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Chlamydia trachomatis/Neisseria gonorrhoeae RNA, TMA

Test code(s) 11363(X), 11361(X), 11362(X)

For women, a vaginal sample is recommended in the absence of a pelvic exam. For men, first-catch urine is the recommended specimen.

The following urogenital specimens are suitable:

  • First-catch urine sample from a male or a female
  • Endocervical, vaginal, SurePath™, or ThinPrep® vial with PreservCyt® specimens from a female patient
  • Male urethral swab
  • Vaginal swab collected by a physician or the patient1-3

For nonurogenital specimens, see Question 2 below.

Rectal and throat swabs are acceptable for C trachomatis (CT) and N gonorrhoeae (NG) 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.

Most persons with C trachomatis detected at oropharyngeal sites do not have oropharyngeal symptoms. Although the clinical significance of oropharyngeal C trachomatis infection is unclear and routine oropharyngeal screening for CT is not recommended, available evidence suggests oropharyngeal C trachomatis can be sexually transmitted to genital sites; therefore, per the 2015 guidelines on sexually transmitted diseases, oropharyngeal C trachomatis should be treated with appropriate antimicrobials.4

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

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

Repeat testing of the same positive sample using the same NAAT methodology is usually not recommended and does not improve the positive predictive value when screening with currently available NAATs.5 Positive results from an NAAT-based screening assay are considered presumptive evidence of infection.

If a false-positive CT or NG NAAT result is expected to have adverse medical, social, or psychological consequences, confirmatory testing should be considered.6 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 settings.5 Treatment probably should not be withheld while awaiting the results of confirmatory testing.

The following tests target alternative nucleic acid regions and can thus be used to confirm positive CT/NG NAAT screening test results:

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

Per the CDC guidelines for chlamydial infections, an NAAT can be used for test-of-cure if performed 3 to 4 weeks after the end of treatment.4 This is appropriate when therapeutic adherence is in question, symptoms persist, or reinfection is suspected.4 Testing earlier than 3 to 4 weeks after treatment may produce a clinically false-positive result due to detection of nucleic acids from nonviable organisms.6

For patients with urogenital or rectal gonorrhea, follow-up testing is not needed to prove eradication after treatment with any of the recommended or alternative regimens. However, if symptoms persist, the patient should be evaluated using N gonorrhoeae culture (with or without simultaneous NAAT), and any gonococci isolated should be tested for antimicrobial susceptibility. Any person with pharyngeal gonorrhea who is treated with an alternative regimen should return 14 days after treatment for a follow-up with either culture or NAAT. If the NAAT is positive, a confirmatory culture is recommended before retreatment. If the culture is positive, antimicrobial susceptibility testing is recommended.

Routine follow-up testing after chlamydia or gonorrhea therapy can be performed using an NAAT approximately 3 months after treatment. If retesting at 3 months is not possible, clinicians should retest at the next opportunity within the 12-month period following initial treatment.

If an NAAT is positive for C trachomatis or N gonorrhoeae 3 or more weeks after the end of treatment,6 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.7

There are many FDA-approved CT/NG NAATs with high specificities. However, TMA methods have a higher clinical sensitivity than other NAATs.8 Please consult reference 8 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, Gail A, Centers for Disease Control and Prevention (CDC). Sexually transmitted diseases treatment guidelines, 2015. MMWR Recomm Rep. 2015;64 (3):1-140.
  5. Laboratory diagnostic testing for Chlamydia trachomatis and Neisseria gonorrhoeae. Expert Consultation Meeting summary report. January 13-15, 2009. Atlanta, GA Accessed June 20, 2014.
  6. 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.
  7. 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.
  8. 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.


Version 1 effective 02/29/2016 to present
Version 0 effective 12/05/2014 to 02/28/2016