Most technical aspects related to sequencing have been solved but data sharing and trust remain key issues, according to experts in Europe.

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.  

Eric Stevens from FDA
Eric Stevens

“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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