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Chlamydia: Evidence-Based Management & Partner Notification

Updated 2026 clinical guide to chlamydia: first-line doxycycline regimen, Nucleic Acid Amplification Testing (NAAT), and contact tracing in Australia.

Epidemiology & The Asymptomatic Nature of Chlamydia

Chlamydia trachomatis is the most frequently notified sexually transmitted bacterial infection in Australia, disproportionately impacting young people aged 15 to 29 years. It is transmitted through unprotected vaginal, anal, or oral sex.

The cardinal clinical challenge of chlamydia is that over 75% of women and up to 50% of men are completely asymptomatic. Left undetected and untreated, silent upward ascent of the organism into the upper reproductive tract causes severe long-term reproductive sequelae:

  • In Women: Pelvic Inflammatory Disease (PID), chronic pelvic pain, tubal scarring, ectopic pregnancy, and tubal factor infertility.
  • In Men: Epididymo-orchitis, scrotal swelling, pain, and potential impaired fertility.

Diagnostic Testing: Nucleic Acid Amplification Testing (NAAT)

Routine serology (blood testing) has no role in the diagnosis of acute chlamydia. Highly sensitive, non-invasive Nucleic Acid Amplification Tests (NAAT / PCR) are the gold standard:

  • In Asymptomatic Women: Self-collected low vaginal swab (first-line preferred method, highly sensitive and acceptable) or first-pass urine.
  • In Asymptomatic Men: First-pass urine (the first 20–30 mL of urine voided after holding urine for at least 1–2 hours).
  • Site-Specific Testing: Rectal and pharyngeal swabs should be collected based on specific sexual practices and exposure history.

Evidence-Based Management Protocol

Standard management comprises five mandatory clinical steps:

  1. Pharmacotherapy: Doxycycline 100 mg twice daily with food for 7 days (remain upright for 30 minutes to prevent pill-induced oesophagitis).
  2. Sexual Abstinence: Strictly no sexual contact (even with condoms) for 7 days after starting treatment, and until 7 days after sexual partners have completed their treatment.
  3. Contact Tracing: All sexual contacts from the past 6 months must be notified, tested, and empirically treated. Anonymous digital notification services (such as Let Them Know - letthemknow.org.au) can assist patients in alerting partners discreetly.
  4. Screening for Co-Infections: Full STI screening including gonorrhoea (usually duplex PCR with chlamydia), syphilis serology, HIV, and hepatitis B/C.
  5. Mandatory Re-Testing at 3 Months: Due to reinfection rates of 10–15% from untreated partners or new exposures, patients must be re-tested 3 months after completing therapy. A 'test of cure' earlier than 4 weeks is not recommended due to shedding of non-viable bacterial DNA producing false-positive PCR results.
Archival Document Available: You can also access Dr Tseng's original reference sheet as a printable PDF.
Download Original PDF
Authored by Dr Jimmy Tseng
BMedSci, MBBS, PGDipSurgAnat, GCUT, FRACGP • Specialist GP, Founder & Senior Lecturer
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