Antimicrobial resistance (AMR), novel foods and emerging risks are some of the main topics facing the food system, according to EFSA’s chief scientist.

Marta Hugas, from the European Food Safety Authority (EFSA), said regulatory agencies face challenges ranging from current priorities, such as tackling AMR and food waste, to identifying emerging risks, wher methodologies or data may be lacking, such as microplastics in the food chain.

Hugas told attendees at IAFP’s European Symposium there are difficulties when providing scientific advice to policy makers and the public.

“First of all is the complexity, every time the volume of evidence keeps increasing so assessing thousands of papers takes a lot of time. We are experimenting with using Artificial Intelligence for pre-selecion of papers and adding some inclusion and exclusion criteria. The methodologies are also evolving and we need to be able to capture and apply this methodology,” she said.

“Societal expectations are also very demanding. They want us to have a holistic approach, so not to look at pesticide by pesticide but the whole exposure of chemicals to public health. Also, they want us to be transparent so they can scrutinize what we do and at the same time, the desire to participate, which is valid but poses some challenges on how to organize that.”

Emerging risks and novel food
Policy developments such as the EU’s Green Deal and product innovation like novel foods require risk assessors to identify potential issues and then advise risk managers to protect European consumers from food-related risks.

One of EFSA’s tasks is emerging risks identification and the Emerging Risks Exchange Network (EREN) met this past month to discuss topics including the health risks of coconut oil, prohibited pesticide residues in food and Shiga toxin producing E. albertii.

“We identify an emerging risk when there is a new hazard that may pose a risk to health with adverse effects or it is a known hazard that has changed with increased exposure, the population has increased susceptibility, the hazard has increased pathogenicity or toxicity or product composition or intake has changed,” said Hugas.

“Initially we call them issues as we don’t know if they are risks or not. We use a process with expert knowledge and literature to help us identify if it may become an emerging risk. However, there is a lot of uncertainty so it is important not to create concerns.”

Hugas said it can be difficult to assess innovation in the food sector.

“Industry is ahead and experimenting with innovation in their products. When an innovative product comes to us we need to be ready with a methodology to assess that product. One of these is alternative proteins, today there is a market and consumer drive for diversification of available proteins also to be less dependent on animal proteins. When we assess applications for novel foods, the focus is on the safety of the product taking into account its intended use,” she said.

AMR and the circular economy
A recent report found resistance levels still were high in bacteria causing foodborne infections.

Hugas said antimicrobial resistance contributes significantly to the burden of disease and is a threat to public health.

“In EFSA we keep working on AMR. We see that it doesn’t really improve a lot so we need to keep investing efforts in reducing consumption. In a report from several years ago it was clear that to combat AMR, we need to reduce the use of antimicrobials and replac them by other substances and rethink the way husbandry systems are implemented in the EU.”

When asked what upcoming hazards in the food chain might be, Hugas said AMR could be the next pandemic if controlling resistance and the usage of antimicrobials is not taken seriously.

In 2020 to 2021, EFSA launched three projects to identify emerging risks related to the circular economy, food fraud, and new food and feed sources and production techniques.

The EU Green Deal calls for a circular economy and while this brings positives there may be some vulnerabilities, said Hugas.

“We have commissioned a project which aims to identify vulnerabilities of the circular economy for food and feed safety, plants and animal health and the environment. We know we have to be vigilant as in the past a threat to public health came from the BSE crisis. We need to be aware of possible disadvantages to prevent them as far as possible.”

Sector’s WGS approach
Another session at the event discussed Whole Genome Sequencing (WGS) from an industry perspective. The Forum for Food Microbiology is a network including 45 members from 28 companies that has quarterly meetings and will soon publish a guidance document.

Adrianne Klijn, of Nestlé, presented findings from a workshop and survey in 2019 involving 33 people from 18 companies although a further 12 firms declined the opportunity.

The included businesses were Arla Foods, Bonduelle, Cargill, Church Brothers Farms, Conagra Brands, Danone, Darling Ingredients, DSM, Fonterra, Greenyard, Hochdorf, Kerry, Kraft Heinz, Mars, Mondelëz International, Nestlé, Unilever, and Vion Food Group.

In total, 83 percent said they used WGS either frequently or infrequently. However, 12 said they were still using serotyping routinely meaning it was unlikely WGS will replac all other typing tools in the near future. Klijn said there are good subtyping tools for Salmonella but there is room for improvement when it comes to Listeria and Cronobacter.

Lab cross contamination is a good example of wher the discriminatory power of WGS is needed, according to Klijn.

From 16 companies, 15 said they were only using WGS for pathogen source tracking while just a few were doing it for strain characterization.

The survey and workshop found the laboratory part is mostly outsourced with only two having in-house sequencing. Most used Illumina sequencing platforms. Bioinformatics was split three ways between in-house, outsourcing and doing both.

“The authorities deal with positive samples with isolates all the time, in the food industry we have a lot less positive samples, so we have fewer isolates and this low sample throughput means the cost per analysis is high with a low return on investment in the equipment. The reason [bioinformatics] is less outsourced is there is a lack of method standardization and analyzing the data in house will ensure a consistent approach,” said Klijn.

Barriers that remain include the regulatory pressure to share WGS data, absence of a legal framework, a lack of clarity on data ownership, time to result and total cost including equipment, IT infrastructure and expertise in sequencing, bioinformatics and microbial genomics.