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Apr 12, 2023Print this page

How to Swab for Gonorrhea and Chlamydia

The gynecologist puts a smear on a slide glass for microscopy, hands close-up - How to Swab for Gonorrhea and Chlamydia

According to the US Centers for Disease Control and Prevention (CDC), a record 2.5 million-plus cases of chlamydia, gonorrhea and syphilis were reported in the United States in 2021.  According to the annual Sexually Transmitted Disease Surveillance Report released in 2021, most of these new diagnoses (1.6 million) were cases of chlamydia.

There were also 710,000 gonorrhea cases and almost 179,000 cases of primary and secondary syphilis – the most infectious stages of the disease.

All three of these STDs can be cured with antibiotics. But if left undiagnosed and untreated, they can have serious health consequences, including infertility, life-threatening ectopic pregnancy, stillbirth in infants, and increased risk for HIV transmission.

Though syphilis is confirmed via blood test, both gonorrhea and chlamydia tests can be conducted with swab samples of the genitals, throat, or anus. That's why we've put together this basic primer on how to take various swab samples used to test for gonorrhea and chlamydia.

*Please note: When collecting samples, it is recommended to wear appropriate personal protective equipment (gloves, surgical mask, eye protection). 

How to Collect an Endocervical Sample

A woman's endocervix, the area around the opening of the uterus, is the preferred site for specimens from females. It's recommended that specimen collection should be done with a sterile swab and not a Cytobrush.  Harsher brushes may cause trauma and bleeding that can corrupt the specimen.

Use two swabs: one to clean the cervix to remove excess mucus,  and another to collect the sample.

For gonorrhea testing, an ideal choice in swab includes a transport and collection system.

  1. Peel open the sterile pouch

  2. Remove plug from sterile tube and discard

  3. Remove swab applicator and collect specimen by rotating the swab against the wall of endocervical canal several times.

  4. Rotate the swab against the wall of the endocervical canal several times for 20-30 seconds

  5. Withdraw the swab without touching the vaginal surface

  6. Insert swab into the transport tube

  7. Record patient information in space provided on the label

  8. Transport specimen to laboratory to be processed

male + female swabbing toolkit for STIs

How to Collect a Urethral Sample 

The urethra is a tube that drains urine from the bladder. This is the preferred culture site in men, or in women with no cervix. Specimens should be taken no earlier than two hours after the patient has last voided his or her bladder. 

  1. Gently insert the swab into the urethra (1-2 cm for women, 2-4 cm for men)

  2. Rotate the swab in one direction for a minimum of 10 seconds

  3. Withdraw the swab

  4. Break the swab handle at scored breakpoint line

  5. Label the vial with appropriate patient information

  6. Seal the transport tube, allowing the specimen to be exposed to the appropriate transport media

How to Collect a Throat Swab

Chlamydia can be spread to the throat during oral sex, despite most frequently infecting the cervix, urethra or rectum. Pharyngeal swabbing is the preferred method of specimen collection, which involves swabbing the area behind the nasal cavities, mouth, and larynx. 

  1. Use a sterile flocked swab that comes with a transport medium filled vial, ex: Universal Transport Media system

  2. Have the patient tilt their head backwards, open their mouth, and stick out their tongue

  3. Without touching the side of the mouth, swab the posterior nasopharynx and the tonsillar arches

  4. Remove swab and insert into a vial containing 1-3 ml of transport media

  5. Break the swab handle at scored breakpoint line

  6. Label the vial with appropriate patient information

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How to Collect a Rectal Swab

Gonorrhea and chlamydia often occur simultaneously because the risk factors are very similar. Patients who are suspected of having one of these sexually transmitted bacterial infections are usually tested for the other as well.

  1. Insert a sterile swab approximately 2.5 cm into the anal canal

  2. Move swab from side to side in the anal canal

  3. Allow swab to remain 10-30 seconds for absorption of organisms onto the swab

  4. Remove swab and insert into a vial containing 1-3 ml of viral transport media

  5. Label the vial with appropriate patient information

Rectal Swab Sample How-To


We hope you find this guide for gonorrhea and chlamydia specimen collection helpful. For more information on these procedures or products to conduct them, feel free to contact our helpful product specialists today.

Contact a sales rep, today!


Topics: Medical, Diagnostics, Specimen Collection Procedure


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