Background:
Several nucleic acid amplification tests (NAATs) are FDA-cleared for detecting urogenital Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infection, but they have not been adequately evaluated for the relatively common oropharyngeal or rectal CT and GC infections in men who have sex with men (MSM).

Objective:
To test the performance of two commercially available NAATs for CT or GC detection using oropharyngeal and rectal specimens from MSM.

Method:
Multiple swabs were collected from the oropharynx and rectum of MSM attending a San Francisco STD clinic. Specimens were tested by APTIMA Combo2 (AC2, Gen-Probe Inc, San Diego, CA) and ProbeTec (PTec, Becton Dickinson, Sparks, MD), and by culture for CT and GC. For apparent false positive specimens, NAATs using alternate primers were performed.

Result:
A total of 1110 men were enrolled; 40% were asymptomatic. CT prevalence was 0.8% (9 positives) in the oropharynx and 6.1% (68 positives) from the rectum, with respective sensitivities for CT detection of 44% and 27% by culture, 100% and 93% by AC2, and 67% and 63% by PTec. GC oropharyngeal prevalence was 8.3% (89 positives) and 8.2% (88 positives) in the rectum, with respective sensitivities for GC detection of 41% and 43% by culture, 84% and 93% by AC2, and 72% and 78% by PTec. NAAT specificities were ≥ 99.4%.

Conclusion:
AC2 and PTec are far superior to culture for detection of CT and GC from the oropharynx and rectum with AC2 detecting twice as many infections as culture. Further analyses with larger pharyngeal samples are needed, but clearly NAATs can improve our ability to diagnose rectal and oropharyngeal infection with CT or GC in MSM.

Implications:
It would be beneficial if manufacturers sought FDA-clearance for rectal and oropharyngeal specimens. Until then, laboratories must validate NAATs for these alternative specimens.