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

Testing Indications

PHO Laboratory accepts swabs from the following specimen sources for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) by a Nucleic Acid Amplification Test (NAAT). Urethral, penile meatal, clinician and patient collected vaginal, endocervical, rectal and pharyngeal site specimens for.  NAAT is the recommended method for initial screening or testing of chlamydia and gonorrhea collected from the approved anatomical sites listed above.

Rectal and pharyngeal testing is recommended in case of unprotected sexual exposure at oral and anal sites only for the following groups:

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

At present, for women, there is insufficient evidence to support a policy of routine screening at rectal and pharyngeal sites for chlamydia and gonorrhea.  However, this may represent a relative lack of studies examining extragenital transmission in this group.  As a result, if there is clinical concern regarding rectal or pharyngeal infection with chlamydia or gonorrhea in a woman presenting to care, testing at these sites can be offered.

In women who have had a hysterectomy, collect a first void urine for NAAT or a vaginal swab for culture or NAAT.  
NAAT for CT and GC at PHO Laboratory is performed using the Hologic® Aptima Combo 2® Assay.   

  • Two different swab collection kits are provided by the manufacturer: the smaller tipped Aptima® Unisex Swab Specimen Collection Kit, and the larger tipped Aptima® Multitest Swab Specimen Collection Kit.  Note: the unisex kit contains a cleaning swab and a collection swab; only the collection swab is optimized and validated for testing.
  • The Hologic® Aptima® Urine Specimen Collection Kit should be used for urine specimen collection. Refer to the PHO Laboratory Test Information Index for Chlamydia trachomatis/Neisseria gonorrhoeae (CT/GC) – Nucleic Acid Amplification Testing - Urine

Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit

Chlamydia trachomatis/ Neisseria gonorrhoeae (CT/GC) NAAT


Chlamydia trachomatis (CT) NAAT

Female endocervical, male urethral, rectal and pharyngeal swabs

Not applicable

PHO Chlamydia trachomatis & Neisseria gonorrhoeae Hologic® Aptima®  Unisex Swab Collection Kit 

Kit order # 300210

Chlamydia trachomatis/ Neisseria gonorrhoeae (CT/GC) NAAT


Chlamydia trachomatis (CT) NAAT

Clinical or patient collected vaginal swabs, penile meatal, rectal and pharyngeal swabs

Not applicable

PHO Chlamydia trachomatis & Neisseria gonorrhoeae Hologic® Aptima®  Multitest Swab Collection Kit

Kit order # 300294

Submission and Collection Notes


Do not use expired kits.


The patient's date of birth must be indicated on the General Test Requisition Form in order for the specimen to be processed for testing.


If the tube contents are spilled, discard and replace with a new Aptima® Swab Specimen Collection Kit.  The preservative contained in the swab collection kit is in the optimal volume required for accurate testing and should not be adjusted.  Failure to use a new kit may invalidate the test results.


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.

Vaginal specimens collected in the Multitest swab collection kit from pregnant women have not been validated, but will be accepted.

Use of the Multitest swab for patient-collected vaginal specimen collection is not designed to replace cervical exams and endocervical specimens for diagnosis of female urogenital infections. Patients may have cervicitis, urethritis, urinary tract infections, or vaginal infections due to other causes or concurrent infections with other agents.

Women who have symptoms suggesting pelvic inflammatory disease (PID) should not use the Multitest swab to obtain patient-collected vaginal swab specimens as a replacement for a pelvic exam.

The patient-collected Multitest swab specimen application are limited to health care facilities where support/counseling is available to explain the procedures and precautions.

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), or suspected treatment failures,
  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 3-7 days 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.

LGV Testing

Male rectal specimens positive for Chlamydia trachomatis will be routinely forwarded to the National Microbiology Laboratory (NML) in Winnipeg for Lymphogranuloma venereum (LGV) testing.  Specimens positive for Chlamydia trachomatis from other sources will only be sent if LGV testing is specifically requested.

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Updated 20 July 2020