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Background: Co-infection with HIV and other STIs is common and enhances transmission. Diagnosis of STIs is often suboptimal due to low sensitivity of culture-based methods and limited testing of at-risk body sites.
Objectives: To evaluate: (i) the benefits of testing for rectal and pharyngeal N. gonorrhoeae (GC) and C. trachomatis (CT) in HIV-infected adolescents and (ii) the non-inferiority of nucleic acid amplified tests (NAAT) for these specimen types.
Methods: A prospective study was performed using NAAT to test for GC and CT at 3 body sites: urethral, rectal, and pharyngeal. Cultures were also used at rectal and pharyngeal sites. All positive tests were confirmed by secondary amplification assays.
Results: 34 (7.8%) of the 434 tests were positive for CT (13 rectal, 2 pharyngeal and 3 urethral) or GC (8 rectal, 5 pharyngeal, and 3 urethral). Rectal and pharyngeal CT infections were never indicated by a CT-positive urethral NAAT (0/2 and 0/13, respectively). However, for GC, 2/4 of positive pharyngeal and 2/6 of positive rectal GC NAATs corresponded to a positive urethral NAAT. Overall, only 4/25 (16%) of rectal or pharyngeal GC or CT infections simultaneously had a urethral infection with GC or CT. 74% of these infections would have gone untreated had only a urethral NAAT been done. Only 5/28 positive NAATs also had a positive culture, whereas all positive cultures also had positive NAATs.
Conclusions: Most pharyngeal and rectal infections are not indicated by urethral NAAT. NAAT improves detection of rectal and pharyngeal CT and GC compared to culture. Implications for Programs, Policy, and/or Research: Given the unexpectedly high rate of rectal CT, public health recommendations should be expanded to improve practitioner attitudes toward STI screening at all body sites. Rectal and pharyngeal NAAT should be FDA-approved, removing the need for internal validation studies. Further studies should examine the resulting improvement of long-term cost-effectiveness.