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Chlamydia trachomatis/Neisseria gonorrhoeae DNA, SDA

Test code(s) 17305

The following specimens are suitable:

  • Urine sample from a male or a female
  • Endocervical, vaginal, SurePath®, or ThinPrep® vial with PreservCyt® specimens from a female patient
  • Male urethral specimens

Use of a vaginal swab collected by a physician or the patient herself is also suitable.1-3


Rectal and throat swabs are acceptable for C trachomatis and 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, young 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 However, some researchers have reported recovering C trachomatis from pharyngeal specimens in certain patient populations, on a relatively frequent basis.9

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

Repeat testing of the same positive sample using the same NAAT methodology is usually not needed and does not improve the positive predictive value when screening with currently available NAATs.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.10 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 settings5). Treatment probably should not be withheld while awaiting the results of confirmatory testing.

The following tests target alternative nucleic acid 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

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 due to detection of nucleic acids from nonviable organisms.

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.6 Such testing is only recommended after C trachomatis therapy is completed in pregnant women.4

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

The BD ProbeTec® (BD Diagnostic Systems) and Aptima Combo 2® (Gen-Probe Incorporated) NAATs have comparable analytical sensitivity and specificity and are both FDA approved.7,8


  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. Laboratory diagnostic testing for Chlamydia trachomatisand Neisseria gonorrhoeae.Expert Consultation Meeting summary report. January 13-15, 2009. Atlanta, GA Accessed June 20, 2013.
  6. 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.
  7. Taylor SN, Van Der Pol B, Lillis R, et al. Clinical evaluation of the BD ProbeTec™ Chlamydia trachomatis Qx amplified DNA assay on the BD Viper™ system with XTR™ technology. Sex Transm Dis. 2011;38:603-609.
  8. Gaydos CA, Theodore M, Dalesio N, et al. Comparison of three nucleic acid amplification tests for detection of Chlamydia trachomatis in urine specimens. J Clin Microbiol. 2004;42:3041-3045.
  9. 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.
  10. Centers for Disease Control and Prevention. Recommendations and Reports: Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections-2002. MMWR. 2002;51(RR-15):1-38.


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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