Pandemics have shown that health crisis-management is a task that goes beyond individual institutions and sectors. Evidence-based forecasts suggest that pathogen-related scenarios will occur again (Jones et al. 2008; Marani et al. 2021) - driven and amplified by various impacts of anthropogenic environmental changes such as intensive land use, loss of biodiversity and climate change (Lefrançois et al. 2022). Accordingly, the role of public health systems will become increasingly important. This will inevitably be accompanied by increased requirements that an individual public healthcare system is currently only able to fulfil to a limited extent with its own capacities due to numerous reasons. Here, we share our experiences in expanding the collaboration between academic medicine and public health authorities to address these challenges. In terms of infection tracing and control, the value of this cooperation was demonstrated in an early period of the SARS-CoV-2 pandemic: initial successes with integrated outbreak management supported by genomic data was achieved (a study of an outbreak in a large meat-processing facility). Second, supra-regional interdisciplinary networks for genomic surveillance have subsequently been established, which have promoted further cooperation between public health sites and academic medicine. Effective participation of our local public health network in the German University Medicine Network (initially founded in response to the pandemic) emphasizes the importance of integrating public health authorities in research. Further, we identified numerous critical obstacles which need to be overcome for achieving sustainable competence clusters.Networking between academic medicine and public health institutions on various levels is an important factor for health and infection management in general. Our experiences from collaborations with the public health sector during pandemic scenarios demonstrate both the benefits and challenges of collaborative infection management, thus highlighting the importance to further develop "bridges" between public health authorities and academic sites in the face of upcoming local and global health crises.