Chlamydia trachomatis/Neisseria gonorrhoeae (CT/GC) – Nucleic Acid Amplification Testing (NAAT) – Swabs

Testing Indications

Rectal, pharyngeal, female endocervical, and male urethral swab, have been validated by Hologic® for Chlamydia trachomatis and Neisseria gonorrhoeae (CT/GC) – Nucleic Acid Amplification Testing (NAAT) using the Hologic® Aptima Combo 2® Assay.

Rectal and pharyngeal testing is recommended only in the following group with unprotected sexual exposure at these sites:

  • men who have sex with men (MSM); 
  • male/female sex workers and their contacts; 
  • patients who are known contacts of those infected with CT or GC

There is weak evidence to support routine rectal and pharyngeal NAA testing for CT and GC in women with a history of unprotected receptive oral or anal sex and therefore is not recommended as routine practice.

Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit
Chlamydia trachomatis/ Neisseria gonorrhoeae (CT/GC) NAAT or Chlamydia trachomatis (CT) NAAT


Swab in media provided in Hologic® Aptima® Unisex Swab Specimen

Chlamydia trachomatis & Neisseria gonorrhoeae Unisex Swab collection kit order # 300210


NAAT testing has not been validated for adolescents (less than 16 years), and medico-legal specimens (pre-pubertal children, sexual abuse in peri-pubertal and pre-pubertal children, sexual assault and legal cases). Culture for Chlamydia trachomatis and/or Neisseria gonorrhoeae is the method of choice in these cases – refer to the appropriate Test Information Sheet for culture.

Preparation Prior to Transport

Label the specimen container with the patient’s full name, date of collection, and one other unique identifier such as the patient’s date of birth or Health Card Number.  Failure to provide this information may result in rejection or testing delay.

Special Instructions

After collection, the swab must be stored and transported to the lab at 2-30°C within 60 days of collection.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Chlamydia trachomatis/Neisseria gonorrhoeae (CT/GC) NAAT swab specimens are tested daily, Monday to Saturday. 

Turnaround time is up to 3 days from receipt by PHO laboratory.



Results are reported to the ordering physician or health care provider as indicated on the requisition.

Critical positive reports (specimens from pregnant patients, pre-pubertal children, i.e. ≤ 12 years and medico-legal specimens, i.e. pre-pubertal children, sexual abuse in peri-pubertal and pre-pubertal children, sexual assault and legal cases) are phoned and faxed if the client is registered for auto fax.

Other positives are only faxed if client is registered for auto fax.

Specimens that are positive for Chlamydia trachomatis or Neisseria gonorrhoeae are reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.

Test Methods

NAA testing is available for Chlamydia trachomatis (CT) alone, or for duplex testing of Chlamydia trachomatis and Neisseria gonorrhoeae (CT/GC) simultaneously from one collection kit. Testing for Neisseria gonorrhoeae (GC) as a single test by Nucleic Acid Amplification is not performed and requests will be tested with the CT/GC combo assay.


NAAT results are interpreted as Detected or Not detected.

Additional Information

Test of Cure (TOC)

Test of Cure for CT/GC is not routinely indicated.  Repeat testing is recommended in the following scenarios: 

  1. when compliance is difficult to ensure (e.g. failure to take or finish medication),
  2. if an alternative treatment has been used,
  3. in all pre-pubertal children,
  4. in all pregnant women, and
  5. in all cases of pharyngeal gonorrhea

The optimal specimen for test of cure is culture and should be performed at 1 - 2 weeks after completion of treatment.   If culture is not available, test of cure by NAAT will also be accepted.  Test of cure by NAAT for GC should be performed 2 - 3 weeks after completion of treatment and for CT should be performed 3 - 4 weeks after completion of treatment. Chlamydia genetic material may persist for longer than 4 weeks and therefore must be considered when interpreting positive test of cure results.


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Updated 21 Feb 2019