Monitoring the dynamics of pathogen spread by public health authorities is a core element for infection prevention during pandemics but also in inter-pandemic phases. Infection management measures that are adaptable to individual and local circumstances can be highly advantageous. One example of this is genome-based or integrated infection chain analysis. This concept combines methods of classic contact tracing with genomic sequence data from molecular pathogen analysis. This enables high resolution infection chain management within the general population or in diffuse local outbreak scenarios. During the SARS-CoV-2 pandemic, we successfully demonstrated applications for digitally supported infection chain analysis, showing its valuable potential (Walker et al. 2022). The aim of the GENTRAIN project is to develop digital applications for the use of genomic-based infection chain analysis by public health authorities in Germany for further relevant pathogens beyond SARS-CoV-2. In order to contribute to a sustainable increase in digital development, the project primarily aims to enhance the dimensions of data interoperability, software and data management as well as the area of employee competence within the German public health authorities. The project expanded the tools of integrated genomic surveillance to analyze genomes of other public-health relevant pathogens (e.g. antibiotic-resistant bacteria). For sustainable improvement of data management capacities in public health authorities, we identified and describe several key factors. For instance, adaptation of existing software is essential with special regard to needs and capacities of local public health authorities. Availability of interfaces for routine data exchange is highly significant, as well as ongoing training for public health personnel. The utilization of this potential by public health authorities is essential, especially for predicted pandemic situations and the threat of increasing antibiotic resistance. Perspectively, this will contribute to more precise, evidence-based and faster reporting systems to support political decisions in terms of preventive measures - at municipal and state level.