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Extragenital Testing: Resources for Providers

and Laboratories

NCSD is collaborating with the National Network of STD Clinical Prevention Training Centers (NNPTC) and the Association of Public Health Laboratories (APHL) to produce resources for clinics and laboratories to ensure that extragenital testing is available across the country.  We are also proud of the ongoing work of the Gay Men's Health Equity Workgroup, a partnership between NASTAD and NCSD, to develop additional tools for Health Departments around extragenital screening best practices.

Extragenital testing for gonorrhea and chlamydia in men who have sex with men (MSM) is a high priority issue for curbing STD rates in the US.  It is important for health departments, medical providers, and laboratories to understand the scope of these issues. 

  • Urine-only chlamydia and gonorrhea misses 70-88% of infections in MSM.  Studies across 11 STD clinics demonstrated that 70% - 88% of rectal chlamydia and gonorrhea infections have no concurrent urethral infection.1
  • Chlamydia and gonorrhea infections are common in MSM and are increasing each year.2
  • Rectal gonorrhea infections are asymptomatic 85% of the time supporting the need for routine screening.3
  • MSM are significantly more likely to demonstrate antimicrobial resistant gonorrhea.4
  • Population-level factors such as overlapping social and sexual networks are associated with higher risk of STDs, including HIV, in MSM.5

Resources for Medical Providers

The CDC recommends the following screening for MSM, regardless of condom use, using Nucleic Acid Amplification Tests (NAATs) as the preferred test:

  • A test for urethral chlamydia or gonorrhea infection in men who had insertive intercourse in the past year.
  • A test for rectal chlamydia or gonorrhea infection in men who had receptive anal intercourse in the past year.
  • A test for pharyngeal gonorrhea infection in men who had receptive oral intercourse in the past year. CDC does not recommend testing for pharyngeal chlamydia infection, but most providers use combination tests for both chlamydia and gonorrhea.

Many clinical settings do not yet have capacity to do extragenital tests.  For assistance with building clinical capacity to conduct extragenital tests, please contact the STD Clinical Consultation Network.  You can submit a request for assistance from the NNPTC to increase your capacity for extragenital testing in your clinical setting.

To support providers in ensuring the maximum billing potential, the STD Technical Assistance Center developed an excellent coding guide for the use of NAATs with extragenital specimens.  

As an additional resource, NCSD and NNPTC developed summary treatment guidelines that can be printed as a poster and put in medical offices for quick reference. 

Resources for Laboratories

NAAT is the recommended test method for both Chlamydia trachomatis and Neisseria gonorrhoeae in men and women. 6 The optimal specimen type to detect chlamydia or gonorrhea infection in men is a first-catch urine which is equivalent to a urethral swab. NAAT is also the recommended test method for rectal and oropharyngeal specimens. While there are several FDA-cleared NAATs for use on urine and urethral swabs, rectal and oropharyngeal samples are not approved specimen types for these tests. Therefore, in order to test these specimen types, laboratories must perform a validation study to modify the test that is compliant with their regulations.  

Many laboratories, including large commercial labs* such as LabCorp, Quest Diagnostics and the Center for Disease Detection, as well as many state and local public health laboratories have gone through the process to validate their FDA-cleared NAAT for use on rectal and/or oropharyngeal specimens.7 Those laboratories still interested in bringing on testing or those  asked to start testing rectal and oropharyngeal samples using NAAT can do the following:

*Mention of specific commercial laboratories is for information only and does not imply endorsement.


[1] Patton ME 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):1564-1570.

2 2015 Sexually Transmitted Diseases Surveillance. Centers of Disease Control and Prevention. October 2016.

3 Kent CK, Chaw JK, Wong W, Liska S, 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(1):67-74.

4 Kirkcaldy RD, Zaidi AA, Hook EW 3rd, et al. Neisseria gonorrhoeae antimicrobial resistance among men who have sex with men and men who have sex exclusively with women. The Gonococcal Isolate Surveillance Project, 2005-2010. Ann Intern Med. 2013; 185(5):321-328.

5 Koblin BA, Husnik MJ, Marla JB, et al. Risk factors for HIV infection among men who have sex with men. AIDS. 2006;20(5):731-739.

6 Papp JR, Schachter J, Gaydos CA, Van Der Pol B. Recommendations for the Laboratory-Based Detection of Chlamydia trachomatis and Neisseria gonorrhoeae — 2014. MMWR. 2014;63(2): 1-18. 

7 Klausner JD, et al. Clinic-Based Testing for Rectal and Pharyngeal Neisseria gonorrhoeae and Chlamydia trachomatis Infections by Community-Based Organizations --- Five Cities, United States, 2007. MMWR. 2009; 58(26):716-719.