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Genital chlamydia infection

Dr Natalie Renaud, Registrar, and Dr Susan Bray, Sexual Health Physician, Sexual Health Clinic, Hamilton, New Zealand. DermNet NZ Editor in Chief: Adjunct A/Prof Amanda Oakley, Dermatologist, Hamilton, New Zealand. Copy edited by Gus Mitchell. September 2019.

Genital chlamydia infection — codes and concepts

What is genital chlamydia infection?

Genital chlamydia infection or chlamydiasis is a sexually transmitted infection (STI) caused by the bacterium Chlamydia trachomatis with the serotypes D-K.

Chlamydia serotypes L1–L3 cause lymphogranuloma venereum (LGV), which is discussed separately.

Chlamydia stain

Who gets genital chlamydia infection?

Genital chlamydia infection is a very common STI.

Risk factors include:

  • Being aged > 25 years old
  • New or multiple sexual partners
  • Inconsistent use of condoms.

What are the clinical features of genital chlamydia infection?

Genital chlamydia infection may cause very mild symptoms or no symptoms at all; it is asymptomatic in approximately 70% of infected women and 50% of infected men.

In men, the most common signs and symptoms of genital chlamydia infection are:

  • Discharge from urethra
  • Urethral irritation
  • Pain on urination
  • Testicular swelling or pain.

In women, the most common signs and symptoms of genital chlamydia infection are:

Chlamydia infection at extra-genital sites

Chlamydia infections can also occur in the rectum, the eyes, and in the throat.

Rectal chlamydia infection usually occurs in men who have sex with men (MSM). It can also occur in heterosexual women who receive anal sex. Rectal chlamydia in females who do not practice anal sex is thought to be a result of the spread of the infection from the vagina. Rectal chlamydia is usually asymptomatic, but can infrequently cause anal discharge and discomfort.

Chlamydia conjunctivitis can occur in adults, where it is sexually acquired. It can also occur in newborn babies due to mother-to-child transmission. Throat chlamydia infection is usually asymptomatic.

What are the complications of genital chlamydia?

Genital chlamydia infection can lead to complications of variable severity and duration, particularly following multiple infections over time.

The possible complications of genital chlamydia infection in men include:

The possible complications of genital chlamydia infection in women include:

  • Pelvic inflammatory disease (PID)
  • Tubal infertility
  • Ectopic pregnancy
  • Sexually acquired reactive arthritis
  • Sexually acquired conjunctivitis
  • Perihepatitis syndrome (Fitz-Hugh Curtis syndrome)
  • Chronic pelvic pain.

Mother-to-child transmission can result in chlamydia conjunctivitis and pneumonia in newborn babies.

A triad of reactive arthritis, conjunctivitis and urethritis is known as Reiter syndrome.

How is genital chlamydia infection diagnosed?

In symptomatic individuals with genital chlamydia infection, examination findings may include urethral discharge, abnormal vaginal discharge, cervicitis and contact bleeding, tenderness on bimanual examination (cervical excitation, pelvic adnexal tenderness) and rectal discharge. As these findings can also occur with other STIs, laboratory tests are required to confirm the diagnosis of chlamydia.

In women with suspected genital chlamydia infection, clinical specimens may include:

  • A vulvovaginal swab taken by a clinician or by the patient; this has the best sensitivity (96–98%)
  • An endocervical swab that is taken after the vulvovaginal swab during speculum examination.

A urine sample is not routinely recommended in women because the bacterial load in urine is much less than in men.

In men with suspected genital chlamydia infection, clinical specimens may include:

  • First void morning urine (or last voided at least an hour earlier)
  • Urethral swab has a similar or increased sensitivity.

Clinical specimens at extra-genital sites

Rectal and pharyngeal swabs can be taken by a clinician or the patient. Proctoscopy should be performed if there are rectal symptoms suggestive of chlamydia infection.


Tests for genital chlamydia infection may include:

  • Chlamydia nucleic acid amplification test (NAAT) — chlamydia NAAT may be combined with tests for Neisseria gonorrhoea (gonorrhoea) and Trichomonas vaginalis (trichomoniasis)
  • Enzyme immunoassay (EIA)
  • A point of care test using NAAT or EIA is not routinely used
  • Chlamydia culture — this is not widely available, has a low sensitivity (60–80%) and is not used for throat and rectal infections.

What is the treatment of genital chlamydia infection?

Individuals receiving treatment for genital chlamydia infection should abstain from sex for at least seven days.

Uncomplicated genital chlamydia infection

  • Doxycycline (100mg twice daily) for 7 days: 98% cure
  • Single-dose (1g) azithromycin: 92–97% cure

Uncomplicated rectal chlamydia infection

  • Doxycycline (100mg twice daily) for 7 days
  • Single-dose (1g) azithromycin: followed by proof of cure test

Asymptomatic infections at extra-genital sites

Note that doxycycline is contraindicated in pregnancy and azithromycin is associated with QT prolongation.

Empiric antimicrobial therapy

Proctitis, epididymo-orchitis and pelvic inflammatory disease due to genital chlamydia infection are treated by an extended course of empiric antimicrobial therapy while waiting for test results.

The treatment should cover other possible causes of these presentations such as gonorrhoea. Supportive measures and clinical review are required.

Other treatments

The management of genital chlamydia infection includes a full sexual health check to look for other STIs and the notifications, treatment and testing of sexual contacts.

If the patient is pregnant or has rectal chlamydia, a test of cure (TOC) by NAAT should be performed at least four weeks after completion of treatment. If taken earlier, a false positive may occur due to remnant chlamydial DNA. Re-testing is recommended in 3 months as re-infection is extremely common.

How can genital chlamydia infection be prevented?

As for other STIs, the risk of acquiring chlamydia infection is reduced by safe-sex practices including limiting the number of sexual partners, using condoms, and avoiding re-infection by not having sexual contact with untreated sexual partners.

If you think you are infected, stop any sexual contact and see your usual doctor or a specialist clinician at a sexual health clinic.

See smartphone apps to check your skin.
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