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Chlamydia trachomatis PCR


chlamydia swab universal

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Nucleic acid amplification assay (PCR) for the detection of Chlamydia trachomatis DNA.

This is performed as a paired test with Neisseria gonorrhoeae PCR


Diagnosis of Genital Chlamydia – Chlamydia is one of the most common sexually transmitted infections in the UK; it is caused by the bacterium Chlamydia trachomatis.

Eye swabs can also be tested on neonates suspected of having opthalmia neonatorum.


Swabs – Endocervical /low vaginal/ rectal/ throat/urethral/ high vaginal swabs

  •  Self-taken female swabs are acceptable for screening purposes.

Urine (Preferably Males only – lower sensitivity than swabs for Females)

  • First voided urine. The patient should not have passed urine in the preceding 1 -2 hours. If the specimen will not reach the laboratory on that day please store in the refrigerator.

Specimen Container

Yellow topped Chlamydia swabs (Cobas PCR)

White Top Universal Pots (20-30ml of initial stream urine)

How To Request On EPIC

For electronic requesting using EPIC (RDUH ONLY):

Search for: ‘Chlamydia trachomatis & Neisseria gonorrhoeae PCR‘ or test code ‘LAB1379

Sample Collection

Risk of invalid result due to lubricants (Click to expand)

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.

    • To minimize the risk of invalid test results:
      • Refrain from using carbomer-containing products to lubricate a speculum as part of the collection procedure, or collect sample prior to use of lubricant/performing pelvic exam
      • Ask patients to refrain from using feminine hygiene products for approximately 24 hours prior to their scheduled visit
      • If patient is known to be using feminine hygiene products at time of collection, an alternative non-vaginal swab sample type may be considered
    • Examples of carbomer-containing products include:
      • DynaLube Lubricating Jelly
      • McKesson Lubricating Jelly
      • Cardinal Health Lubricating Jelly
      • Medline Lubricating Jelly
      • RepHresh Clean Balance
      • RepHresh Vaginal Gel Prefilled
      • Vagisil Anti-itch Cream
      • Vagisil Crème Regular Strength
      • Vagisil ProHydrate
      • Vagisil Sensitive Cream
      • IsoLove Balancing Gel
      • Replens Long-Lasting Vaginal Moisturizer
      • Metronidazole Vaginal Gel


Endocervical & Low Vaginal Swabs (Click to expand)

The specimen collection kit consists of a paper packet containing 2 swabs and a yellow topped plastic tube containing transport media.

    • For an endocervical swab, it is essential to visualize the cervix. Any discharge or blood should be wiped away. Insert the swab into the cervix and rotate with the aim of removing epithelial cells.
    • For taking a low vaginal swab, ensure the patient is not wearing a tampon. The labia should be parted to open the vagina. Insert a swab gently to about 5cm. Rotate all the way around the vagina
    • If preferred the patient can take her own low vaginal swab ( instructions below)
    • Please take only one sample per patient (vials with 2 swabs in will be rejected)



How to collect a Low Vaginal Swab (self-swab) (Click to expand)

1. Open the plastic bag. Open the paper packet which contains two swabs. Throw away the thin ended swab – you need to use the THICKER swab ONLY.

2. Stand with your feet apart and your knees bent, or sit down with your knees apart.

3. Take the thicker of the two swabs by the non-fluffy end. With your free hand hold open the skin around the vaginal opening.

4. Place the soft swab tip into the vagina approximately the length of your finger. Rotate the swab all the way around the vagina. Remove the swab and continue to hold it. Do not put it down.



5. Holding the yellow topped tube upright, unscrew the cap and put the swab inside with the fluffy end down. There is a faintly scored ring around the white stick about 2/3 of the way up. Hold the swab stick firmly with the score mark against the top of the tube; bend it until it breaks off at the top of the tube. (There is liquid in the tube – DO NOT pour this away as it is meant to be there, without it the specimen cannot be processed.)


6. Screw the cap on firmly. Label the tube with your full name, date of birth and the date of the sample. Ensure that the tube only contains the thicker swab. The laboratory will not be able to process the sample if both swabs are in the tube.



7. You may discard the broken stick, packaging and unused swab into a household rubbish bag.


Special Instructions

  • Please state time of collection and label with the minimum patient identification. Labelling must include the following:
    • Surname
    • First Name
    • Date of Birth
    • Unique Identifier – NHS Number  (or Hospital No.)
  • Samples from patients known to have blood transmissible viral infections should be clearly labelled “High Risk” or “Danger of Infection”.
  • Please include relevant clinical details and any antimicrobial therapy the patient is taking
  • If patient is symptomatic / high suspicion of infection please also send charcoal swab for MC&S  – Genital Swab Culture

LGV (Lymphogranuloma Venereum) Testing

(Click here to expand)

Caused by a subset of C. trachomatis (Serovars L1, L2 or L3), which can cause a more severe infection (attacking lymph nodes, causing inflammation and invasive disease.)

  • As standard practice we refer all Chlamydia positive rectal swabs from Males for LGV testing. (Also from all sites for HIV+ MSM if Chlamydia positive.)
  • We can refer Chlamydia positive rectal swabs from females on request, but do not do so routinely (LGV in females is rare in the UK.)
      • Please note the reference lab will only test samples from females who either:
          • Have proctitis
          • Are a contact of a LGV positive patient
          • Are trans-gender female
      • Please provide this information with the request
  • We DO NOT refer samples for LGV that have tested NEGATIVE for Chlamydia on our in-house PCR test.
      • All requests received for LGV only will be tested for Chlamydia in-house prior to referral for LGV testing

LGV testing is performed by the Bacteriology Reference Department, UKHSA Colindale – UKHSA – Referral form for LGV Testing

For further information on LGV – Terrence Higgins Trust – LGV



Processed locally in Microbiology at RDUH

LGV testing: Sent to Sexually Transmitted Infections Reference Laboratory (STIRL), UKHSA Colindale, London

Processing Time

Please allow up to 6 days for result

LGV testing: Please allow up to 7 days after sending to STIRL

Repeat Interval

Do not repeat this test within 1 month.


Routine Testing: Roche Cobas 6800

Urgent Testing: Cepheid GeneXpert

For Patients:

Chlamydia – Devon Sexual Health

Chlamydia – Lab Tests Online UK

Chlamydia – NHS

Chlamydia – Sexwise

For Healthcare professionals:

Chlamydia: surveillance, data, screening and management – UKHSA

British Association for Sexual Health and HIV

National Chlamydia Screening Programme (NCSP) – UKHSA

The National Chlamydia Screening Programme offers annual (or on change of sexual partner) opportunistic screening to all sexually active men & women under 25 years.


(Sounds Like: Chlamidia)

Specimen Labelling Procedure
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