Testing men who have sex with men for urethral infection with Chlamydia trachomatis and Neisseria gonorrhoeae is only half the job, and we need the right tools.

Standard operating procedure in STD clinics commonly has been to test urethral specimens when evaluating males, whether they are heterosexual or men who have sex with men (MSM). Rectal or oropharyngeal specimens may be tested in MSM with symptoms, or in some clinics as screening tests if individuals report sexual practices that would indicate risk of infection at these sites. In a report in this issue of Sexually Transmitted Diseases, Marcus and colleagues studied the prevalence of infection with Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in the urethra, the oropharynx, and rectum in asymptomatic MSM visiting the San Francisco STD clinic.1 A retrospective analysis of 3398 patient visits found CT or GC at 549 (16.2%) of those visits. The prevalence of infections among these asymptomatic men ranged from a high of 7.8% for rectal CT to a low of 0.4% for urethral GC. Strikingly, 83.8% of CT and GC infections would have been missed if only urethral screening was performed. What was found in the Marcus study, and in others, as well, is that the majority of infections with CT/GC in MSM are not in the urethra. The first major study to make this point was performed by Kent and colleagues, in 2 clinics in San Francisco, where they found that 50% of chlamydial and gonococcal infections were extraurethral.2 That finding has been confirmed by a number of approaches, including retrospective chart reviews and prospectively designed studies (Table 1). While these studies have focused on rectal and pharyngeal CT/GC infections in MSM, it must be noted that such infections are far from rare in women.12,13 In many clinical settings, the infections in women will be seen more often than those in men. These extragenital infections should not be ignored now, and we need more research to better define their potential consequences. Both CT and GC are recognized as causes of proctitis, and even asymptomatic infections have been associated with HIV transmission.14 Current CDC recommendations call for routine screening of the oropharynx and rectum in MSM who may be exposed to GC or CT at those sites. It is not clear whether pharyngeal infections have a major direct impact on health. But evidence is emerging that infection can be transmitted from the oropharynx to the urethra of sex partners, thus continuing chains of infection.15 All of the cited studies have been made possible by the introduction and application of highly sensitive and specific nucleic acid amplification tests (NAATs) for the diagnosis of CT and GC infections. NAATs are recommended for routine diagnosis of CT/GC infections.15 Where direct comparisons have been done, it has been shown that the increment in sensitivity for NAATs as compared to culture is greater with pharyngeal and rectal specimens than it is with cervical and urethral specimens. An approximate doubling of the number of infections detected has been obtained with NAATs.4,11 Alas, there remains a gap wherein the best tests are not readily available to the patients and providers who need them. Several NAATs are commercially available and have received FDA clearance for male and female urine specimens, urethral swabs from men, and cervical and vaginal swabs from women. Unfortunately, none have been cleared by the FDA for pharyngeal or rectal specimens. But the CDC, recognizing the superior performance of these tests used on these specimens, has taken an unusual step and recommended the use of NAATs for diagnosis of CT/GC in oropharyngeal and rectal specimens, even though such use has not received FDA clearance.16 The