Sexual Health  |  Chlamydia Pathway - Sampling

Sexual Health

Chlamydia Pathway - Sampling


  • submit a self-taken vulvovaginal swab for nucleic acid amplification test (NAAT/PCR):
    • vaginal specimens have been demonstrated to produce a similar sensitivity to cervical testing
    • recent studies indicate that vulvovaginal swabs are better than endocervical swabs for chlamydia and gonorrhoea NAAT/PCRs
  • alternatively, a first-void urine sample may be obtained but is not the preferred female sample for N. gonorrhoea
  • urine is less sensitive than endocervical or self-taken vulvovaginal swabs


  • submit a first-void urine
  • urine should be held in the bladder for at least 1 hour
  • if the man cannot pass urine, a urethral swab may be used

Men who have sex with men and sex workers - take pharyngeal and rectal swabs in addition to the above:

  • NAAT/PCRs are routinely used and are the test of choice, however they are not licensed
  • pharyngeal specimens:
    • rub swab over the posterior pharynx and tonsillar crypts
  • rectal specimens:
    • self-taken and physician-taken rectal swabs are of equal efficacy and either may be used (LGV), refer them to a clinic


  • technological advancements in NAAT/PCRs make it possible and inexpensive to simultaneously test for gonorrhoea alongside¬†chlamydia in a single assay
  • problems that may be associated with dual NAAT/PCRs include:
    • false positive results, leading to:
      • incorrect and stigmatising diagnoses
      • unnecessary antibiotic treatment
      • incorrect partner notification
    • patients not always consenting to or being informed that their sample is being tested for both infections
  • it is important to obtain informed consent
  • screening of asymptomatic individuals in low-risk populations with a low prevalence of gonorrhoea can result in high rates of¬†false positives:


  • a repeat test, for confirmation, if/when there is an unexpected positive result for gonorrhea.

Last updated : Monday, April 09, 2018
Next review date : Tuesday, April 09,2019

Disclaimer: This site is intended to be flexible and frequently updated. While every effort has been made to ensure accuracy, all information should be verified.