FDA supports EU’s WGS outbreak plan; food industry groups voice concerns

The U.S. Food and Drug Administration (FDA) has backed European plans to use whole genome sequencing (WGS) to help solve outbreaks.

The European Commission recently asked for comments on potential legislation requiring EU countries to do WGS during foodborne outbreaks.

The FDA said the proposed regulation would “significantly improve food safety and public health within the European Union.”

The genomic sequence of isolates collected from clinical, food, or environmental samples in the United States is publicly available, with limited metadata, through the National Center for Biotechnology Information (NCBI).

International angle
The FDA suggested data submitted to ECDC and EFSA’s One Health database could also be uploaded to the International Nucleotide Sequence Database Collaboration (INSDC).

“The inclusion of sequence data plus limited metadata, such as date of collection, isolate source, and geographic area, collected from samples in the European Union in the INSDC could make a greater impact when combined with data from the rest of the world on food safety both within the EU and globally, allowing public health professionals and food safety authorities to more rapidly detect and address foodborne illness affecting multiple countries or regions.

“The food supply chain is becoming increasingly global, and the U.S. and the EU share many common importers of food; thus, having integrated data systems and working together greatly benefits consumers in the United States and European Union.”

Under the EU Commission plans, member states would collect Salmonella, Listeria monocytogenes, E. coli, Campylobacter jejuni, and Campylobacter coli isolates from food, animal feed, and related environmental samples from businesses and during official inspections, where the isolates are suspected to be associated with a foodborne outbreak. They would also need to carry out WGS on those isolates.

EU countries would send results to the European Food Safety Authority (EFSA), which developed the One Health WGS system with the European Centre for Disease Prevention and Control (ECDC). EFSA would compare the WGS results on these isolates with findings from human isolates communicated to ECDC to identify the source of outbreaks.

Because of the time needed to adapt to the new rules and technical and financial considerations, the regulation would not come into force until 18 months after the proposed rules are finalized.

Pushback from industry
FoodDrinkEurope was one of several respondents who raised concerns about financial feasibility, data protection, technical accessibility, regulatory burden, and international competitiveness.

The group, representing the EU’s food and drink manufacturing sector, said implementing WGS can be costly, especially for small and medium-sized enterprises (SMEs), plus the rising costs for product insurance policies due to the increasing likelihood of recalls.

FoodDrinkEurope said the regulation should adopt a risk-based approach, where WGS is mandated only for high-risk or large-scale outbreaks.

The European Chilled Food Federation said any data on test results submitted by firms to a government agency stays in that system, so if a match is found in the future, the company having sent the data can be blamed for an outbreak, with allegations made of persistent contamination.

CLITRAVI, the European Association for the Meat Processing Industry, said government agencies are pressuring firms to share their WGS data, although the companies have paid for the tests and own the data.

The Dutch Meat Association (COV) and Dutch Meat Products Association (VNV) said the proposal would not result in a representative dataset from EU companies, as only a few with enough resources are carrying out WGS. This could lead to a large company being blamed for a finding because other firms with fewer resources are not performing WGS. This will make businesses less willing to invest in WGS research and result in less research being carried out.

They added that there is no mutually agreed international nomenclature for genetic variations. This is a barrier to utilizing WGS data and needs to be resolved internationally prior to making data sharing mandatory. Otherwise, the data will not be able to be interpreted clearly.

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Source: https://www.foodsafetynews.com/2024/09/fda-supports-eus-wgs-outbreak-plan-food-industry-groups-voice-concerns/