HIV and Colonization with Staphylococcus aureus in two Maximum-Security Prisons in New York State.

•Staphylococcus aureus was isolated from the anterior nares and/or oropharynx of 44% HIV infected and 48% of uninfected prison inmates.•HIV was not associated with S. aureus colonization of the anterior nares and/or oropharyngeal.•HIV was associated with a decreased likelihood of exclusive S. aureus oropharyngeal colonization.•Strain diversity was similar among HIV infected and uninfected inmates.•Spa type t0571 and t064 were both more prevalent among HIV infected inmates.