis more effective public health interventions.
Milestones
2023
September
Together with the Inter-EURL working group on Next Generation Sequencing, EFSA organises the conference “Science meets policy”: Using Next Generation Sequencing to tackle foodborne threats”. The conference advances discussions on data sharing methodologies and standards, identifying areas for action with a view to a stakeholder-conceived roadmap while also addressing legal barriers and solutions related to food safety.
2022
July
EFSA launches a platform for the collection and analysis of Whole Genome Sequencing (WGS) data on Salmonella, Listeria monocytogenes, and Escherichia coli in food and animals, following a request from the European Commission. The platform is accessible to national competent organisations in the field of food safety, which will be uploading data that come from the annual monitoring of foodborne diseases. It will interact with the equivalent ECDC data collection system.
The platform will support the work of EFSA and ECDC on rapid outbreak assessments, and ultimately help protect European consumers.
2019
December
Experts evaluate the possible use of whole genome sequencing and metagenomics to investigate foodborne outbreaks, in source attribution analysis and microbiological risk assessment A specialised field of applied science that involves reviewing scientific data and studies in order to evaluate risks associated with certain hazards. It involves four steps: hazard identification, hazard characterisation, exposure assessment and risk characterisation. They also analyse the advantages and limitations of next generation sequencing-based methodologies for characterising Salmonella and STEC and detecting antimicrobial resistance The ability of microbes to grow in the presence of substances specifically designed to kill them; for example, some human infections are now resistant to antibiotics, raising concerns about their widespread use genes in bacteria.
May
Following a request from the Commission, EFSA and the European Centre for Disease Prevention and Control (ECDC) provide technical support for the collection and analysis of whole genome sequencing (WGS) data. Experts assess the state of the art of existing tools and identify needs and requirements for the joint EFSA-ECDC data collection system.
EFSA's role
EFSA plays a significant role in coordinating the collection of WGS data of foodborne bacterial pathogens and, jointly with ECDC, uses these data for the preparation of assessments of multi-country foodborne outbreaks (known as rapid outbreak assessment or ROA reports).
One Health WGS system
EFSA and ECDC have developed the "One Health WGS system”, a sophisticated IT tool designed to gather and analyse WGS data from EU Member States. Operational since July 2022, this system collects and analyses genomic profiles of significant bacterial foodborne pathogens, such asListeria monocytogenes, Escherichia coli, and Salmonella enterica.
A video released by EFSA showcases how WGS data are used to combat foodborne outbreaks and explains how the ‘One Health WGS system’ works.
The system consists of two interconnected platforms, one hosted by EFSA and the other by ECDC. These platforms independently collect genomic sequencing data from each sector (human health and food safety) and generate profiles for cross-sectoral analysis. The platforms automatically exchange genomic profiles and continuously generate reports, enabling scientists at EFSA and ECDC to promptly identify and assess potential foodborne outbreaks.
The One Health WGS system provides several benefits by:
- Allowing Member States to share WGS data with EFSA and ECDC;
- Building databases of genomic profiles from human and food isolates to detect clusters and identify foodborne outbreaks;
- Supporting real-time investigations of multi-country foodborne outbreaks;
- Facilitating cross-sectoral collaboration and partnership among Member States in the food safety and public health sectors.
EFSA and ECDC use the information collected in the One Health WGS system, along with relevant traceability The ability to track the journey of a foodstuff or ingredient through all stages of production, processing and distribution and epidemiological evidence, to assess multi-country foodborne outbreaks. The goal of the two agencies is to identify the sources of such outbreaks, and specifically to pinpoint the food vehicle involved.
The rules of use for data stored in the EFSA and ECDC databases linked to the One Health WGS system are included in the EFSA ECDC collaboration agreement.
Ensuring secure and effective data sharing
The WGS system is designed to facilitate secure, efficient and flexible data sharing while respecting national priorities and ensuring stakeholder trust. It is based on the following key principles:
Data sharing occurs in a secure environment, ensuring data confidentiality and integrity;
- Countries maintain full ownership of their data, and the system guarantees their control and responsible use;
- The tool addresses the complexities of the EU context by allowing each country to designate data providers according to their national priorities;
- The tool supports national implementation processes for seamless integration with national systems while providing an intuitive portal for non-technical users;
- Data visibility is designed to protect country-specific information without compromising the effectiveness of the sharing process.
The outlined approach aims to build trust among stakeholders, foster effective cooperation, and enhance the protection of public health. It aligns national policies with broader EU objectives, yielding more effective and coordinated results across Member States.
Other relevant resources:
EU framework
- Implementing regulation (EU) 2025/179 outlines obligations for the collection and transmission of molecular analytical data related to food-borne outbreaks. The regulation was published on 31 January 2025 and will enter into force on 23 August 2026.
- Directive 2003/99/EC establishes rules on the monitoring and reporting of zoonoses and zoonotic A term given to diseases and infections that can be transmitted between animals and humans agents, forming the legal basis for the new requirements on molecular analytical data collection.
- EC FAQs FAQs on WGS in foodborne outbreak Two or more people developing the same foodborne illness after eating or drinking the same food investigations - European Commission
FAQs
- EU agencies: dedicated EFSA staff can access the EFSA platform and dedicated ECDC staff can access the ECDC platform.
- Food safety sector: access to the EFSA platform is granted only to data providers and country officers appointed by the food safety authorities of reporting countries.
- Public health sector: access to the ECDC platform (i.e. EpiPulse – which includes the ECDC platform as part of the One Health WGS system) is granted to users nominated by the National Coordinators of EU/EEA countries, in accordance with the ECDC Coordinating Competent body policy.
- The ECDC system detects “clusters” of isolates or identifies “events” of human cases; for each of the identified clusters or events, ECDC sends a request to the EFSA platform to search for any relevant data linked to it (i.e. genomic allelic related to alleles, which are different versions of a gene found at the same location on a chromosome profiles generated from raw sequences submitted by data providers). The EFSA platform then identifies profiles that closely match one or more members of the cluster, using allelic distance thresholds that EFSA and ECDC have jointly established and periodically review.
- The EFSA system responds to ECDC queries by transferring only genomic profiles (excluding raw sequences), along with other typing data and limited metadata. The metadata includes the year of sampling, country of sampling, country of the organisation and food category for any match found.
- During joint ECDC-EFSA assessments of multi-country foodborne outbreaks, all relevant information available for the investigation is exchanged between the two agencies.
- EFSA staff can access, view and fully manage all the data in the EFSA database.
- Data providers can access, view and fully manage the data from their own organisation.
- Country officers can access, view and fully manage the data from their own country on behalf of any data provider organisation.
- As result of a query, both data providers and country officers can access the following information related to data that does not belong to their organisation or country:
- Typing information (MLST, serotype, AMR profile, pathotype);
- Year of sampling (when available);
- Category: either “food” or “human”;
- Country: only if it matches the user’s country.
- It is not possible to download any data (sequencing data, typing data and other metadata) from the system unless it is owned and submitted by the data provider of the organisation.
- It is not possible to download the cross-sectoral analysis or results from interactions between EFSA and ECDC databases; users can visualise the results only on the EFSA platform.
- Cross-sectoral clusters are shown to public health users in EpiPulse.
- Clusters can only be seen by users of involved countries (i.e. those with human cases in the cluster) unless it is upgraded by ECDC to an event.
- Country users can access the results of the queries performed by ECDC automatically, following specific rules; data related to food, year of sampling, food category (e.g. fish and fishery product thereof) and country of sampling can only be seen by the involved countries (i.e. those with cases in the cluster).
- Food data cannot be downloaded by the users of the ECDC platform.
- Member States are the owners of their own data in the EFSA platform and can manage it within the system.
- They can share their data by making it accessible for other system users, including ECDC, based on the access, process and visibility rules described in the EFSA-ECDC collaboration agreement.
- They can edit their data to correct or integrate information.
- They can withdraw their data at any time if not locked by EFSA due to their inclusion in a published Joint EFSA ECDC outbreak assessment.
- ECDC and EFSA use the data collected in the One Health WGS system to make intersectoral analyses (i.e. joint microbiological cluster and outbreak detection and investigations) for joint ECDC-EFSA food-borne outbreak assessments and/or to support investigations linked to cross-border food-borne clusters, outbreaks and crisis events.
- ECDC and EFSA must obtain the consent of the data providers, who are in charge of securing approval from the data owners, before any publication or communication of the data (except for food-borne public health risk assessments) or of any work that reproduces or uses the data, unless explicitly authorised.