Tracing the source of an infectious human disease can save lives. It allows for measures to be taken to prevent further spread of the disease. Although the mode of transmission for many human pathogens is known, it often remains difficult to trace the exact source of an outbreak of a disease with laboratory methods. Viruses, bacteria, fungi, parasites and protozoa can cause human diseases, but here we focus on bacterial pathogens. The currently used techniques to obtain DNA fingerprints of bacterial agents of infectious diseases frequently cannot discriminate between all bacterial strains of the same outbreak, making it impossible to follow the spread of the disease. A recent solution to this problem is the application of next‐generation whole‐genome sequencing techniques, which allows all available genetic information of each clinical isolate to be determined.