Most Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infections in men who have sex with men (MSM) are not in the urethra. This has been confirmed often since it was shown by Kent and colleagues, in 2 clinics in San Francisco, ( J. Infect. Dis. 2003). All of these studies have been made possible by the use of highly sensitive and specific nucleic acid amplification tests (NAATs) that are currently recommended for routine diagnosis of CT/GC infections. The increment in sensitivity for NAATs compared to culture is greater with pharyngeal and rectal specimens than with cervical and urethral specimens; doubling the number of rectal or pharyngeal infections detected.

In MSM attending STD clinics the prevalence of rectal or urethral CT and GC is often in the 7–10% range. GC is found in the oropharynx at about the same level, but CT is less common there, typically 1–2%. Most STD clinics’ routine has been to test urethral specimens when evaluating males, with rectal or oropharyngeal specimens tested in symptomatic MSM. We need a paradigm shift: in MSM routine testing of oropharyngeal and rectal sites, as well as urethra, must become the norm. Whether testing should be based on a history of sex practises needs more research.

Unfortunately, no NAATs have received FDA clearance for pharyngeal or rectal specimens. But CDC, recognising the superior performance of NAATs with these specimens, took an unusual step recommending NAATs for diagnosing CT/GC in oropharynx and rectum, despite absence of FDA clearance.

It is possible to use tests that have not received FDA clearance for patient management. Large laboratories can verify use of NAATs for rectal and pharyngeal specimens by following Clinical Laboratory Improvement Act (CLIA) guidelines. We need NAATs with FDA clearance for use on oropharyngeal and rectal specimens to further expand clinical access to these tests.