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The University of Chicago Medicine Laboratories

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Mayo Clinic Laboratories

Test Code CTNG Chlamydia trachomatis and Neisseria gonorrhea PCR (CT/NG PCR)

Important Note

For Cobas PCR Urine Sample Kit and cobas® PCR Media Dual Swab Sample Kit

call Clinical Microbiology Laboratory 773-702-6133

Infectious

Additional Codes

Not Applicable

Specimen and Container/Tube

Specimen Types: Swab and Urine
Container for Urine samples: cobas® PCR Urine Sample Kit 
Container for Swab samples: cobas® PCR Media Dual Swab Sample Kit


Specimen Sources:
Urine
Endocervical Swab (clinician collected)
Vaginal Swab (clinician-collected)
Vaginal Swab (self-collected in a clinical setting) 
Oropharyngeal Swab (clinician collected)
Anorectal Swab (clinician collected)    
Ocular (corneal/conjunctiva) 

Collection Instructions

Urine for CT/NG:
Recommended urine sample is first catch urine (first 10 to 50mL of the urine stream). 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.                          The liquid media included in the PCR transport kit must remain inside the container prior to adding sample.
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.

 

Endocervical specimens for CT/NG:

First use the large woven swab provided in the Roche cobas® PCR Media Dual Swab Sample Kit to clean and remove excess mucous. Discard the swab after cleaning.

Use only the flocked swab in the cobas® PCR Media Dual Swab Sample Kit to collect endocervical specimens.

Hold flocked swab with the scoreline above your hand and insert into the endocervical canal.

Gently rotate the swab 5 times in one direction in the endocervical canal. Do not over-rotate.

Carefully withdraw the swab, avoiding any contact with the vaginal mucosa.

Align: Remove the cap from the cobas® PCR Media Tube.

Lower the swab specimen into the tube until the visible scoreline on the swab shaft is aligned with the tube rim. The bud of the swab should not be submerged into the liquid prior to breaking the shaft.

BREAK:  Carefully leverage the swab against the tube rim to break the swab shaft at the scoreline.

CLOSE: Tightly close the cobas® PCR Media Tube. The specimen is now ready for transport. - Discard the top portion of the swab.

 

Vaginal, Oropharyngeal, Anorectal for CT/NG:

Use only the woven polyester swab in the cobas® PCR Media Dual Swab Sample Kit to collect vaginal, anorectal and oropharyngeal swab specimens. Do not use the flocked swab; these specimens will be cancelled.

The liquid media included in the PCR transport kit must remain inside the container prior to adding sample. A properly collected swab specimen should have a single swab with the shaft broken at the score line.

 

Ocular (corneal/conjunctiva) for CTNG      COLLECT TWO SPECIMENS:

  • One Aptima Multitest Swab Collection Kit, call Laboratory Service Center for supplies, (773)702-1316
  • One cobas® PCR Media Dual Swab Sample Kit

Use only the woven polyester swab in the cobas® PCR Media Dual Swab Sample Kit to collect Ocular Specimen.

Place collection swabs in transport tube provided. Snap off swab at score line so swab fits into closed tube.

 

Specimen Handling and Transport Instructions

Do not freeze any samples                                                                                                                                                        

All specimen types can be stored and transported at 2-30°C.

Swabs in the cobas® PCR Media should be transported to the Microbiology laboratory within 48 hours of collection.                

Urine in the cobas® PCR Media should be delivered to the Microbiology laboratory within 48 hours of collection.

Rejection Criteria

Endocervical swab specimens that have both the large woven polyester swab used for cleaning and the flocked swab used to collect the sample inside of the cobas® PCR media tube.

Swab specimens that contain dry swabs with no liquid inside of the cobas® PCR media tube.

Swab specimens that contain NO swab or two swabs inside the cobas® PCR media tube

Urine samples that are above or below two black lines on the cobas® PCR Media

If the liquid level is above or below these lines, the specimen has not been collected properly and cannot be used for testing

If the collected specimen contains excess blood (specimen has a red or brown color), it should be discarded and not used for testing.

Reference Values

Chlamydia trachomatis: Negative

Neisseria gonorrhea: Negative

Critical Values

Not Applicable

Clinical Indications

Nucleic acid amplification testing (NAAT) is the recommended method for initial screening or testing for Chlamydia trachomatis (CT) and Neisseria gonorrhea (NG) infections.

Neisseria gonorrhea (NG) culture is recommended plus NAAT when suspecting antimicrobial resistance, test of cure, symptomatic patients, pelvic inflammatory disease (PID), pregnancy, and sexual abuse/sexual assault.

Vaginal lubricants, speculum jellies, creams, and gels containing carbomer(s) may interfere with the test and should not be used during or prior to sample collection.

If the collected specimen contains excess blood (specimen has a red or brown color), it should be discarded and not used for testing.

Avoid contact of the cobas® PCR Media with the skin, eyes or mucous membranes.

If contact does occur, immediately wash with large amounts of water.

Do not pre-wet the swab in cobas® PCR Media before collection.

Test Components

Chlamydia trachomatis (CT)
Neisseria gonorrhoeae (NG

Methodology

Roche cobas® 6800, DNA PCR

CPT Codes

87491 for Chlamydia trachomatis (CT)
87591 for Neisseria gonorrhoeae (NG)

LOINC Codes

21613-5 Chlamydia trachomatis 
24111-7 Neisseria Gonorrhoeae

Last Review Date

5/22/2025

Turnaround Time

72 hours, Priority: Routine 

Volume

Urine Specimens

Recommended urine sample is first catch urine (first 10 to 50mL of the urine stream). 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.  

Swab Specimens

The liquid media included in the cobas® PCR Media Dual Swab Sample Kit must remain inside the container prior to adding sample.

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