The European Food Safety Authority (EFSA) and EU Commission’s Inter-European Union Reference Laboratories (EURL) Working Group on Next Genome Sequencing (NGS) organized the second Science Meets Policy conference this week. More than 100 people from 20 countries attended in-person while online viewers peaked at 257.

Stefano Morabito, from the Italian National Institute of Health (ISS); George Haringhuizen, at the Dutch National Institute for Public Health and the Environment (RIVM); João André Carriço, of bioMérieux; Katja Alt, from the German Federal Ministry of Food and Agriculture and Coen van der Weijden, from the Netherlands Food and Consumer Product Safety Authority (NVWA) were featured on a panel discussion.

Panelists highlighted the need for flexibility, especially as there are 27 countries in Europe at different stages in use of Whole Genome Sequencing and as outbreaks can involve nations outside the EU. They discussed the types of data needed, data quality and comparability, resource issues, how to build trust and the role of different parties including regulators and industry.

EFSA and ECDC’s One Health WGS system has been operating since July 2022 and while things are going well, not all member states are contributing equally.

Data sharing dilemmas

Bernhard Url, EFSA’s executive director, said genomic data sharing is now at a turning point.

“We believe that from a technological and methodological point of view we are ready to use WGS data more widely and with more impact. Many of the problems have been solved and the technical infrastructure has been built. There is no doubt, at least within the community, that data sharing adds value, because it leads to faster outbreak detection and better tracing. It increases the likelihood of connecting sporadic cases to clusters and to detect outbreaks and there is measurable economic impact,” he said.

However, despite the knowledge that sharing data helps, there are still some obstacles that prevent wider use, said Url.

“There are technological gaps as not all member states or organizations use WGS on a routine basis. There is also a worry that people and countries say we don’t have a robust legal basis to share data. There is a fear that people lose control of data, they produce the data, share it but don’t know what happens afterwards. There is a concern that if this technology would be used widely, many more clusters would be detected, which is good from a public health point of view, but it also would increase the workload of national authorities to follow-up and deal with these clusters.”

Url said it would be “unwise” to wait for legislators to define the rules of the game.

“The WGS community must do our part to create the conditions for success. We think there is a lot we can do to move data sharing forward in the current legislative framework. We still have to work on creating a mutual understanding about benefits and limitations of this technology. We have to agree on common guidelines, processes and procedures, otherwise we wouldn’t know how to compare different outcomes,” he said.  

“We want to act as openly as possible but as confidential as needed, there is a fine line that we have to find. EFSA has invested resources in creating a technological infrastructure for enabling WGS data sharing, mainly to tackle foodborne threats. We will continue to do our part to move genomic data sharing forward.”

United States perspective

Eric Stevens, from the U.S. Food and Drug Administration, said the GenomeTrakr network is the result of 12 years of work. At the end of 2021, there were 600,000 genomes in the public database, today it is more than 1,000,000 sequences.

“After more than a decade of experience, it is not the sequencing that is the challenge when transitioning to this data, it is how you are going to analyze it, train staff, gain the skills and enable the entire system to utilize it effectively,” he said.  

“Metadata helps to tell a complete picture, without it you have a DNA sequence, which can only tell you some stuff. Contextual data gives that data life, it tells you where those bacteria came from, how they were living and when we are starting to think about the interventions we can make, we need that information to understand the complete picture.

“For us, the best use is making it open data available to anyone because somebody maybe interested in Salmonella, somebody else in E. coli and sometimes they overlap with interventions you can make for preventive controls and reducing contamination.”

Stevens said once data is in the database, a variety of things can be looked at.

“When you start thinking of the global food chain you can think where do we need more data from and start doing some projects to tackle those problems to better understand how food becomes contaminated in the first place. You wouldn’t know any of this unless you had the data that can help point the way,” he said.

“GenomeTrakr is responsible for almost 100,000 food and environmental isolates to tell a more complete picture of linking clinical isolates back to their sources, so we can not only respond to foodborne outbreaks but then try to prevent them. When you start looking at where your sources of food and environmental isolates linked to human illnesses come from, you can start doing source attribution and more preventive targeting. If we can get to a point where we can upload data in real time we can start to make those connections as early as possible to get a contaminated product out of the market.”

It can also help in moving from responding to outbreaks to trying to prevent contamination occurring.

“In a facility for example, you are not going to do WGS to identify a pathogen, you can do a quick culture method to see presence or absence. But if you have a facility that is concerned about whether they have a resident pathogen you would 100 percent like this information from WGS. You could expand that further to farms and potential water sources,” said Stevens.  

“When you start doing projects in different parts of the world you start understanding that everybody has issues that maybe aren’t issues for you. We’ve done a lot of work in Latin America and the big problem in getting started in sequencing is availability of reagents. We hear it costs five to seven times more than what we pay. When we talk about this being utilized by the world we have to start focusing on those issues that are going to make the most impact.”

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“What we say about food safety matters, what we write about food safety matters but most important is what we do,” said Frank Yiannas at the ONE – Health, Environment, Society – Conference in Brussels and online.

The event, from June 21 to 24, is organized by the European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control (ECDC), the European Chemicals Agency, European Environment Agency, European Medicines Agency and the European Commission’s Joint Research Centre (JRC).

Yiannas gave two examples of what the FDA is doing to increase consumer trust.

“The first one is food traceability, we are in the process of issuing a final rule later this year. We know from a food safety perspective, if there is a food scare, tracing that food back to source quickly can allow us to remove product from the market and shorten the epidemic curve, perform a secondary intervention and prevent additional illnesses. We believe better food traceability is about transparency and increasing this in the food system will breed trust,” he said.

“What’s the opposite of transparency in food? To me it’s what we have in today’s food system, too much anonymity, we really don’t know where those products come from, under what conditions were they produced, what certifications have they truly got and consumers also don’t know this.”

Data and consumer trust issues

The second action involves data, said Yiannas.

“I often say better food safety will begin and end with better quality data. We have the possibility of using tools to convert large volumes of big data that exists into actionable, preventive information. There is this big divide but new tools such as artificial intelligence, machine learning and the Internet of Things are causing this divide to close,” he said.

“In the data age, collaboration will increasingly involve public to public and private and public organizations sharing data and converting that into information and the entire food system getting smarter together. At FDA we are working on data trusts and have started a few projects to do just that.”

Yiannas said we are living through a “mega consumer trust bust”.

“Social scientists tell us consumers are less trusting of institutions, governments, companies, corporations and even of non-profits. On top of that people are increasingly polarized on issues of politics, climate change and how to deal with the pandemic. What about food? Do you think we, as a society, are increasingly polarized on food? I think the answer is yes,” he said.

“After three decades in the profession, I am sad to say I increasingly see food dividing us. I think food should unite us. We hear people talk about I want local food, others say they are ok with global food. Some people want organic and others are ok with conventional food, it tends to be more affordable. Some eat only natural and others are ok with processed foods. Today, we have an issue in many countries with too much food being as harmful as too little food.

“Never before in history has the responsibility to provide safe, available and sustainable food to so many rested on the shoulders of so few and never before have the consequences for not getting this right been more important.”

More than 4,200 participants registered online for the four day event, and around 1,000 signed up to attend in person. Of the latter, almost 90 percent come from Europe, with the rest from Africa, Asia and North America.

EFSA viewpoint on One Health and collaboration

Bernhard Url, EFSA’s executive director, said the speed of change creates widespread uncertainty and anxiety.

“The food system is in a state of crisis: hunger, obesity, food waste, resource depletion and biodiversity losses. With this conference, we would like to explore how food safety and more integrated health assessments can contribute to the transformation of food systems,” he said, when opening the conference.

“The One Health concept aims at balancing and improving the health of humans, animals and the environment. We think the principles of One Health make it ideal to support our work on addressing the complexity and urgency of the health challenges ahead. At EFSA, we think by applying these features, our food safety work will advance and be more fit for purpose and better inform policies which aim to transform the food system. One Health acts as a stepping stone, it connects food safety to sustainable food systems.”

Url said there is a need to see faster innovation in science methodologies to confront the challenges ahead.

“There is a trust issue – how can we anchor our scientific advice in a society that is ready to accept it. Even if the outcome is not liked because of value differences, people trust the process,” he said, during a later panel discussion.

“Everybody talks about collaboration and says yes we need to collaborate more, it’s a no-brainer but it’s not done enough, so what are the obstacles? I think here something is fundamentally wrong, so lets rectify it. Collaboration adds a layer complexity, you lose autonomy and give something for the bigger purpose which means it takes longer. There can be cultural or language differences, budgetary cycles and objectives of organizations are different. Maybe we have to put collaboration as an objective of organizations and not just something that could help us from the sidelines.”

EU Commission on regulation and EFSA’s role

Stella Kyriakides, EU Commissioner for Health and Food Safety, said trust in the food safety system underpins more sustainable food systems.

“The COVID-19 pandemic and Russia’s invasion of Ukraine have highlighted how we need a robust and resilient food system supplying sufficient, affordable food at all times,” she said.

“It has also brought home to us how our health, ecosystems, supply chains, consumption patterns and planetary boundaries are all interlinked. The increasing recurrence of droughts, floods, forest fires and new pests are a constant reminder that our food system is under threat and must become more sustainable and resilient.”

Kyriakides also mentioned the 20 year anniversary of the General Food Law Regulation and creation of EFSA. 

“The regulation’s common definitions, aims and general principles have redefined and shaped EU food law and policy. Chief among them is the risk analysis principle, under which food law must be science-based,” she said.

“EFSA’s scientific excellence has served to give EU measures a solid scientific basis. It has maintained confidence in the EU food supply. It has raised EU food safety and standards and it has definitely helped raise international standards in the process. Thanks to EFSA and the General Food Law, the European Union can pride itself on having one of the most robust and efficient food safety systems in the world.”

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Anne Bucher, a French national, has worked for the Commission for 35 years across several departments and will head the Directorate-General for Health and Food Safety (DG SANTE) beginning Oct. 1.

The DG SANTE is a department of the Commission. It is responsible for EU policy on food safety and public health and monitoring implementation of related laws.

Vytenis Andriukaitis is European Commissioner for Health and Food Safety and Jean-Claude Juncker is head of the European Commission until European Parliament elections next year.

Bucher is currently chair of the commission’s Regulatory Scrutiny Board and will succeed Xavier Prats Monné who will retire at the end of September to work with non-profit organizations in the education sector. He became the head of DG SANTE in September 2015.

Bucher has been a senior manager in the Commission’s Directorates-General for Economic Affairs and for Communications Networks, Content and Technology, respectively, since 2008.

Her career has focused on policy areas including economy and finance, development and social policy, taxation and information society.

Bucher will bring a broad view of European Commission policies in a variety of areas, to help with situations when health and food safety management is interlinked with economy and technology.

The European Commission also proposed to the administrative board of the European Food Safety Authority (EFSA) to extend the term of its current executive director, Bernhard Url, for five years as of June 2019. Url has been managing EFSA since 2013, following a role at the Austrian food safety authorities.

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The Authority is an agency of the EU, but one that is housed in Parma, Italy, not Brussels, Belgium, where the EU governmental operations are headquartered.

Now, however, the European Food Safety Authority’s (EFSA) Management Board Chair Jaana Husu-Kallio says the agency has adopted a new, robust and well-balanced independence policy that includes several new measures to further strengthen the Authority’s impartiality and protection against improper influence.

“The policy we agreed today (June 21)  is the result of months of debate and consultation,” said Husu-Kallio. “We thank our stakeholders and the public for their important suggestions, which were considered with great care. The system already in place was robust and effective and we have further strengthened it.

“Independence is not black and white – we have to strike a balance between attracting experts and securing ourselves against undue influence. Some people might think we have gone too far or could have gone further, but I am confident that we have got the balance right.”

Husu-Kallio said the next challenge is to implement the policy.

“We will do this by the end of 2017 so that the new rules can be used in the renewal process for our scientific panels, which begin new terms in 2018,” Husu-Kallio said.

EFSA’s existing range of safeguards rests on a comprehensive system for avoiding conflicts of interest among its external scientific experts. These measures include:

• A multi-layered scrutiny system of annual declarations of interest (ADoIs), specific declarations of interest (SDoIs) and oral declarations of interest (ODoIs). ADoIs are submitted by all members of EFSA’s Scientific Committee, Scientific Panels and Working Groups.
• All DoIs are screened to identify potential conflicts related to an expert’s professional activities and financial interests. A range of options is available to resolve conflicts – e.g. the expert may be considered ineligible for membership or chairmanship of a panel, or can be asked to relinquish a position, or shares in a company.
• Compliance checks are performed on a sample of DoIs twice a year by staff members not involved in the assessment and validation process. Regular external audits are carried out by the European Court of Auditors, the Internal Audit Service of the European Commission, and external contractors.

The revised policy now includes:

• A new definition of what constitutes a conflict of interest, which brings EFSA into line with the most recent rules adopted by the European Commission for its expert committees.
• A comprehensive set of “cooling-off” rules: external experts will be automatically barred from joining EFSA’s scientific panels if in the preceding two years they have been employed by, acted as consultants to, or have offered scientific advice to organisations that work in areas covered by EFSA’s remit. The cooling-off rules also apply to experts who have received research funding from such organisations over the same period.
• A requirement that experts declare the proportion of their annual earnings received from any organization, body or company whose activities fall within EFSA’s areas of work. This information will be published and used as part of the DoI assessment.
• Publication of the list of EFSA’s partner organisations, such as national and international authorities, universities or research institutes.
• Member State experts who take part in peer review meetings to be subject to the same scrutiny and transparency measures as panel experts.

“I am pleased that our governing body has equipped us with such a strong set of measures,” said Bernhard Url, EFSA’s executive director. “EFSA’s scientific advice has little value unless it is trusted, and the public will grant us that trust only if they can see that we are independent.”

EFSA was set up in 2002 following a series of food crises in the late 1990s to be a source of scientific advice and communication on risks associated with the food chain. The agency was legally established by the EU under the General Food Law – Regulation 178/2002.

The General Food Law created a European food safety system in which responsibility for science-based risk assessment and risk management policy are kept separate. EFSA is responsible for the former area, and also has a duty to communicate its scientific findings to the public.

• EFSA’s policy on independence
• Outcome of the public consultation on EFSA’s draft Policy on independence