In response to the COVID-19 pandemic, the European Commission established the European Health Emergency Preparedness and Response Authority (HERA). Generally, it aims to strengthen the European Health Union by improving preparedness and response to future national, cross-border, or pandemic outbreaks of infectious diseases. The HERA-Incubator, funded by the European Centre for Disease Prevention and Control (ECDC), allows investments to upscale the national infrastructure for collecting Whole Genome Sequencing (WGS) data to be linked with epidemiologic data as well as building a sustainable infrastructure that can be used more broadly in the context of outbreak preparedness and risk management. As a result, the current HERA-Incubator-WGS project covers a proof-of-principle of a national genomic-epidemiologic eHealth framework for five national reference centers (NRCs) for human microbiology