Microbial genomics has revolutionized infectious diseases and epidemiology research and is facilitating the tracking and containment of emerging biological threats. Among the most serious contemporary infectious agents are multiple antibiotic-resistant strains of the human pathogen Staphylococcus aureus, which present a formidable public health challenge that is no longer limited to hospitalized patients. To address key hypotheses regarding microbial strain evolution or virulence, conventional genotyping methods do not offer enough power to resolve minor changes between closely related strains. The application of next-generation high-throughput genotyping technologies, as illustrated in a recent analysis of a highly resistant S. aureus strain, can provide new clues about the geographical origin and intrahospital spread of important microbial pathogens.