Whole-genome sequencing delivers high-resolution typing and insights into pathogen biology. In this hypothetical example, the two large ovals represent sets of isolates (small ovals) that have been assigned to genotypes using conventional laboratory typing. Clouds indicate clusters within those genotypes built using epidemiological data. Whole-genome sequencing provides a more detailed view of pathogen epidemiology, revealing previously unseen links (red lines) between genome-sequenced isolates (filled small ovals) within and between genotypes. Whole-genome sequencing also provides insights into pathogen biology, including the factors associated with virulence (represented here by toxin gene X) and drug resistance (represented here by resistance gene Y).