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

Testing Indications

Nucleic acid amplification testing (NAAT) is the recommended method for initial screening or testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections. PHO’s laboratory accepts urine and swabs for CT/NG NAAT.

First-void urine is the specimen of choice for males. A vaginal swab is the specimen of choice for females. In women who have had a hysterectomy, collect a first void urine for NAAT or a vaginal swab for culture or NAAT. Refer to the Specimen Collection and Handling section for additional acceptable specimen types.

Rectal and/or pharyngeal testing is recommended for individuals who have had unprotected sexual

  • exposures at these sites and are in specific at-risk groups or have risk factors, including:
  • gay, bisexual, and men who have sex with men, including trans women;
  • individuals engaged in sex work or have had sexual contact with someone engaging in sex work;
  • individuals who are known contacts of those infected with CT or NG;
  • individuals who have signs or symptoms of rectal or pharyngeal infection.

Rectal and/or pharyngeal testing in individuals who have had exposures at these sites and are not in specific risk groups above may be considered in individual circumstances based on clinical evaluation or local epidemiology. 

Please refer to PHO’s Bacterial STI Testing: Quick Reference Guide for guidance on testing based on risk factors and clinical presentation.

Rectal bacterial sexually transmitted infections, including CT and NG, have been associated with increased risk of HIV infection in gay, bisexual, and other men who have sex with men, and transgender women.  Screening for HIV is highly recommended in these individuals. Details about HIV serology testing at PHO can be found on the HIV Serology Test Information Sheet. Consider initiation of Pre-Exposure Prophylaxis (PrEP) for HIV-negative individuals. For more information on PrEP, refer to ontarioprep.ca.
For additional information on the CT/NG NAAT, refer to: LAB-SD-005, Chlamydia trachomatis and Neisseria gonorrhoeae - Nucleic Acid Amplification Testing

Specimen Collection and Handling

Specimen Requirements

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

Chlamydia trachomatis/ Neisseria gonorrhoeae (CT/NG) NAAT

First-void urine2,15

Transfer first-void urine from a sterile container to the Roche cobas® PCR Urine Sample Kit until the fluid level is between the two black fill lines.3,4,5,6,7

Roche cobas® Urine Sample Kit (Item # 300316)1

Chlamydia trachomatis/ Neisseria gonorrhoeae (CT/NG) NAAT

Endocervical9,13,15

Flocked swab

Roche cobas® PCR Media Dual Swab Sample Kit (kit order # 300317)1,8

Chlamydia trachomatis/ Neisseria gonorrhoeae (CT/NG) NAAT

Clinician or patient-collected specimens in a clinical setting10,11,13:

  • Female vaginal15
  • Rectal12
  • Pharyngeal12

Woven swab

Roche cobas® PCR Media Dual Swab Sample Kit (kit order # 300317)1,8

Submission and Collection Notes

1

Do not use expired kits.

2

Prior to sampling, the patient should not have urinated for at least one hour. Female patients must not clean the labial area before collection. If the patient has used Replens® vaginal moisturizer, the specimen should be recollected as it will not be tested.

3

Collect approximately 10-50 mL of first-void urine in a sterile container. Using the provided disposable pipette, transfer urine from the sterile container to the Roche cobas® PCR Urine Sample Kit until the fluid level is between the two black fill lines. Tightly re-cap the Roche cobas® PCR Urine sample tube, and invert 5 times to mix. Urine specimens must be transferred into the Roche cobas® PCR Urine sample tube immediately for stabilization. If specimens cannot be transferred immediately, they can be stored at 2-30°C for up to 24 hours.

4

The Roche cobas® PCR Urine Sample Kits serve as a nucleic acid stabilizing transport and storage medium for urine specimens. The transferred urine must be between the black fill lines for accurate testing. Inadequate volumes (i.e. insufficient or excess) will be cancelled.

5

If there is an excess of blood in the urine specimen (i.e. >35%; specimen will be dark red or brown in colour), it should be discarded and recollected when appropriate. If received at the laboratory, these specimens will be cancelled. The Roche cobas® PCR Urine Sample Kits serve as a nucleic acid stabilizing transport and storage medium for urine specimens. The transferred urine must be between the black fill lines for accurate testing. Inadequate volumes (i.e. insufficient or excess) will be cancelled.

6

Neat urines, and urine submitted in a kit other than the Roche cobas® PCR Urine Sample Kit will be rejected. The Roche cobas® PCR Urine Sample Kit is the only acceptable collection kit for testing.

7

If the tube contents are spilled, discard and replace with a new Roche cobas® PCR Media Dual Swab Sample Kit or PCR Urine Kit. The transport media 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. Clean spills with a suitable detergent and water. Do not use sodium hypochlorite (bleach) or other highly reactive reagents, or a noxious gas could be released.

8

The Roche cobas® PCR Media Dual Swab Sample Kit contains two swabs: a flocked swab and a woven swab. Each swab is optimized and validated for testing of a specific genital/extragenital site. The flocked swab is used for endocervical specimens, and the woven swab is used for vaginal, rectal and pharyngeal specimens. Do not pre-wet swabs in Roche cobas® PCR Media or any other liquid before collection of any specimens. Primary swab specimen tubes with no swabs or with two swabs have not been collected according to the collection instructions and therefore will not be tested.

9

For either swab type, lower the swab specimen into the tube until the visible scoreline on the swab is aligned with the tube rim. The tip of the swab should be just above and not submerged into the liquid prior to breaking the shaft at the dark scoreline. Discard the top portion of the swab. Specimens received with no swab in the sample kit will be cancelled.

10

The presence of mucous in endocervical specimens may cause process delays. Mucous-free specimens are required for optimal test performance. For endocervical specimen collection, use the large woven swab provided in the Roche cobas® PCR Media Dual Swab Sample Kit or equivalent device to clean and remove excess mucous. Discard this swab after use. Use only the flocked swab for specimen collection. Specimens received with two swabs in the sample kit will be cancelled.

11

Vaginal, rectal and pharyngeal specimens should be collected using the woven swab. Do not let the woven swab touch any surface before placing it into the sample kit. Do not use the flocked swab; these specimens will be cancelled.

12

The patient-collected swab specimen collection is limited to health care facilities where support/counseling is available to explain the procedures and precautions. At home patient-collected specimens is not accepted at PHO’s laboratory.

13

The Roche cobas® CT/NG assay is currently not approved by Health Canada for testing of extragenital sites; however, a limited validation of rectal and pharyngeal specimens was performed at PHO to support NAAT for these collections sites.

14

If there is an excess of blood in the swab specimen (i.e. >5%; specimen will have a red or brown colour) or the specimen is grossly contaminated with feces, it should be discarded and recollected. If received at the laboratory, these specimens will be cancelled.

15

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.

16

Specimen collection instructions using the Roche cobas® CT/NG kits can be found here: Roche Educational Resources.

Limitations

Medico-legal investigations: CT and NG culture is the preferred and recommended method for medico-legal investigations; however, NAAT specimens will also be accepted. A positive NAAT result will be confirmed by another NAAT using a different set of primers as per the current Public Health Agency of Canada (PHAC) Canadian Guidelines on Sexually Transmitted Infections. Specimens received on patients <14 years of age have not been validated by the manufacturer; however, they will be tested by PHO with a disclaimer added.

Products containing carbomer(s), including vaginal lubricants, creams and gels may interfere with the test and should not be used during or prior to collecting urogenital specimens.

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 of pelvic inflammatory disease (PID) should not use a self-collected swab to obtain patient-collected vaginal swab specimens as a replacement for a pelvic exam.

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.

After collection, the urine and/or swab specimen must be stored and transported to PHO’s laboratory at 2-30°C. Specimens in the Roche cobas® PCR Media are stable within 12 months of collection.

Special Instructions

Complete all fields of the General Test Requisition Form.  Include, the patient’s full name, date of birth (must be indicated in order for the specimen to be processed for testing), Health Card Number (must match the specimen label), enter the name of the test requested under test description, source of specimen, date of onset, date of collection, physician name and address, and clinical diagnosis.

Chlamydia trachomatis & Neisseria gonorrhoeae Urine Sample kit item # 300316; order using Requisition for Containers and Supplies.

Chlamydia trachomatis & Neisseria gonorrhoeae Roche cobas® PCR Media Dual Swab Sample Kit order # 300317; order using Requisition for Containers and Supplies.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Daily, Monday to Saturday.

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

Reporting

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

Critical positive reports, including specimens from pre-pubertal children (<12 years old) and medico-legal specimens (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 CT or NGare reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.

Test Methods

NAAT for CT/NG is performed using the Roche cobas® CT/NG Assay, a duplex real-time PCR assay for the qualitative detection of CT and NG. Simultaneous testing of both CT and NG occurs from a single specimen (i.e. one collection kit). Testing for CT or NG as a single test request by NAAT is not available and requests will be tested with the CT/NG duplex assay.

Algorithm

Confirmatory testing:

  • NG confirmatory testing is performed on NG-positive specimens for extragenital sites, children <12 years of age, cases of sexual abuse/sexual assault, and medico-legal investigations. Confirmatory testing for NG is performed using the Roche cobas omni Utility Channel with the PivNG Assay V2 (IDT). This assay is not currently approved by Health Canada but has been validated for use at PHO’s laboratory.
  • CT confirmatory testing is performed on CT-positive specimens for children <12 years of age, cases of sexual abuse/sexual assault, and medico-legal investigations. CT confirmatory testing is performed using the Cepheid Xpert® CT assay.

Lymphogranuloma venereum (LGV) testing:

Rectal specimens positive for CT from males, trans-female and/or individuals identifying as male at birth will be routinely forwarded to the National Microbiology Laboratory (NML) for LGV testing. Specimens positive for CT from other sources will only be sent if LGV testing is specifically requested.

Interpretation

CT and NG are interpreted individually and reported as Detected or Not detected.

Test of Cure

Test of cure is recommended for all cases of pharyngeal gonorrhea, suspected compliance issues or treatment failures, if first line treatment was not used, for CT and NG infections during pregnancy, and in cases of sexual abuse/sexual assault.
Refer to the PHAC Canadian Guidelines on Sexually Transmitted Infections for additional indications and information on repeat testing.

Culture for NG is the optimal method for test of cure 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 and should be performed 2-3 weeks after completion of treatment.

In occasional cases where test of cure is recommended for CT infection, NAAT should be performed 3-4 weeks after completion of treatment. In rare circumstances, CT 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 1 Dec 2021