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Chlamydia trachomatis

In Australia, the term ‘chlamydia’ commonly refers to genital infections with C. trachomatis. The infection is widespread in the community and approximately 10 times as common as gonorrhoea.

Spectrum of disease

  • Commonly an asymptomatic genital infection, particularly in females
  • Urethritis
    • 60% of non-gonococcal urethritis is due to chlamydia
    • A common cause of sterile pyuria among young adults
  • Cervicitis
  • Pelvic inflammatory disease, peri-hepatitis
  • Epididymo-orchitis
  • Reactive arthritis
  • Conjunctivitis in infants born to infected mothers or in adults who get genital secretions into an eye
  • Pneumonia in infants born to infected mothers


C. trachomatis infection is a molecular diagnosis (PCR) on a variety of different samples, as below. The majority of current assays in clinical laboratories on the market will test for both chlamydia and gonorrhea in the same assay.

Female:Urethral swab or first-catch urine or cervical swab
Male:Urethral swab or first-catch urine
Conjunctivitis:Conjunctival swab specifically requesting chlamydia
Neonatal infection:Conjunctival swab specifically requesting chlamydia. For respiratory symptoms, nasopharyngeal swab specifically requesting chlamydia

When to test for chlamydia

  • As part of the evaluation of a patient with urethritis, sterile pyuria, epididymitis, proctitis, cervicitis, pelvic inflammatory disease, reactive arthritis.
  • Screening of an asymptomatic patient at risk of a sexually transmitted infection (STI), for example, sexually active and under 25 years of age, diagnosed with another STI, for example, trichomoniasis, gonorrhoea, syphilis, HIV, acute hepatitis B, history of previous STI, history of new or multiple partners.
  • During pregnancy, because infection can be passed to the infant during birth
  • Evaluation of a neonate developing conjunctivitis within four weeks of age or developing respiratory symptoms (persistent dry cough, respiratory distress) within the first eight weeks of life.


Uncomplicated chlamydia infection in adults is treated with single dose azithromycin, 1 g, including during pregnancy. An alternative is oral doxycycline, 100 mg, twice daily for seven days.

Sexual partners should be treated concurrently to prevent re-infection. If a first-catch urine is the only specimen that has been tested and is positive for chlamydia, concurrent STIs are not necessarily excluded. Further swabs and serological tests are needed for a full sexual health evaluation.

C. trachomatis conjunctivitis – azithromycin 1 g (child: 20 mg/kg up to 1 g) orally, as a single dose. Regardless of age, topical antibiotics are inadequate and are unnecessary when oral treatment is given.

Except for pregnant women, patients do not need to be re-tested shortly after treatment with azithromycin or doxycycline unless symptoms persist or re-infection is suspected.

A high prevalence of C. trachomatis infection is found in women who have had chlamydial infection in the preceding several months. Most result from re-infection, often occurring because the patient’s sex partners were not treated or because the patient resumed sex among a network of persons with a high prevalence of infection. Therefore, recently infected men and women should have repeat screening for C. trachomatis after three months, not as a test of cure, but to detect reinfection.

A positive chlamydia test in a person below 16 years old may indicate a child protection issue. Medical practitioners are reminded that they must report a reasonable suspicion of child abuse immediately and directly to the Department of Child Safety or equivalent in any jurisdiction.

Diseases caused by other subtypes of C. trachomatis

  • Trachoma, a chronic conjunctivitis, which is a major cause of conjunctival scarring and blindness in remote Aboriginal communities and developing countries.
  • Lymphogranuloma venereum (LGV) is a sexually transmitted disease caused by a specific type of Chlamydia trachomatis (serovars L1, L2, and L3). Unlike other forms of C. trachomatis, LGV is invasive and affects the lymphatic system. The symptoms of LGV vary according to the site of infection and may include inflamed and swollen lymph nodes in the groin (inguinal syndrome) and acute haemorrhagic proctitis (anorectal syndrome).
  • LGV is endemic in certain areas of Africa, Asia, South America and the Caribbean. In Australia, cases of LGV have been detected in men who have sex with men (MSM). Many patients reported multiple unprotected sexual contacts abroad, including Europe and the US. Most cases present with anorectal symptoms or proctitis, are HIV positive and many have concurrent STIs.
  • LGV is detectable by conventional Chlamydia trachomatis PCR, but requires specific subtype PCR at a reference laboratory to distinguish it from regular chlamydia. A specific request should be made if LGV is suspected, that is, proctitis in MSM.


  1. eTG complete [Internet]. Therapeutic Guidelines, 2022. [Accessed Apr 2022] <> (Keywords chlamydia trachomatis)
  2. Sexually transmitted infections (STI) [Internet]. Australian Government Department of Health, 2020. [Accessed Apr 2022] <>
  3. Sexually Transmitted Infections Treatment Guidelines, 2021 [Internet]. Centers for Disease Control and Prevention (CDC), 2021. [Accessed Apr 2022] <>
  4. Melbourne Sexual Health Centre [Internet]. Melbourne Sexual Health Centre (MSHC), 2022. [Accessed Apr 2022] <>
  5. NSW STI Programs Unit [Internet]. NSW Government Department of Health, 2017. [Accessed Apr 2022] <>