The rapid development of whole genome sequencing technologies and the subsequent integration of pathogen and human genomic information into routine public health activities has the potential to benefit the population-level management of infectious diseases. The comprehensive description of the current landscape of infectious disease surveillance, the identification of priority pathogens, and the assessment of the perception and needs of a wide range of stakeholders provide a solid base to guide the implementation of pathogen genomics. Subsequent pathogen-specific study cases within a real-world public health setting enabled to demonstrate the added value and pointed important challenges for the integration of genomic information in epidemiological analyses. As such, the findings of this thesis can further guide the integration of genomic information for the surveillance and control of infectious diseases within the national public health institute in Belgium. ; (SP - Sciences de la santé publique) -- UCL, 2022