Guidelines for reporting Whole Genome sequencing-based typing data through the EFSA One Health WGS System

The European Union (EC) tasked the European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control (ECDC) to implement and manage the system Whole Genome Sequence(WGS)for food pathogens. The pathogens include Salmonella enterica, Listeria monocytogenes, and Escherichia coli,  including Shiga toxin-producing E. coli (STEC) from humans and food, feed, animals, and the related environment. In response to this mandate, EFSA has developed the EFSA One Health WGS System that interoperates with the ECDC Molecular Typing system exchanging core genome Multi Locus Sequence Typing (cgMLST) profiles and minimum metadata. The technical report describes the EFSA One Health WGS system, including its architecture, the users, and their relative data visibility, as well as data ownership and intellectual property. @ https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2022.EN-7413