Need to Know

• Regulation (EU) 2025/179, which came into effect on August 23, requires EU Member States to conduct WGS on five key pathogens during foodborne illness outbreak investigations
• Faster, more complete sharing of WGS data through the EFSA–ECDC One Health WGS System can reveal cross-border outbreak connections and facilitate rapid responses
• Food business operators must cooperate with competent authorities by providing pathogen isolates and WGS upon request during outbreak investigations
• Dr. Frank Verdonck, Head of EFSA’s BIOHAW unit, explained the importance of Regulation (EU) 2025/179, how it will work in practice, and how food system stakeholders should prepare
• EFSA’s Science Meets Policy conference, taking place September 2–3 in Rome, will address implementation challenges, industry concerns and misconceptions, public-private collaboration, and how WGS data will be leveraged under the new regulation.

Regulation (EU) 2025/179 came into force on August 23. What problem was the regulation intended to solve, and what will fundamentally change about how WGS data are generated, shared, and used during foodborne illness outbreak investigations in the EU?

Foodborne illness outbreaks increasingly involve cases that initially appear sporadic and unrelated, often involving products that may be distributed across multiple countries. In these situations, identifying whether cases reported in different locations are linked to the same source requires detailed comparison of pathogens isolated from food, animals, production environments, and infected people. WGS provides this level of resolution by generating the genetic fingerprint of a microorganism, allowing scientists to determine whether isolates are closely related and may be part of the same outbreak.

Regulation (EU) 2025/179 addresses three practical gaps in the way WGS is used during foodborne illness outbreak investigations in the EU:

1. First, on data generation: WGS is already used in many countries, but implementation remains uneven across the EU because of differences in capacity, costs, expertise, and infrastructure. By requiring WGS data for relevant outbreak-related isolates, the regulation acts as an important driver for accelerating national implementation and for promoting a more consistent use of WGS in outbreak investigations. 
2. Second, on data-sharing: The regulation provides a clearer legal framework for when and what information should be shared at the EU level. This helps competent authorities take decisions on data-sharing in a more consistent way, clarifying why certain data are essential for EU-wide outbreak assessment. The scope remains focused on outbreak-related data, but it is an important starting point for broader and more systematic data-sharing in the future.
3. Third, on data use: WGS data still need to be interpreted together with epidemiological and food-chain information. The regulation is expected to improve the completeness and timeliness of the data available at the EU level, supporting stronger EU-wide comparisons and improving the detection and investigation of cross-border outbreaks.

The regulation requires competent authorities to collect isolates for Salmonella enterica, Listeria monocytogenes, Escherichia coli, Campylobacter jejuni, and Campylobacter coli when associated or suspected to be associated with an outbreak, and transmit WGS results “without undue delay.” In practice, what does sufficiently timely data collection and sharing look like, and how could this help investigators?

The benefits of WGS are realized only when genomic data are made available for sharing, enabling comparisons across sectors and borders. In practice, "without undue delay" means that competent authorities should collect relevant isolates, generate WGS data, and share the results as soon as they are available, rapidly enough to support investigations while an outbreak is ongoing. The intention is to avoid situations where data are generated and used nationally but shared at the EU level only much later, when their value for detecting wider links has been reduced. 

Faster and more comprehensive data-sharing can help reveal links that might otherwise remain unnoticed, helping identify cross-border links that individual countries may not see on their own. 

There is no single fixed timeframe, as this depends on the investigation and the availability of isolates and sequencing results.

EFSA and ECDC's One Health WGS System allow food, feed, animal, and environmental isolates to be compared with isolates from human cases. How can bringing these different streams of genomic information together improve multinational outbreak investigations?

The key advantage of EU-level genomic data-sharing is that it provides a broader view than any single country can have on its own. This is especially relevant in an open market, where contaminated products may be produced in one country, distributed in others, and cause cases across borders.

By bringing these different streams of information together, the One Health WGS System allows investigators to compare the genetic fingerprints of pathogens from multiple sources within a common framework. This can help identify links that may not be apparent when data are analyzed separately at the national or sector level, facilitating early signal detection in human populations and in the food chain before they become larger outbreaks.

WGS can establish that isolates are genetically related, but epidemiological and traceback information are still needed to understand what that relationship means. How should genomic, epidemiological, and traceback evidence be integrated to move from detecting a cluster to identifying a source and taking action?

At the Member State level, competent authorities have the primary responsibility for investigating and controlling outbreaks, in line with the EU Zoonoses Directive. Microbiologists, epidemiologists, food-chain experts, risk assessors, and risk managers all contribute different pieces of evidence that are needed to understand the event and decide on appropriate action.

When an outbreak may be multinational, the role of EFSA, ECDC, and the European Commission becomes essential. Their collaboration helps bring together information from the food and public health sectors, coordinate the Member States involved, and support a rapid common understanding of the outbreak and the possible risk management measures needed.

Previous Food Safety Magazine content written by EFSA authors highlighted differences among sequencing platforms, bioinformatics pipelines, infrastructure, and national capacity as barriers to WGS implementation and data harmonization. How much progress has been made, and what practical or interoperability challenges remain?

Significant progress has been made in recent years in building the technical and organizational foundations needed for wider use of WGS in foodborne illness outbreak investigations. Multiple Member States have expanded their sequencing capabilities and are applying WGS systematically. Collaboration has increased across sectors, and the EFSA–ECDC One Health WGS System now provides a common framework for collecting and analyzing outbreak-related data at the EU level. Bioinformatics workflows are becoming more harmonized, and the EFSA workflow for the food sector, interoperable with ECDC’s system, is increasingly used as a reference at the national level. EU Reference Laboratories have also played an important role in supporting training, knowledge transfer, and more consistent implementation across countries.

The remaining challenges are now less about whether WGS can be used, and more about how to ensure that data are used in a comparable, timely, and interpretable way. New sequencing technologies will continue to emerge, making it essential to maintain comparability across sequencing platforms and bioinformatics workflows. Interpreting WGS clusters also remains complex and requires integration with epidemiological, traceback, and contextual data, as well as a shared understanding of bacterial population dynamics and evolution.

As the new regulation becomes applicable, attention is increasingly focused on ensuring consistent implementation across countries and sectors. Continued efforts will be needed to support data quality, interoperability, timely sharing of information, and the effective use of WGS in outbreak investigations. The September Science Meets Policy conference will provide an opportunity to discuss these practical challenges and exchange experiences among stakeholders.

Under Regulation (EU) 2025/179, food and feed business operators may be required to provide available pathogen isolates and related WGS results during suspected outbreaks. What should companies understand about this obligation, and how should businesses, particularly smaller firms with more limited access to resources, prepare?

This will be one of the central themes of the Science Meets Policy conference. Food business operators are legally required to cooperate with competent authorities during foodborne illness outbreak investigations. Article 15 of Regulation (EU) 2017/625 clearly stipulates that operators must assist and cooperate with competent authorities during official controls and other official activities, including outbreak investigations. This cooperation is also in their own interest: by helping identify the source of contamination and the affected consignments, companies can help limit the public health impact of an outbreak and reduce the consequences for their own operations.

Although cooperation with competent authorities is already part of the EU legal framework, Regulation (EU) 2025/179 is clear on the specific role of business operators in relation to WGS. It does not require operators to systematically perform WGS or routinely share genomic data. Instead, when requested by the competent authorities during an outbreak investigation, operators must provide pathogen isolates, if available, and share any WGS results that they have generated or commissioned on their own initiative.

Therefore, the main expectation for companies, and especially for small and medium enterprises (SMEs), is not that they invest directly in implementing WGS capacity. Rather, they should be ready to cooperate actively with competent authorities during outbreak investigations, understand what WGS is and how it is used by authorities, and consider investing time in training relevant staff so they can engage effectively when isolates or existing WGS results are requested.

What aspects of Regulation (EU) 2025/179 implementation might still limit the regulation’s effectiveness, and how might such challenges be overcome?

The main bottlenecks are likely to be at the Member State level, particularly in the capacity to collect and organize all the information required for submission. The regulation requires the sharing not only of WGS results, but also of the contextual metadata needed to interpret them. This requires coordination among laboratories, epidemiologists, food safety authorities, and risk managers, so that the relevant information is collected, structured, and shared with EFSA in a timely way. In some Member States, this may require adjustments to existing outbreak investigation workflows to ensure that genomic and contextual data are available together when they are needed.

For some countries, another challenge will be the practical implementation of WGS itself. Where WGS capacity is not yet fully established, additional time may be needed before the system becomes fully effective. Continued training, knowledge transfer, and support from EFSA and the EU Reference Laboratories will be important to overcome these gaps and ensure more consistent implementation across the EU.

EFSA will remain available to provide further technical and operational support where needed.

The September 2–3 Science Meets Policy conference in Rome comes just days after the regulation becomes applicable. What misunderstandings or uncertainties about the new requirements are you hearing most frequently from food business operators, and what do you hope the conference will clarify?

We hope the conference will first help create a clearer and more realistic understanding of what WGS can and cannot do. Some concerns from food business operators are linked to real questions about implementation, but others are driven by misconceptions about how WGS results are interpreted. For this reason, the keynote presentation will focus on the scientific value and limitations of WGS, including what conclusions can and cannot be drawn from genomic data alone.

One recurring concern that will be addressed at the conference is that WGS data may remain in databases after an outbreak assessment and could later be used to support regulatory action simply because a genomic cluster is detected. In actuality, the scientific need to understand pathogen population dynamics and the need to identify outbreak sources are complementary, not contradictory. In outbreak investigations, source attribution cannot rely on WGS alone; it requires the combined assessment of genomic, epidemiological, and traceback evidence.

Another area of uncertainty is how competent authorities use and share WGS data. The conference will present examples from Member States showing how they are preparing for the new regulation, how WGS is being incorporated into national systems, and how authorities interact with food business operators. We also invited U.S. speakers to present how agencies and operators interact in the U.S. context, offering a useful comparison for EU stakeholders.

Finally, the program will address the practical value of WGS for industry. Some operators are concerned about whether sequencing is useful in a business context, beyond regulatory requirements. Sessions with multinational food business operators and representatives from sectors such as meat, fresh produce, and slaughterhouses will show how WGS can support internal investigations, prevention, and participation in EU and global data-sharing. The final moderated discussion will bring these issues together and focus on the main remaining challenges at the Member State and operator levels.

The conference will also address examples of collaboration between competent authorities and industry. What would a successful public-private WGS data-sharing partnership look like?

For food business operators, the most important contribution is good cooperation with competent authorities. This collaboration starts at the national level: the first interaction is between food business operators and the national competent authority. Any sharing of data at the EU level is mediated by the national competent authority, which remains the data controller and ensures the chain of custody of the data. A successful public-private WGS partnership features clear roles, timely communication, and a mutual understanding that sharing data and isolates through the appropriate authority can help identify contamination sources more quickly and reduce the impact of an outbreak.

If implementation works as intended, what would you expect a foodborne illness outbreak investigation in Europe to look like a few years from now, compared with one conducted before Regulation (EU) 2025/179?

If implementation is effective, the main change will not be only technical, but also cultural. Regulation (EU) 2025/179 has the potential to promote a broader understanding that timely data-sharing at the EU level is essential for managing outbreaks effectively.

Compared with the past, investigations will be more connected. Genomic and contextual data will be available more rapidly for EU-level comparison, allowing authorities to assess earlier whether a signal is limited to one country or is part of a wider event involving several countries.

In the longer term, this could support a more proactive system. When food safety and public health data are shared and compared in a timely way, some outbreak signals may be detected already at the food sector level, allowing authorities and operators to act earlier and prevent contamination events from developing into full outbreaks.

About Dr. Verdonck

Dr. Frank Verdonck holds a master’s degree in biotechnology and a Ph.D. in Veterinary Sciences from Ghent University in Belgium. He has developed his career at the interface of science, policy, and management, with a focus on food and feed safety, as well as animal health and welfare.

He joined EFSA in 2012, where he initially supported the Panel on Animal Health and Welfare. Between 2018 and 2021, he led the FEED Unit, responsible for the scientific assessment of feed additives. Since September 2022, he has been heading the BIOHAW unit, overseeing risk assessment and monitoring activities related to biological hazards, antimicrobial resistance, and animal health and welfare.