Cervical Swabs vs Vaginal Swabs for Chlamydia and Gonorrhea NAATs
Cervical Swabs vs Vaginal Swabs for Chlamydia and Gonorrhea NAATs

Cervical Swabs vs Vaginal Swabs for Chlamydia and Gonorrhea NAATs

Female gynecologist unrecognizable woman patient in gynecological chair during gynecological check up.

Chlamydia and gonorrhea infections remain major public health concerns. The Centers for Disease Control and Prevention (CDC) reported over 1.5 million chlamydia cases and 350,000 gonorrhea cases in the United States in 2018. As most cases are asymptomatic, screening is crucial for timely diagnosis and treatment. Traditionally, endocervical swabs have been considered the optimal specimen for diagnosing cervical infections. However, studies in recent decades have evaluated self-collected vaginal swabs as an alternative. Vaginal discharge and conditions like bacterial vaginosis can also complicate endocervical sampling and interpretation. This raises the question: Are endocervical swabs still the best specimen type for chlamydia and gonorrhea testing?

What specimen types have been used for chlamydia and gonorrhea testing?

Nucleic acid amplification tests (NAATs) are recommended for chlamydia and gonorrhea diagnosis due to their high sensitivity and specificity. When NAATs were first introduced in the 1990s, endocervical swabs were the standard specimen. Other options like urine or vaginal swabs were initially considered suboptimal.

This changed as studies in the 2000s demonstrated comparable performance of self-collected vaginal swabs and first-void urine to endocervical swabs for NAATs. In a 2003 study, Schachter et al. evaluated the Gen-Probe Aptima assays on 1464 women at US clinics. Using positive results from two FDA-cleared NAATs as reference, they found self-collected vaginal swabs had similar sensitivity and specificity to clinician-collected cervical swabs for detecting chlamydia (98.3% and 96.5% vs. 97.2% and 95.2%) and gonorrhea (96.1% and 99.3% vs. 96.2% and 99.3%).

How do self-collected vaginal swabs compare to clinician-collected endocervical swabs?

Several studies have directly compared self-collected vaginal swabs and clinician-collected endocervical swabs for NAATs.

In a 2005 study, Chernesky et al. had 1077 women attending Canadian STI clinics provide both specimen types. Aptima assays demonstrated nearly equal sensitivity and specificity for chlamydia (vaginal 98.3% and 99.7%, cervical 98.1% and 99.0%) and gonorrhea (vaginal 98.3% and 99.9%, cervical 96.7% and 99.7%). Patients also reported preferring self-collection over pelvic exams.

A 2009 study by Schachter et al. across 10 US sites compared self-collected vaginal swabs to clinician cervical swabs using Gen-Probe Aptima and BD Probetec assays. Sensitivities were 96.1%-97.9% for chlamydia and 95.5%-96.7% for gonorrhea, while specificities exceeded 98.9% for both infections. Furthermore, more infections were detected using vaginal swabs.

Recent studies using newer NAATs have affirmed this equivalence. A 2015 CDC study reported comparable sensitivity and specificity between self-collected vaginal and clinician cervical swabs when tested with the Hologic Aptima combo assay.

Collectively, these studies demonstrate self-collected vaginal swabs perform similar to clinician-collected endocervical swabs for chlamydia and gonorrhea NAATs.

What are the advantages of using self-collected vaginal swabs?

Beyond comparable accuracy, self-collected vaginal swabs offer multiple benefits over endocervical swabs:

  • - Increased screening access: Self-collection eliminates the need for pelvic exams, which is a barrier for some women. At-home self-collection also enables screening outside clinics.
  • - Patient preference: Studies show most women prefer self-collecting vaginal swabs over clinician cervical sampling. Self-collection enhances privacy and comfort.
  • - Ease of collection: Patients can easily collect vaginal swabs themselves following simple instructions. Endocervical swabs require proper insertion by a clinician.
  • - Specimen stability: Vaginal swabs can be stored dry and shipped without refrigeration, unlike endocervical swabs. This enables remote collection and transport.
  • - Detection at multiple sites: Vaginal secretions may capture pathogens from the cervix, vagina, and urethra, while endocervical swabs sample only the cervix.

The CDC currently recommends self-collected vaginal swabs as an alternative to endocervical swabs for chlamydia and gonorrhea screening in women. Given the advantages, self-collected vaginal swabs will likely become the preferred approach.

What about use in symptomatic women?

Most studies on self-collected vaginal swabs focused on asymptomatic screening. However, a 2017 study by Gaydos et al. evaluated self-collected vaginal, clinician endocervical, and urine samples from 513 symptomatic women using Hologic Aptima assays.

For chlamydia, sensitivities were 88.4% for vaginal swabs, 89.8% for endocervical swabs, and 72.3% urine. For gonorrhea, sensitivities were 100% for vaginal swabs, 92.9% for endocervical swabs, and 78.6% for urine. This demonstrates self-collected vaginal swabs perform similar to endocervical swabs in symptomatic women too.

Are there any limitations to self-collected vaginal swabs?

While self-collected vaginal swabs have proven accuracy for NAATs, some limitations exist:

  • - Insufficient sampling: Patient errors in collection could lead to inadequate samples. However, studies show most women collect swabs properly when given instructions.
  • - Interfering flora: Vaginal swabs contain mixed microflora that could inhibit NAATs, unlike endocervical swabs. But clinical evaluations demonstrate minimal impact.
  • - Uncertain lesion location: Endocervical swabs directly sample any cervical lesions. Vaginal swabs may miss cervical infections. However, they detect most clinically relevant cases.
  • - No cytology: Endocervical swabs enable Pap smears. But co-testing for cytology is not recommended and rarely done with chlamydia/gonorrhea testing.

Overall, self-collected vaginal swabs have demonstrated excellent performance despite these limitations. Any drawbacks appear outweighed by the benefits for screening.

In summary, current evidence affirms self-collected vaginal swabs are comparable to clinician-collected endocervical swabs for detecting chlamydia and gonorrhea using NAATs. Offering advantages in accessibility, acceptability, and logistics, self-collected vaginal swabs are becoming the preferred specimen type for chlamydia and gonorrhea screening programs. However, endocervical swabs still play a role in evaluating symptomatic individuals when pelvic exams are clinically indicated. Further studies may help refine best practices for specimen types in different testing scenarios. But for routine screening, self-collected vaginal swabs appear to be the optimal approach moving forward.

Click to View: Mantacc Cervical Swabs


  1. 1. Chernesky M, Jang D, Gilchrist J, Hatchette T, Poirier A, Flandin JF, Smieja M, Ratnam S. Head-to-head comparison of second-generation nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae on urine samples from female subjects and self-collected vaginal swabs. J Clin Microbiol. 2014 Jul;52(7):2305-10. doi: 10.1128/JCM.03552-13. Epub 2014 Apr 2. PMID: 24696024; PMCID: PMC4097753.
  2. 2. Schachter J, Chernesky MA, Willis DE, Fine PM, Martin DH, Fuller D, Jordan JA, Janda W, Hook EW 3rd. Vaginal swabs are the specimens of choice when screening for Chlamydia trachomatis and Neisseria gonorrhoeae: results from a multicenter evaluation of the APTIMA assays for both infections. Sex Transm Dis. 2005 Dec;32(12):725-8. doi: 10.1097/01.olq.0000190092.59482.96. PMID: 16314767.
  3. 3. Masek BJ, Arora N, Quinn N, Aumakhan B, Holden J, Hardick A, Agreda P, Barnes M, Gaydos CA. Performance of three nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae by use of self-collected vaginal swabs obtained via an Internet-based screening program. J Clin Microbiol. 2009 Jun;47(6):1663-7. doi: 10.1128/JCM.02387-08. Epub 2009 Apr 22. PMID: 19386838; PMCID: PMC2691063.

Related Posts

Everything You Need To Know About Cervical Specimen Collection

Cervical Swab: A Vital Tool in Detecting Precancerous Cells

Cervical Cancer 101: Symptoms, Causes, Screening Tests, Treatment and Prevention Strategies

Keep Away from Cervical Cancer

At-Home HPV Testing: The Gift of Cervical Cancer Prevention

White Blood Cells in Cervical Swab Without Infection: Causes and Clinical Approach

The Cervical Swab: Leading the Charge in Women's Diagnostics

Product Catalog