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STIs

  • Anogenital warts
  • Chlamydia
  • Donovanosis
  • Ectoparasites
  • Genital Herpes Simplex Virus
  • Gonorrhoea
  • Hepatitis A
  • Hepatitis B
  • HIV
  • Lymphogranuloma venereum
  • Mycoplasma genitalium
  • Syphilis
  • Trichomoniasis

Infections associated with sex

  • Bacterial Vaginosis
  • Candidiasis
  • Hepatitis C
  • Monkeypox (mpox)
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Endorsement: These guidelines have been endorsed by the Blood Borne Viruses and Sexually Transmitted Infections Standing Committee (BBVSS). 

Developed by: the Australasian Society for HIV, Viral Hepatitis and Sexual Health Medicine (ASHM) ABN 48 264 545 457 | CFN 17788

Funded by: The Australian Government Department of Health

Disclaimer: Whilst the Australian Department of Health provides financial assistance to ASHM, the material contained in this resource produced by ASHM should not be taken to represent the views of the Australian Department of Health. The content of this resource is the sole responsibility of ASHM. www.ashm.org.au

Last updated: April, 2024

© ASHM, Australia, 2024

  • Standard Asymptomatic Checkup
  • STIs
    • ← Back
    • Chlamydia
    • Gonorrhoea
    • Hepatitis A
    • Hepatitis B
    • Syphilis
    • Donovanosis
    • Trichomoniasis
    • Anogenital warts
    • HIV
    • Lymphogranuloma venereum
    • Ectoparasites
    • Mycoplasma genitalium
    • Genital herpes simplex virus (HSV)
    • Bacterial vaginosis
    • Candidiasis
    • Hepatitis C
  • Syndromes
    • ← Back
    • Anogenital lumps
    • Anogenital ulcers
    • Cervicitis
    • Epididymo-orchitis
    • Skin rash and lesions – general
    • Sex-associated diarrhoea
    • Anorectal syndromes
    • Genital dermatology
    • Pelvic inflammatory diseases (PID)
    • Vaginal discharge
    • Urethritis – penile
  • Populations
    • ← Back
    • Aboriginal and Torres Strait Islander People
    • Sex workers
    • People in custodial settings
    • Adult sexual assault
    • People who use drugs
    • Regional and remote populations
    • Trans and gender diverse people
    • Women who have sex with women
    • Refugees and migrants to Australia
    • Young people
    • Pregnant people
    • Men who have sex with men
    • People living with HIV
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Self-collection of samples for NAAT testing

Vaginal swab: Instruct the patient to insert the swab into the vagina like a tampon and then remove and place into the correct transport tube for NAAT testing.

Rectal swab: Instruct the patient to insert the swab into the anal canal 2-4cms and then remove and place into the correct transport tube for NAAT testing.

First pass urine (FPU): Collect approximately 20 ml (1/3 of the standard urine jar) of the first part of the urine stream in a specimen jar at the time you are consulting the patient. The patient does not need to have held their urine for more than 20 minutes prior to specimen collection. A midstream urine (MSU) or early morning specimen (i.e. first void urine) are not required for NAAT.

Click here for information on how to describe self-collection technique to a patient.

Clinician collected for NAAT/culture/microscopy

Urethral swabs for microscopy: Collect only if the patient has frank urethral discharge and when the patient has not urinated for at least 1 hour. Squeeze the urethra to express the discharge and collect on urethral swab. It is not necessary to insert the swab into the urethra.

Anorectal swabs: Should be collected by inserting a sterile swab 2-4cm into the anal canal. To reduce patient discomfort, the swab can be moistened prior to insertion, using either saline or tap water. If using a proctoscope, rub the swab on the rectal mucosa.

Pharyngeal swabs: Collect from the tonsils and oropharynx.

High vaginal swab: Smear onto a glass slide, air dried and sent for microscopy. Insert swab into transport medium for culture.