Chlamydia trachomatis (genital) diagnosis and management

Last updated: December 2017


Nucleic Acid Amplification Test

NAAT refers to Nucleic Acid Amplification Test, such as PCR

Current nucleic acid amplification test (NAAT) technology is very sensitive and has been validated for urine, cervical and vaginal specimens.

NAATs for chlamydia are not validated at extra genital sites but due to the absence of a Gold Standard alternative test, NAATs are used in clinical practice at rectal, pharyngeal and conjunctival sites.

Diagnosis is made on a positive sample from an infected site such as:

  • first catch urine in males
  • self-collected vaginal swab
  • clinician collected endocervical swab
  • clinician collected or self-collected rectal swab in males and females
  • clinician or self-collected throat swabs in men who have sex with men (MSM) and in female sex workers
  • in females without a cervix or in whom swabs cannot be taken, a first catch urine is tested
  • conjunctiva
  • Nasopharynx in infants at risk of neonatal transmission.

Note: Women should be asked about anal sex and appropriately tested.

Specimen collection

Self-collected anal and vaginal swabs are only appropriate for asymptomatic patients. If patients have any symptoms, a physical examination and clinician-collected swab samples are recommended.

Self-collection of specimens by patients is acceptable, and can be helpful in situations where the patient is uncomfortable with the clinician collecting the sample directly, or where consultation times are limited.

A self-obtained vaginal swab or first-void urine is acceptable in women even though the first void urine is slightly less sensitive.

First-void urine is best collected at least 20 minutes after urine was last passed, collecting the first 20 mL of urine passed. Note, first void urine is not the first urination after waking in the morning.

Recommendations for testing:


  • Endocervical swab- if undergoing a speculum exam for an evaluation of symptoms
  • In asymptomatic women - a self-collected vaginal swab or a first pass urine sample is acceptable.
  • Rectal swab if history of anal sex
  • For female sex workers include additional pharyngeal swab, and rectal swabs if history of anal sex


  • First-void urine sample
  • Men who have sex with men (MSM): Regardless of sexual practice, rectal and throat swabs should be taken.
  • If anorectal symptoms are present, consider referral to specialist sexual health clinic.

Women with symptoms of PID such as pelvic pain, deep dyspareunia and intermenstrual or post coital vaginal bleeding, should be assessed, and if indicated, treated for PID – see PID Diagnosis and Management Guideline


Serology is of no value in the diagnosis of genital tract chlamydial infection.


Standard therapy for oropharyngeal, urethral, endocervical, conjunctival sites

Azithromycin 1 g orally as one dose (B1)


Doxycycline 100 mgs orally twice a day for 7 days (D).


Doxycycline (and ofloxacin) are contraindicated in pregnancy and breastfeeding.

Azithromycin 1 g orally as one dose (B1)


Amoxycillin 500 mgs orally tds for seven days (A).

Standard therapy for rectal site

Doxycycline 100 mg orally twice a day for 7 days (D).

Please note that if lymphogranuloma venereum (LGV) is considered, 21 days of doxycycline is required – see LGV guidelines

Rectal site in pregnancy

Azithromycin 1 g weekly for two doses (B1).

Partner notification (contact tracing)

Stress the importance of partner notification and treating sexual partners.

Inform patients about asymptomatic infections, potential complications of untreated infection and the possibility of re-infection if a partner is not treated.

Advise patients to have no sexual contact for 7 days after treatment.

Patients should be advised to contact all sexual partners in the last six months for testing and treatment. 

All contacts should have appropriate investigations for chlamydia and treatment with standard therapy as above.

Patient delivered partner therapy (PDPT) for chlamydia, using azithromycin, is advocated in some jurisdictions. This practice is not recommended in South Australia due to the presence of circulating strains of azithromycin resistant gonorrhoea and mycoplasma genitalium.  Appropriate testing for chlamydia and gonorrhoea is recommended for asymptomatic contacts of chlamydia, on the day of treatment.

Web resources are available for patients to inform partners anonymously:

The Australasian Contact Tracing Guidelines are a resource for medical professionals.

Patient education

The following points should be discussed:

  • chlamydia is sexually transmitted
  • chlamydia is a common infection
  • infection is asymptomatic in up to 50% of men and 90% of women
  • re-infection may occur during or after treatment
  • abstinence from sex (including oral sex) until doxycycline is completed by patient and partner/s, or 1 week after patient and partner treatment if azithromycin is used
  • chlamydia is a notifiable disease
  • advise on the side effects of medications
  • a test of cure is required at six weeks
  • discuss window periods for other STI and HIV
  • reinforce safe sex.

Follow up

Clinical review 1 week after treatment for symptomatic patients allows

  • Confirmation of patient adherence with treatment if directly observed single dose therapy not used, and assessment for symptom resolution.
  • Confirmation that partner notification procedures have been undertaken or offer of more partner notification support.
  • Provision of further sexual health education and prevention counselling.

Test of Cure (TOC)

Not routinely recommended, except in the following groups:

  • Pregnant women
  • Rectal chlamydia

TOC by Nucleic Acid Amplification Test (NAAT) in these situations should be performed at 4 weeks or more after treatment is completed. (The best time interval is unknown). An earlier TOC could yield a false positive result due to the presence of non-viable chlamydia DNA remnants.


  • Re-infection is common
  • Re-testing at 3 months is recommended for all treated patients, to detect re-infection.
  • Screen for Human Immunodeficiency Virus (HIV) and syphilis at 3 months.

Further information

For further information on the diagnosis and management of genital chlamydia trachomatis contact Adelaide Sexual Health Centre.


These guidelines are based on review of current literature, current recommendations of the United States Centres for Disease Control and Prevention, World Health Organization, the British Association for Sexual Health and HIV, Australian national and state guidelines, and expert opinion. Local antimicrobial sensitivities are reflected in these recommendations.

They are written primarily for use by Adelaide Sexual Health Centre in the setting of a specialist Sexual Health Clinic, with on-site laboratory facilities. Some flexibility is required in applying them to other clinical settings.