The ODIN project aims at strengthening capacity for genomics and bioinformatics database management skills for generating, maintaining, and querying large genomic epidemiology data sets in sub-Saharan countries. To reach this goal, ODIN will develop a genomic surveillance system relying on environmental monitoring of major communicable disease agents and antimicrobial resistance in community wastewater and other environmental samples containing human and animal excreta. In a socially and ethically acceptable anonymous manner, environmental surveillance systems follow the trends in prevalence and may detect the outbreaks of communicable diseases in human communities and to convey this information to key stakeholders for the efficient implementation of data-driven public health policies. A strong and innovative aspect of this project is the combination of various semi-automatic bioinformatics tools for the processing and analysis of genomic epidemiology data, disseminated through a visual dashboard, providing means for timely public health interventions. The ODIN project implements the three pillars of the One Health framework: human health, animal health and the environment, which is crucial for communicable disease epidemiology in resource- and infrastructure-poor regions. Together with extensive training activities, ODIN implementation will result in a substantial strengthening in the capacity and infrastructure in sub-Saharan countries for genomic epidemiology. Networking and capacity building are an integrated part of the project activities and will comprise communication activities with stakeholders and training of MSc and PhD students. By its multi-disciplinary team, ODIN will contribute to setting up a sustainable model for how environmental surveillance systems can support the control of poverty-related and emerging/re-emerging infections in sub-Saharan Africa and promote the public health interventions targeting safe water supply and sanitation.