The US Food and Drug Administration (FDA) has backed European plans to use whole genome sequencing (WGS) to help tackle outbreaks.
The European Commission recently asked for comments on potential legislation requiring EU countries to apply 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 corner
The FDA suggested that data submitted to ECDC and EFSA’s One Health database could also be uploaded to the International Nucleotide Sequence Database Collaboration (INSDC).
“Including sequence data plus limited metadata, such as date of collection, isolated source and geographical area, collected from samples in the European Union in the INSDC could have 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 quickly detect and tackle foodborne diseases affecting multiple countries or regions.
“The food supply chain is becoming increasingly global, and the US and EU share many common food importers; So having integrated data systems and working together provides major benefits for consumers in the United States and the European Union.”
Under the European Commission’s plans, Member States would collect isolates of Salmonella, Listeria monocytogenes, E. coli, Campylobacter jejuni and Campylobacter coli from food, feed and related environmental samples from establishments and during official inspections, where the isolates are suspected of contamination are. associated with a foodborne outbreak. They should also perform WGS on those isolates.
EU countries would send the results to the European Food Safety Authority (EFSA), which developed the One Health WGS system together with the European Center for Disease Prevention and Control (ECDC). EFSA would compare WGS results for these isolates with findings from human isolates reported to ECDC to identify the source of outbreaks.
Due to the time needed to adapt to the new rules and technical and financial considerations, the regulation would not enter into force until 18 months after the proposed rules have been finalized.
Backlash from the industry
FoodDrinkEurope was one of many respondents who expressed concerns about financial viability, data protection, technical accessibility, regulatory burden and international competitiveness.
The group, which represents the EU’s food and drink manufacturing sector, said implementing WGS could be costly, especially for small and medium-sized enterprises (SMEs), plus rising costs for product insurance policies due to the increasing likelihood of recalls.
FoodDrinkEurope said regulations should adopt a risk-based approach, with WGS only mandatory for high-risk or large-scale outbreaks.
The European Chilled Food Federation said any test result data submitted by companies to a government agency will remain in that system, so if a match is found in the future, the company that submitted the data could be blamed for an outbreak , with accusations of continued pollution.
CLITRAVI, the European Meat Processing Industry Association, says government agencies are pressuring companies to share their WGS data, even though the companies paid for the tests and own the data.
The Dutch Meat Association (COV) and the Dutch Meat Products Association (VNV) say the proposal will not result in a representative dataset of EU companies, as only some with sufficient resources carry out WGS. This could lead to a large company being blamed for a finding because other companies with fewer resources do not conduct WGS. This will ensure that companies are less willing to invest in WGS research and that less research is done.
They added that there is no mutually agreed international nomenclature for genetic variations. This is a barrier to the use of WGS data and needs to be resolved internationally before data sharing becomes mandatory. Otherwise the data cannot be interpreted clearly.
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