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Chlamydia trachomatis and Neisseria gonorrhoeae RNA, TMA

Test code(s) 11361, 11362, 11363

This is an outdated version of this FAQ. It was effective 12/05/2014 to 02/28/2016.

The current version is available here.

Question 1. Which specimen types are suitable for C trachomatis and N gonorrhoeae nucleic acid amplification tests (NAATs)?

For women, a vaginal specimen is recommended if no pelvic exam. For men, urine is the recommended specimen.

The following urogenital specimens are suitable:

  • Urine sample from a male or a
  • Endocervical, vaginal, SurePath®, or ThinPrep® vial with PreservCyt® specimens from a female patient
  • Male urethral
  • Vaginal swab collected by a physician or the patient.1-3

For nonurogenital specimens see Question 2 below.

Question 2. Are samples other than genital samples, such as throat and rectal swabs, acceptable for C trachomatis and N gonorrhoeae NAATs?

Rectal and throat swabs are acceptable for C trachomatisand N gonorrhoeae NAAT testing. C trachomatis and N gonorrhoeae have been isolated from extra-genital sites in men who have sex with men (MSM) and sexually active heterosexuals who engage in unprotected oral or anal sex. The CDC currently recommends oral and anal testing of MSM who have had receptive oral or anal sex, respectively, within the previous year.4 Both C trachomatis and N gonorrhoeae testing are recommended on the anal specimens, but only N gonorrhoeae testing is recommended on the oral specimens.4 Some researchers, however, have reported recovering C trachomatis from pharyngeal specimens in certain patient populations, on a relatively frequent basis.5

Quest Diagnostics offers throat- and anal (rectal)-based testing:

  • Test code 16506-Chlamydia trachomatis/Neisseria gonorrhoeae RNA, TMA, Rectal
  • Test code 70051-Chlamydia trachomatis/Neisseria gonorrhoeae RNA, TMA, Throat
  • Test code 16505-Chlamydia trachomatis RNA, TMA, Rectal
  • Test code 70048-Chlamydia trachomatis RNA, TMA, Throat
  • Test code 16504-Neisseria gonorrhoeae  RNA, TMA, Rectal
  • Test code 70049-Neisseria gonorrhoeae RNA, TMA, Throat

Question 3. What are the guidelines for additional diagnostic testing?

Repeat testing of the same positive sample using the same NAAT methodology is usually not needed and does not improvethe positive predictive value when screening with currently available NAATs.6 Positive results are considered presumptive evidence of infection.

If a false-positive result is expected to have adverse medical, social, or psychological consequences, confirmatory testing should be considered.7 Confirmatory testing using an alternative nucleic acid target region should also be considered in low-prevalence settings, where the positive predictive value (likelihood that a positive result is a true positive) of assays is reduced (note that testing of asymptomatic people is not recommended in extremely low-prevalence settings6). Treatment probably should not be withheld while awaiting the results of confirmatory testing.

The following tests target alternative nucleic acid target regions and can thus be used to confirm positive test results:

  • Test Code 15031-Chlamydia trachomatis RNA, TMA, Alternate Target
  • Test Code 91046-Chlamydia trachomatis RNA, TMA, Alternate Target, Rectal
  • Test Code 15033-Neisseria gonorrhoeae RNA, TMA, Alternate Target
  • Test Code 90990-Neisseria gonorrhoeae RNA, TMA, Alternate Target, Rectal

Question 4. Can NAATs be used for test-of-cure? How long after treatment should one wait before retesting?

NAATs can be used for test-of-cure if performed 3 or more weeks after the end of treatment. Testing earlier than that may cause a false-positive result. Residual nucleic acid from bacteria rendered noninfective by antibiotics might still be detected.7

Per the CDC, however, follow-up testing is not recommended after first-line treatment for C trachomatis or N gonorrhoeae infection to prove eradication of the infection.8 Such testing is only recommended after C trachomatis therapy is completed in pregnant women.4

Question 5. What do I do if test-of-cure test results are positive?

If an NAAT is positive for C trachomatis or N gonorrhoeae 3 or more weeks after the end of treatment7, first ensure that the patient has complied with the prescribed therapy and that the patient denies having sex after treatment with an untreated or new sex partner. If these conditions are met, treatment is considered to be a failure. In such cases, the CDC recommends contacting the local or state health department to get guidance and to arrange for antimicrobial susceptibility testing.8

Question 6. Is performance of one NAAT any different from that of another NAAT?

There are many FDA approved NAATs. Most have a high specificity, ie, minimal false-positive results. However, TMA methods have a higher clinical sensitivity than other NAATs.9 Please read reference 9 for further details.


  1. Schachter J, McCormack WM, Chernesky MA, et al. Vaginal swabs are appropriate specimens for diagnosis of genital tract infection with Chlamydia trachomatis. J Clin Microbiol. 2003;41:3784-3789.
  2. Wiesenfeld HC, Heine RP, Rideout A, et al. The vaginal introitus: a novel site for Chlamydia trachomatis testing in women. Am J Obstet Gynecol. 1996;174:1542-1546.
  3. Wiesenfeld HC, Lowry DL, Heine RP, et al. Self-collection of vaginal swabs for the detection of chlamydia, gonorrhea, and trichomoniasis: opportunity to encourage sexually transmitted disease testing among adolescents. Sex Transm Dis. 2001;28:321-325.
  4. Workowski KA, Berman S, Centers for Disease Control and Prevention (CDC). Sexually transmitted diseases treatment guidelines, 2010. MMWR Recomm Rep. 2010;59(RR-12):1-110.
  5. Centers for Disease Control and Prevention. Recommendations and Reports:Clinic-Based Testing for Rectal and Pharyngeal Neisseria gonorrhoeae and Chlamydia trachomatis Infections by Community-Based Organizations. MMWR. 2009;58(26):716-719.
  6. Laboratory diagnostic testing for Chlamydia trachomatis and Neisseria gonorrhoeae. Expert Consultation Meeting summary report. January 13-15, 2009. Atlanta, GA http://www.aphl.org/aphlprograms/infectious/std/Documents/ID_2009Jan_CTGCLab-Guidelines-Meeting-Report.pdf. Accessed June 20, 2014.
  7. Centers for Disease Control and Prevention. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae—2014. MMWR Recomm Rep. 2014;63(RR-02):1-19.
  8. Johnson RE, Newhall WJ, Papp JR, et al. Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections-2002. MMWR Recomm Rpt. 2002;51(RR-15):1-38.
  9. Chernesky M, Jang D, Gilchrist J, et al. Head-to-head comparison of second-generation nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae on urine samples from female subjects and self-collected vaginal swabs. J Clin Microbiol. 2014;52:2305-2310.
This FAQ is provided for informational purposes only and is not intended as medical advice. A clinician’s test selection and interpretation, diagnosis, and patient management decisions should be based on his/her education, clinical expertise, and assessment of the patient.

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