NGS have made bacterial genome seq routine. However, the genomics-based clinical strategies for monitoring infection outbreaks in hospitals is lagging. The SkyNet platform we are developing integrates state-of-the-art comparative genomics techniques, principles from epidemic spreading modelling and available patients metadata to support the work of the microbiology units for outbreak surveillance. In doing so, we set the basis for a digital epidemiology in several hospitals of the Lombardia Region. A second branch of the platform pertains the analysis of historical records and the sequencing of the corresponding strains with the ambition of building models able to predict infection outbreaks or potentially critical situations.