The use of Whole Genome Sequencing (WGS) for food- and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries

A survey among the EU/EFTA laboratory Networks for Salmonella, Listeria monocytogenes, Escherichia coli (VTEC), Campylobacter, Coagulase Positive Staphylococci, Antimicrobial Resistance and bacteriological and viral contaminants of bivalve mollusks was conducted. By the end of 2016, WGS was in use in reporting laboratories from 17 out of 30 EU/EFTA countries. The main reason for not implementing WGS was the lack of capacity (budget and expertise). WGS was mainly used for outbreak investigations, followed by surveillance, and mostly for L. monocytogenes, E. coli and Salmonella analysis. WGS was used only to type subsets of isolates, and normally, in parallel to other molecular techniques (PFGE and MLVA). The intention to switch to only WGS for typing was indicated by some laboratories. This report provides a first picture of the state of the art in relation to the use of WGS in European food safety laboratories at the end of 2016. A new questionnaire to tackle the state of the art in 2018 has been recently launched @ https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2018.EN-1432