The European Food Safety Authority (EFSA) is responsible for the evaluation of registration dossiers applied by commercial manufacturers for the use of (genetically modified) micro-organisms in food/feed applications. Whole-genome sequencing (WGS), i.e. the reading out of the content of the genetic material contained within a sample, allows a thorough risk assessment of these micro-organisms to ensure the safety of the European consumers. In this service project, EFSA calls upon our expertise in this domain to analyse data for specific dossiers and assist with the development of bioinformatics software for the routine analysis of the WGS data.
Micro-organisms, genetically modified or not, may be used in the food chain as active agents or as production strains of substances of interest. In Europe, such micro-organisms or derived substances/products are subject to a pre-market authorisation process which defines the need to perform a risk assessment. In this process, companies wishing to place their products in the EU market need to submit a technical dossier with information on such products to the European Food Safety Authority (EFSA). Recently, EFSA has introduced the use of Whole Genome Sequencing (WGS) and WGS-based data analysis for the micro-organism’s identification, characterisation, and safety assessment. Currently EFSA has launched a tender aimed at developing and implementing standardised pipelines to analyse WGS data from these technical dossiers. The first objective of the project consists of assisting to the analysis of WGS data for a number of applications for regulated products dealing with micro-organisms, more specifically by conducting quality control of the data, taxonomic identification of the organism, and detection of the presence of genes of concern. The second objective is to carry out testing, debugging and provide advice on the creation of three pipelines for WGS-based analysis of bacteria, yeasts/filamentous fungi and viruses.