To evaluate the association between HIV and Staphylococcus aureus colonization after confounding by incarceration is removed.

A cross sectional stratified study of all HIV infected and a random sample of HIV-uninfected inmates from two maximum-security prisons in New York State. Structured interviews were conducted. Anterior nares and oropharyngeal samples were cultured and S. aureus isolates were characterized. Log-binomial regression was used to assess the association between HIV and S. aureus colonization of the anterior nares and/or oropharynx and exclusive oropharynx colonization. Differences in S. aureus strain diversity between HIV-infected and uninfected individuals were assessed using Simpson's Index of Diversity.

Among 117 HIV infected and 351 HIV uninfected individuals assessed, 47% were colonized with S. aureus and 6% were colonized with methicillin resistant S. aureus. The prevalence of S. aureus colonization did not differ by HIV status (PR = 0.99, 95% CI = 0.76–1.24). HIV infected inmates were less likely to be exclusively colonized in the oropharynx (PR = 0.55, 95% CI = 0.30–0.99). Spa types t571 and t064 were both more prevalent among HIV infected individuals, however, strain diversity was similar in HIV infected and uninfected inmates.

HIV infection was not associated with S. aureus colonization in these maximum-security prison populations, but was associated with decreased likelihood of oropharyngeal colonization. Factors that influence colonization site require further evaluation.