EFSA: requirements for WGS analysis of microorganisms intentionally used in the food chain

Microorganisms can be employed as food or as producing organisms of substances of interest in the food chain, regardless of whether they have been genetically modified or not.    

The introduction of such microorganisms or derived substances/products onto the European market may be subject to a pre-market authorization procedure. The approval procedure specifies the requirement to conduct a risk assessment to determine the safety and/or efficacy of microorganisms when employed in the food chain as such or as production strains of compounds of interest. The microorganisms that are subject to the application for authorization must be characterized in order to undertake a risk assessment.    

In relation to the latter, the data obtained from whole genome sequence (WGS) analysis is able to present the information on the strains' unambiguous taxonomic identification as well as the characterization of their potential functional traits of concern, such as virulence factors, resistance to antimicrobials of clinical relevance for humans and animals, and the production of known toxic metabolites.    

In reality, the use of WGS-based data has been established as a prerequisite for risk assessment in several sectors of regulated goods. For these reasons, the European Food Safety Authority (EFSA) has developed a paper that advises applicants on how to describe the procedure and findings that should be submitted to the risk assessor in the context of a market authorization application for a regulated product. There are instructions on how to execute WGS, as well as the quality criteria/thresholds that must be met, as well as the data and pertinent information that must be provided along anytime such data is needed.      

 

Sources:  

https://efsa.onlinelibrary.wiley.com/doi/full/10.2903/j.efsa.2021.6506