In October 2021 the Scientific Committee of the Federal Agency for the Safety of the Food Chain (FASFC) published the opinion 18-2021 regarding whole genome sequencing (WGS) for the detection of foodborne outbreaks and bacterial risk assessment. This opinion was prepared using a self-tasking mandate and published after public consultation.

The added value of WGS for the detection of foodborne outbreaks and bacterial risk assessment has been demonstrated on many occasions in the last couple of years. Therefore, the implementation of WGS in the Belgian context needs some serious reflection. In the future, WGS will largely replace the various older typing methods in the field of bacterial food safety investigation, due to its high discriminatory power and the general use at the international level. Therefore, the Scientific Committee advises the FASFC to gradually make the transition to WGS for the analysis of food isolates.

While the advantages of the WGS method are considerable, some challenges still need to be taken into account for routine and uniform implementation. As with the implementation of any method the validations of the WGS methodology requires a significant effort. Furthermore, the interpretation of the results should be done with care. Therefore, in outbreak investigations it is recommended that WGS-based results be interpreted by a multidisciplinary team (microbiologists, molecular biologists, bioinformaticians, epidemiologists) with sufficient expertise. Only by putting the WGS-based results, the epidemiological evidence and the strains metadata together can a hypothesis be formulated. Further care should be given to the communication of these interpretations or hypotheses to the different actors (competent authority, food business operator, consumer). Finally, effort should be made to facilitate data sharing in an appropriate way.