Whole genome sequencing (WGS) by companies in Norway will likely be used for certain samples or in particular situations instead of all the time, according to a report.

The report looks at the legal rules that may affect WGS implementation of bacterial pathogens in the food industry, using Listeria monocytogenes as a case study.

Work was part of the PathoSeq project that began in 2019 and ended in 2023. It involved Nofima, the University of Oslo, the University of Veterinary Medicine in Vienna, Austria and companies in the meat and salmon sector.

The EU legal framework distinguishes between ready-to-eat (RTE) foods and food that is supposed to be cooked before consumption and between foods supporting the growth of Listeria and those that don’t. Stricter rules are applied for smoked salmon, sushi, deli meat, and soft cheeses.

Under EU law, firms are not obligated to notify the authorities upon detection of Listeria monocytogenes in their processing environments. Notification occurs mainly if foodstuff with Listeria has been sent to the market above the legal maximum levels.

Understanding findings
Detailed genomic sequences can allow companies to map the bacterial variants within their factories and discover sources and spread, enabling more informed risk assessments, control measures, and targeted responses, said experts.

Sequencing takes days or weeks, which is too long to be useful as part of daily hygiene monitoring or product release programs. Also, analyses may be too expensive for companies, especially compared to only considering the presence or absence of Listeria, which is sufficient to comply with current regulations.

From interviews, Norwegian firms generally have not yet applied WGS as part of their internal Listeria monocytogenes control programs. However, many companies were interested in the technology and the information it could provide.

Most interviewees said suppliers would not notify them upon detection of Listeria monocytogenes. Suppliers are not legally required to provide such information. Firms also don’t sample every batch of raw materials they receive. However, notice from suppliers appears common for the detection of Salmonella.

One producer of RTE fish products said it used to export to the U.S. but stopped since should any Listeria monocytogenes be detected during a control, the whole container would be returned or destroyed, presenting too high an economic risk for the business. While the U.S. has a zero-tolerance approach, EU law permits Listeria up to 100 CFU/g at the end of the shelf life in RTE products.

Data concerns
Concerns may relate to using WGS data, particularly how it may be interpreted and acted upon by regulatory authorities. Data, including metadata, needs to be assessed by experts, and there are risks of misinterpretation and overreaction. Industry interviews showed that trust in authorities’ competence and use of WGS data was low and fragile. They also worry about what other firms or customers might discover about their factories and food safety controls.

Highly similar Listeria monocytogenes may exist independently in multiple locations simultaneously, and many firms have the same supplier. Biases may arise because sampling is not performed to the same extent or equally by all parties.

Companies feared being incorrectly blamed and suffering the financial and reputational consequences if they were not the source of an outbreak.

Standards for assessing the data may also differ, for instance, regarding how many genetic differences one considers can exist between isolates while concluding that they originate from a common contamination source.

One example was given of a company requesting WGS data from Mattilsynet. only limited data was provided, and the report said refusing to grant companies access risks increasing the divide and hindering their willingness to cooperate.