* IWTK is NOT able to test throat (oropharyngeal) swabs at this time *
Although commercially available nucleic acid amplification tests (NAATs) are recommended for testing genital tract specimens, they have not been cleared by the FDA for the detection of C. trachomatis and N. gonorrhoeae infections of the rectum and throat. Results from commercially available NAATs can be used for patient testing IF the laboratory has established specifications for the performance characteristics according to CLIA regulations. The International STD Laboratory at Johns Hopkins University has performed the required validation study to test rectal samples by the NAAT assay currently in use by the IWTK program. The validation study to test throat/oropharyngeal specimens has not been completed, so IWTK is NOT able to test throat specimens at this time.
Infections with C. trachomatis and N. gonorrhoeae are common in extragenital (rectal and throat/oropharyngeal) sites in certain populations such as MSM. Because extragenital infections are common in MSM, and most infections are asymptomatic, routine annual screening of extragenital sites in MSM is recommended. No recommendations exist regarding routine extragenital screening in women because studies have focused on genitourinary screening, but rectal and oropharyngeal infections are not uncommon.
The scope of the problem of extragenital infection in MSM is not known at the national level. In 2007, CDC coordinated an evaluation of MSM attending several community-based organizations and public or STD clinics and found that of approximately 30,000 tests performed, 353 (5.4%) MSM were positive for rectal infection with N. gonorrhoeae, and 468 (8.9%) were positive for rectal C. trachomatis. Pharyngeal N. gonorrhoeae tests were positive for 759 MSM (5.3%), and 54 (1.6%) were positive for C. trachomatis. In the United Kingdom, some studies on screening MSMs have been performed, and in one study of 3,076 MSM attending an STD clinic, there was an 8.2% prevalence of infection with C. trachomatis in the rectum and 5.4% in the urethra. The majority (69%) of the men with C. trachomatis were asymptomatic, stressing the need for screening.
A 2003 study assessed nucleic acid amplification testing (NAAT) for diagnosing C. trachomatis and N. gonorrhoeae infections in multiple anatomic sites in MSMs using Becton Dickinson's ProbeTec, which had been validated previously for such use. Among 6,434 MSM attending an STD clinic or a gay men's clinic, the study found that the prevalence by site for C. trachomatis was 7.9% for the rectum, 5.2% urethral, and 1.4% pharyngeal; and prevalence by site for N. gonorrhoeae was 6.9% for the rectum, 6% urethral, and 9.2% pharyngeal. The great majority (84%) of the gonococcal and chlamydial rectal infections were asymptomatic. More than half (53%) of C. trachomatis and 64% of N. gonorrhoeae infections were at non-urethral sites and would have been missed if the traditional approach to screening of men by testing only urethral specimens had been used.