Flow chart of data generation, data management and quality control. dcc_vivaldi8: a private datahub (https://www.ebi.ac.uk/ena/pathogens/login) set up for data sharing and hosted at the European Nucleotide Archive (ENA). Computerome: a local server used by DTU Food (https://www.computerome.dk). Prokka: Rapid Prokaryotic genome annotation32. Roary: Rapid prokaryotic genome annotation33. cgMLST and wgMLST obtained using the Enterobase scheme11 in BioNumerics version 7.6 (Applied Maths, Sint Martens Latem, Belgium).