The recognition of infection clusters via determination of clonal relationships between pathogen isolates represents the major aim of pathogen subtyping during outbreaks. In addition, a continuing and comprehensive subtyping of pathogen isolates is a prerequisite for early recognition of changes within pathogen populations, especially of new pathogen types and variants. Here, in an exemplary manner, we outline the current practice in Germany for three important agents of food-borne infections, Salmonella enterica, Listeria monocytogenes and enterohemorrhagic Escherichia coli (EHEC). Pathogen subtyping is mostly performed in specialized laboratories. Collection of representative pathogen isolates is therefore critical for comprehensive pathogen surveillance. Salmonella and L. monocytogenes are usually isolated by sample culturing in primary diagnostic laboratories and a considerable number are sent to the respective reference laboratories for further subtyping. However, the current situation in terms of EHEC is problematic. As the detection of shiga toxin (or gene) is sufficient for diagnosis and case reporting, primary diagnostic laboratories actually rarely isolate EHEC; therefore, a concept for appropriate retrieval of isolates is needed to ensure effective EHEC surveillance in Germany.