Anti-microbial resistance surveillance systems in Europe are limited by the inability to link laboratory data and patient data. The OMOP Common Data Model (OMOP CDM) is an option to store and use patient data in an international context supporting observational research. Detailed medical microbiology laboratory data are usually not stored in OMOP CDM. We propose here a solution to deal with the inherent complexity of microbiology data and store those in the OMOP CDM v5.4. We demonstrate the feasibility of our approach by capturing data from a microbiology in vitro diagnostic middleware, modeling in OMOP CDM 5.4 and querying for visualization.