Staphylococcus aureus is a persistent companion bacterial species in one-third of humankind. Reservoirs include the nasal and nasopharyngeal cavities, skin, and gastrointestinal (GI) tract. Despite earlier claims that colonization of individuals is caused by clonal organisms, next-generation sequencing (NGS) has revealed that resident type heterogeneity is not exceptional. Carriage, whether overt or hidden, is correlated with a risk of autoinfection. In a recent article in mBio, it was shown that, based on staphylococcal genome sequencing, low-level GI persistence may cause long-term nosocomial outbreaks [L. Senn et al., 7(1):e02039-15, 2016, doi:10.1128/mBio.02039-15]. Institutional endemicity with methicillin-resistant S. aureus (MRSA) sequence type 228 (ST228) is shown to originate not from high-level nasal carriage or poor compliance with infection control practice but from low-grade asymptomatic GI colonization. This shows the power of NGS in elucidating staphylococcal epidemiology and, even more important, demonstrates that (drug-resistant) microorganisms may possess stealthy means of persistence. Identifying these persistence mechanisms is key to successful infection control.