The European Food Safety Authority (EFSA) released an updated statement on the use of whole genome sequence analysis of micro-organisms intentionally used in food and feed applications. Micro-organisms, genetically modified or not, may be used in food and feed either as active agents, biomass, or as production organisms. Selling micro-organisms or their derived substances/products in the European market may be subjected to a premarket authorization process. The premarket authorization process requires the implementation of risk assessment strategies to establish the safety and/or efficacy of the proposed micro-organism(s) when used in the food chain. The risk assessment strategy includes conducting a full molecular characterization of the micro-organism(s). For certain regulated products, whole genome sequence (WGS) data of the microorganism is required as a part of the assessment strategy.

In this statement, EFSA refers to relevant regulations and guidance for the premarket authorization process for various applications of micro-organisms, such as food enzymes, animal nutrition, food additives, and plant protection products. EFSA also lists the guidance documents and opinions available for the characterization and risk assessment of micro-organisms. This document does not define when WGS data are necessary and it does not provide assessment criteria for drawing conclusions from the WGS analyses. This information is provided in the relevant Regulatory framework and/or Guidance documents.

This document provides recommendations to applicants on describing and reporting the results of WGS analyses for market authorization applications. Information is provided on how to conduct genome sequencing, the quality criteria/thresholds, and the data and information to be reported. This document reflects the current state of WGS, which is rapidly evolving both in knowledge and technology.

The micro-organisms covered in the document include bacteria, yeasts, filamentous fungi and viruses (including bacteriophages). For applications using other taxonomical groups, the same principles apply on a case-by-case basis.

The WGS methodology includes the following steps: nucleic acid extraction, sequencing and data quality control, de novo assembly and annotation, reference-based assembly, and the use of the WGS data for characterizing the micro-organism. The statement also describes the standard data formats in which the collected data should be submitted in addition to the file naming conventions. WGS data can be used to identify the micro-organism, compare genetic modifications to wildtype micro-organisms, and identify genes or genetic elements of concern. The types of genes or genetic elements of concern include those which code for antimicrobial resistance, toxigenicity, pathogenicity, production of antimicrobials, ability to transduce (mobilize) DNA, and absence of lysogenic activity.