April 2023 Q&A Readers’ questions answered

March 27, 2023

What is the standard laboratory workup for pharyngeal STI detection? CT-NG from a throat cx? Should this include VCM, aerobic, and/or anaerobic swabs?

Sexually transmitted infections (STIs) involving extragenital sites (pharynx and rectum) of particular public health concern include both Neisseria gonorrhea (GC) and/or Chlamydia trachomatis (CT).1 These infections represent a substantial proportion of overall STIs.2-4 In addition, extragenital STIs at rectal or pharyngeal sites are most often asymptomatic. For these reasons, depending on an assessment of patient risk factors as well as community prevalence, screening may be recommended or considered. For example, different studies have demonstrated that approximately one third to two thirds of gonococcal and chlamydial infections might be missed if urogenital-only testing is performed among Men Who Have Sex with Men (MSM).5-9 The primary diagnostic methods for detection of GC and CT at extragenital sites include culture and nucleic acid amplification tests (NAATs) and either may be used. However, for CT infections at rectal and oropharyngeal sites, NAATs have been shown to have higher sensitivity and specificity when compared to culture methods.10-14 For GC, culture and NAATs are also available for diagnosis of infection at extragenital sites. Commercially available NAATs have been cleared by the FDA for rectal and pharyngeal swabs for both men and women.14

However, not all commercially available GC and CT NAATs with FDA clearance for urogenital samples have been cleared for use with extragenital samples. There are examples where testing of oropharyngeal specimens for GC might have reduced specificity due to detection of commensal organisms. Additionally, although it is generally true that NAAT sensitivity for detecting N. gonorrhoeae from extragenital sites is superior to culture, it does vary by NAAT type and some commercially available NAATs that have been cleared for urogenital testing have not been cleared for extragenital testing. For this reason, it is suggested that the product inserts from each NAAT manufacturer be carefully reviewed to best understand approved sample types and associated performance. However, product inserts for each NAAT manufacturer should be consulted carefully because collection methods and specimen types vary. Certain NAATs that have been demonstrated to detect commensal Neisseria species might have comparable low specificity when testing oropharyngeal specimens for N. gonorrhoeae.  Finally, it is worth noting that self-collected swabs have been reported to be an acceptable means of collection for pharyngeal and rectal specimens, which can enhance patient comfort and reduce clinical workloads.15-17

The clinical utility of extragenital testing for other organisms such as Mycoplasma genitalium has not been established yet since there is no evidence of it causing disease. In the case of HSV infection, an appropriate swab of an active oral lesion submitted in viral transport media for testing real-time HSV PCR testing has been demonstrated to be the most sensitive method of HSV detection.

For details regarding sample collection, transport, and culture of CT and GC, please refer to the Centers for Disease Control and Prevention recommendations at: https://www.cdc.gov/std/laboratory/2014labrec/recommendations.htm.


1.     Walensky RP, Houry D, Jernigan DB, et al. Centers for disease control and prevention. Cdc.gov. Accessed February 15, 2023. https://www.cdc.gov/std/treatment-guidelines/STI-Guidelines-2021.pdf.

2.       Barbee LA, Khosropour CM, Dombrowski JC, Manhart LE, Golden MR. An estimate of the proportion of symptomatic gonococcal, chlamydial and non-gonococcal non-chlamydial urethritis attributable to oral sex among men who have sex with men: a case-control study. Sex Transm Infect. 2016;92(2):155-60. doi:10.1136/sextrans-2015-052214. 

3.       Lafferty WE, Hughes JP, Handsfield HH. Sexually transmitted diseases in men who have sex with men. Acquisition of gonorrhea and nongonococcal urethritis by fellatio and implications for STD/HIV prevention. Sex Transm Dis. 1997;24(5):272-8. doi:10.1097/00007435-199705000-00007. 

4.       Bernstein KT, Stephens SC, Barry PM, Kohn R, et al. Chlamydia trachomatis and Neisseria gonorrhoeae transmission from the oropharynx to the urethra among men who have sex with men. Clin Infect Dis. 2009;15;49(12):1793-7. doi:10.1086/648427.

5.      Patton ME, Kidd S, Llata E, et al. Extragenital gonorrhea and chlamydia testing and infection among men who have sex with men—STD Surveillance Network, United States, 2010–2012. Clin Infect Dis. 2014;58(11):1564-70. doi:10.1093/cid/ciu184.

6.      Kent CK, Chaw JK, Wong W, et al. Prevalence of rectal, urethral, and pharyngeal chlamydia and gonorrhea detected in 2 clinical settings among men who have sex with men: San Francisco, California, 2003. Clin Infect Dis. 2005;41:67–74. doi: 10.1086/430704.

7.      Koedijk FD, van Bergen JE, Dukers-Muijrers NH, van Leeuwen AP, Hoebe CJ, van der Sande MA; Dutch STI centres. The value of testing multiple anatomic sites for gonorrhoea and chlamydia in sexually transmitted infection centres in the Netherlands, 2006–2010. Int J STD AIDS. 2012;23(9):626-31. doi:10.1258/ijsa.2012.011378.

8.       Rieg G, Lewis RJ, Miller LG, Witt MD, et al. Asymptomatic sexually transmitted infections in HIV-infected men who have sex with men: prevalence, incidence, predictors, and screening strategies. AIDS Patient Care STDS. 2008;22(12):947-54. doi:10.1089/apc.2007.0240. 

9.       Marcus JL, Bernstein KT, Kohn RP, Liska S, Philip SS. Infections missed by urethral-only screening for chlamydia or gonorrhea detection among men who have sex with men. Sex Transm Dis. 2011;38(10):922-4. doi:10.1097/OLQ.0b013e31822a2b2e. 

10.    Centers for Disease Control and Prevention. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae--2014. MMWR Recomm Rep. 2014;14;63(RR-02):1-19.  

11.   Schachter J, Moncada J, Liska S, Shayevich C, Klausner JD. Nucleic acid amplification tests in the diagnosis of chlamydial and gonococcal infections of the oropharynx and rectum in men who have sex with men. Sex Transm Dis. 2008;35(7):637–42.  doi:10.1097/OLQ.0b013e31817bdd7e.

12.    Mimiaga MJ, Mayer KH, Reisner SL, Gonzalez A, et al. Asymptomatic gonorrhea and chlamydial infections detected by nucleic acid amplification tests among Boston area men who have sex with men. Sex Transm Dis. 2008;35(5):495-8. doi:10.1097/OLQ.0b013e31816471ae. 

13.    Bachmann LH, Johnson RE, Cheng H, Markowitz LE, Papp JR, Hook EW 3rd. Nucleic acid amplification tests for diagnosis of Neisseria gonorrhoeae oropharyngeal infections. J Clin Microbiol. 2009;47(4):902-7. doi:10.1128/JCM.01581-08. 

14.    FDA clears first diagnostic tests for extragenital testing for chlamydia and gonorrhea. U.S. Food and Drug Administration. Accessed February 15, 2023. https://www.fda.gov/news-events/press-announcements/fda-clears-first-diagnostic-tests-extragenital-testing-chlamydia-and-gonorrhea.

15.    van der Helm JJ, Hoebe CJ, van Rooijen MS, Brouwers EE, et al. High performance and acceptability of self-collected rectal swabs for diagnosis of Chlamydia trachomatis and Neisseria gonorrhoeae in men who have sex with men and women. Sex Transm Dis. 2009;36(8):493-7. doi:10.1097/OLQ.0b013e3181a44b8c.  

16.    Alexander S, Ison C, Parry J, Llewellyn C, et al. Self-taken pharyngeal and rectal swabs are appropriate for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in asymptomatic men who have sex with men. Sex Transm Infect. 2008;84(6):488-92. doi:10.1136/sti.2008.031443.  

17.     Freeman AH, Bernstein KT, Kohn RP, Philip S, Rauch LM, Klausner JD. Evaluation of self-collected versus clinician-collected swabs for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae pharyngeal infection among men who have sex with men. Sex Transm Dis. 2011;38(11):1036-9. doi:10.1097/OLQ.0b013e318227713e.