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Chlamydia PCR

CT, chlamydia, STI

Test Codes

EPIC: LAB1230886, Beaker: ICNG

Department

Molecular Pathology

Instructions

Nucleic acid amplification testing (NAAT) is the preferred option for the detection of Chlamydia trachomatis (CT). Swabs (vaginal, endocervical, rectal or oropharyngeal swabs) in Alinity m Multi-collect media, urine in Alinity m Multi-collect media, and ThinPrep^® PreservCyt liquid-based cytology specimens are acceptable for testing. ThinPrep^® PreservCyt specimens offer the patient and physician an efficient means to perform CT testing in conjunction with routine cytology and HPV testing as clinically indicated.

Specimen Collection Criteria

Collect: Swab, urine, or ThinPrep^® PreservCyt specimen, as described below:

SWABS: Vaginal (patient-collected or clinician-collected), Endocervical, Rectal, Oropharyngeal

• Note: Patient-collected vaginal samples must be collected in a healthcare setting
• Collect swab in Alinity M Multi-collect media
  

URINE (Male or Female):  

Preferred specimen: First void urine in Alinity m Multi-collect media. To ensure specimen integrity, collecting locations should refrain from sending urine in sterile collection cups and should instead transfer urine into Alinity m Multi-Collect Media prior to transport.

Also acceptable:

• First void clean catch urine in a sterile collection container or yellow top urine tube. (Minimum: 5.0 mL)
• Midstream urine in a sterile container or yellow top urine tube. Midstream specimens have decreased clinical sensitivity and are of limited diagnostic value. (Minimum: 5.0 mL)

Urine Collection Instructions:

1. First void ("dirty") urine is included in this collection, this is collected before a UA specimen, if both are needed.
2. Do not cleanse the genital area prior to specimen collection.
3. Patient should not have urinated for at least one hour prior to sample collection.
4. Follow directions above to obtain a first void urine specimen.
5. Discard specimen collection swab, it is not required for urine specimen collection.
6. Unscrew the transport tube cap, taking care not to spill the transport buffer within.
7. Handle the cap and tube carefully to avoid contamination.
8. Use the plastic transfer pipette to transfer urine from the collection cup into the transport tube until the liquid level in the tube falls within the clear fill window of the transport tube label or else a new specimen should be collected.
9. Do not overfill. Slightly more than one full squeeze of the transfer pipette bulb may be required to transfer the necessary volume of urine specimen.
10. Recap the transport tube carefully. Ensure the cap seals tightly.
11. Label the transport tube with sample identification information, including date of collection. Take care not to obscure the fill window on the transport tube.

Chlamydia trachomatis MUST be ordered at the time of collection.

Add-on tests CANNOT be performed on urine specimens following testing on other Instrumentation (i.e., urinalysis).

ThinPrep^® PRESERVCYT LIQUID BASED CYTOLOGY (Female endocervical or vaginal):

• Chlamydia trachomatis MUST be ordered at the time of collection.
• Add-on tests CANNOT be performed once the ThinPrep^® specimen has been processed for cytology and/or HPV testing.
• Chlamydia trachomatis test results WILL be reported separately, and NOT as a component of the combined PAP/HPV report. 

Preparation for Courier Transport

Transport: Swabs and urine collected in Alinity m Multi-Collect Media can be stored and transported at room temperature (20 to 26°C or 68 to 78.8°F) or refrigerated  (2 to 8°C or 36 to 46°F). Unpreserved/neat urine samples must be refrigerated (2 to 8°C or 36 to 46°F) and transported to Alinity m Multi-Collect Media within 24 hours of collection. Samples beyond this will be rejected. ThinPrep^® specimens can be transported at room temperature (20 to 26°C or 68 to 78.8°F) or refrigerated (2 to 8°C or 36 to 46°F).

Rejection Criteria

• Unlabeled specimens.
• Specimens submitted in transport media other than Alinity m multi-collect specimen collection media.
• Urine specimens sent in a sterile container that were not refrigerated or have not been transferred to Alinity m Multi-Collect Media within 24 hours of collection.
• SurePath liquid-based cytology specimens.
• Add-on requests for samples that have been previously run on other instrumentation.
• Requests for testing on patients <14 years old. Please refer to Send Outs LAB1231875- Chlamydia trachomatis DNA w/Confirmation (<14 years).
• Conjunctival or eye specimens. Please refer to Send Outs LAB1231872- Chlamydia trachomatis/Neisseria gonorrhoeae RNA, TMA, Conjunctiva.

Inpatient Specimen Preparation

Specimens should be sent to the main Laboratory if received at Royal Oak. Specimens received at other campuses must be added to a packing list before being sent to Royal Oak Laboratory.

Storage

Abbott Alinity m Multi-collect specimens- Urines, swabs (Endocervical, vaginal, oropharyngeal,  or Rectal)
Room Temperature (20-26°C or 68-78.8°F): 14 days
Refrigerated (2-8°C or 36-46°F): 14 days
Frozen (-20°C/-4°F or below): 60 days

Unpreserved / Neat Urine Specimens
Refrigerated (2-8°C or 36-46°F): 24 hours
Frozen (-20°C/-4°F or below): Unacceptable

ThinPrep^® PreservCyt Specimens
Room Temperature (20-26°C or 68-78.8°F): 14 days
Refrigerated (2-8°C or 36-46°F): 14 days
Frozen (-20°C/-4°F or below): 60 days

Specimen Storage in Department Prior to Disposal:

Alinity m Multi-collect urines and swabs): Room Temperature (20-26°C or 68-78.8°F) for 7 days

ThinPrep^® PreservCyt Specimens: Room Temperature (20-26°C or 68-78.8°F) for 30 days

Unpreserved / Neat Urine Specimens: Refrigerated (2-8°C or 36-46°F) for 7 days

Laboratory

Royal Oak Molecular Pathology Laboratory

Performed

Monday – Saturday.
Results are usually available within 24-48 hours of receipt in the Laboratory (excluding weekends and holidays).

Reference Range

Chlamydia PCR not detected.

Test Methodology

Nucleic acid amplification testing performed using the FDA-cleared Abbott Alinity m STI assay (Abbott Alinity m System).

Interpretation

By report.

Clinical Utility

Infection with Chlamydia trachomatis (CT) is the most frequently reported bacterial sexually transmitted disease (STD) in the United States. CT is the leading bacterial cause of sexually transmitted diseases worldwide, with approximately 89.1 million cases occurring annually. CT is a gram-negative, nonmotile, obligate intracellular bacterium with a unique biphasic lifecycle and is the causative infectious agent for a variety of diseases. CT can cause urethritis, cervicitis, proctitis, conjunctivitis, endometritis, and salpingitis; if left untreated, the infection may ascend to the uterus, fallopian tubes, and ovaries causing pelvic inflammatory syndrome, ectopic pregnancy, and tubal factor infertility. Reiter’s syndrome (urethritis, conjunctivitis, arthritis, and mucocutaneous lesions) has also been associated with genital CT infection.  Many infections remain asymptomatic, and high numbers of infected patients may not seek care. Patients often become re-infected if their sexual partners are not treated.  Infants born to infected mothers can develop conjunctivitis, pharyngitis, and pneumonia. The predominant symptoms in men and women are increased discharge and dysuria; women may also present with irregular uterine bleeding.

Reference

1. Package insert, Alinity m STI AMP Kit. Revised August 2023: Abbott Molecular, Inc. Ref 09N17-095. 53-608012/R3

CPT Codes

87491

Contacts

Last Updated

3/17/2025