Use of integrated genomic surveillance by local public health authorities: Recommendations based on a mixed-methods study of current adoption, applications and success factors, Germany, 2023

BackgroundIntegrated genomic surveillance (IGS), i.e. the integrated analysis of pathogen whole genome sequencing and classical epidemiological data, can contribute substantially to the disease surveillance and infection prevention activities of local public health authorities (LPHAs).AimOur aim was to characterise how LPHAs use IGS, and factors required or important for their implementation, in the context of the German public health system.MethodsWe employed a mixed-methods design combining a quantitative survey of 60 LPHAs in three German states with five qualitative case studies based on LPHAs in four German localities and one state-level public health authority.ResultsApproximately half of LPHAs reported adoption of IGS; applications included outbreak analysis (n = 25), targeting and evaluation of infection control measures (n = 25 and n = 18, respectively) and characterisation of pathogen transmission chains (n = 25). Factors identified as required or important for the implementation of IGS in LPHAs included fast sample-to-result turnaround times, organisational data interpretation capabilities and clearly defined surveillance sampling strategies. Based on the case studies in which the adoption of IGS was successful, we formulate recommendations for implementing IGS at the level of LPHAs, including establishment of dedicated IGS analysis teams within LPHAs, use of user-friendly digital solutions (e.g. browser-based dashboards) for data exchange and analysis, and implementation of IGS in collaboration with local academic institutions.ConclusionOur analysis paves the way for increasing the implementation of IGS by LPHAs in Germany and other countries with similarly structured public health systems.