Whole Genome Sequencing (WGS) provides new opportunities for improving bacterial food safety but also brings with it some concerns, according to Belgian experts.

An opinion by the Scientific Committee of the Federal Agency for the Safety of the Food Chain (FASFC) made several recommendations about implementing the technology in Belgium.

Different foodborne pathogens including Salmonella, Listeria monocytogenes and Shiga Toxin-producing E. coli (STEC) are covered in the report. These are the initial focus of a WGS database developed by the European Food Safety Authority (EFSA) and European Centre for Disease Prevention and Control (ECDC).

The committee advised FASFC, also known as AFSCA or FAVV, to start making the transition to WGS for the analysis of food isolates in the near future. This would allow labs time to get experience and ensure they have the necessary infrastructure.

Current situation and future potential
In Belgium, the use of WGS for food safety monitoring and control purposes is not yet harmonized but some labs are using the technique. Whole genome sequencing is mainly done to confirm an outbreak and only in specific cases to proactively detect a potential incident. For the food industry, available WGS data is limited and there is not yet a centralized database.

In the future, WGS will be the preferred method for bacterial food safety investigation, because of its high discriminatory power and the phasing out of older typing methods internationally. It will become the technology of choice for outbreak investigation, pathogen strain typing, national surveillance, and source attribution, said the experts.

Despite the fact that WGS methods and pipelines for data analysis are still evolving and improving, WGS is ready to be used in outbreak investigation and surveillance activities. However, there are limitations for routine and uniform implementation. Efforts should be made to validate the WGS methodology and to facilitate data sharing and comparison.

When using WGS for subtyping strains, as part of an outbreak investigation, validated or internationally recognized methods and bioinformatics tools should be used, and interpreted according to the pathogen involved and taking into account the epidemiological evidence and metadata on the strains. This data should include things such as location, isolation source, collection date, the organization performing collection and sample and strain names.

Role of epidemiological investigation
The technology could also be used to investigate presence of pathogens in food processing environments and to follow up cleaning and disinfection processes.

By June 2022, the joint European database will be operational between EFSA’s WGS database with isolates from food products and ECDC’s TESSy with clinical isolates from humans.

The committee warned about correctly interpreting results and communicating about the source of contamination during an outbreak. They recommended that WGS-based results on the relatedness of strains in outbreak investigations are interpreted by a multi-disciplinary team including microbiologists, bio-informaticians and epidemiologists with sufficient expertise.

It is not possible to define a clear threshold for the number of genetic differences between strains from a common source. WGS data should be combined with metadata informing the epidemiological part of outbreaks, according to the scientists.

It is also difficult to estimate to what extent food businesses will adopt WGS in their self-monitoring and how willing they will be to share data.