Patient presentation and specimen collection

Asymptomatic females

The following investigations should be undertaken:

  • physical examination is important as often patients may not be aware of lesions or other clinical signs. 
  • endocervical swabs for NAAT (no transport medium) for those examined
  • endocervical swabs for MC&S (glass slide and swab in charcoal [black] or non-charcoal [clear] agar gel transport medium), if pus is present or cervix is inflamed
  • HVS for MC&S (glass slide and swab in charcoal [black] or non-charcoal [clear] agar gel transport medium) if vaginal discharge appears normal or vaginal walls are inflamed
  • a self-obtained low vaginal swab (SOLVS) for NAAT (no transport medium) is the preferred specimen in an asymptomatic female who declines to have a physical examination. Add first void urine (FVU) for NAAT if possible
  • FVU for NAAT only, is acceptable if a woman declines to give either vaginal or endocervical swabs
  • If GeneXpert point-of-care test is available, test specimen/s with point-of-care test. If patient has no discharge from the cervix and the cervix is not inflamed, collect an additional swab and urine sample for sending to the laboratory for NAAT testing. If patient has discharge from the cervix and/or the cervix is inflamed, collect two endocervical swabs for sending to the laboratory for antibiotic susceptibility testing; one for microscopy, culture and sensitivity (MC&S) and another for NAAT testing.
Essential tests

As a general rule, patients who are suspected of having an STI should be offered testing for:

  • chlamydia
  • gonorrhoea
  • syphilis
  • hepatitis B
  • HIV.

If an ulcer is present take a NAAT swab from the ulcer and request a genital ulcer multiplex test for herpes, syphilis and donovanosis. 

Test for hepatitis A if symptomatic or if there is a history of male-to-male and/or oro-anal sex and vaccination is contemplated if negative.

Test for hepatitis C if there is a history of injecting drug use or other high risk factors based on an individual client's risk assessment.

HIV testing should also be considered in the presence of:

  • possible seroconversion illness (fever, myalgia, rash)

        or

  • atypical or severe prolonged infections without other apparent cause (e.g. oral candidiasis, oral hairy leukoplakia, severe persistent genital herpes, persistent lymphadenopathy, persistent gastro-intestinal symptoms with significant weight loss).

Consider testing for other non-notifiable diseases, e.g. genital herpes, trichomoniasis, if clinically indicated based on history and/or examination findings. 

Access the national HIV, HCV and HBV testing policies from the Australian Society for HIV Medicine (ASHM) testing portal (external site) or download the latest HIV testing policy (external site).

Specimen collection and handling checklist

All specimens

  • Specimens must be clearly labelled with the patient's name, date of birth, or medical record number, site of collection, date and time of collection.
  • Specimens should reach the laboratory within 24 hours, whenever possible. Gonorrhoea culture yield will diminish after this time.
  • If necessary, tests may be coded so that the person being tested is not personally identified. This is rarely necessary.

Urine samples

  • Keep urine samples for NAAT refrigerated. Transport as soon as possible.
  • For patient instructions for taking a self-obtained urine sample, please see the STI self testing card (PDF 346KB).

Self-obtained vaginal swabs

  • Self-obtained vaginal swabs enable specimen collection from the genital tract of asymptomatic women for chlamydia and gonorrhoea tests when a vaginal examination is declined and if they cannot provide a urine specimen.
  • A physical examination, including a vaginal speculum examination is recommended for all women with genital or STI symptoms.
  • For patient instructions for taking a self-obtained low vaginal swab (SOLVS), please see the STI self testing card (PDF 346KB).

Self-obtained anal swabs

Gonorrhoea culture swabs

  • Make a smear on a glass slide and place the swab in charcoal (black) or non-charcoal (clear) agar gel transport medium.
  • Smears and swabs will have a diminished yield if processed more than 24 hours after collection. NAAT at the same time will improve detection of gonorrhoea.
  • Keep specimens in an insulated container between 10 °C and 25 °C.
  • Avoid extremes of temperature. Never place gonorrhoea swabs for culture in the refrigerator.
  • All smears should be allowed to air dry before sealing and labelling.

Chlamydia and gonorrhoea NAAT specimens

  • Keep as close as possible to 4 °C during storage and transport. Avoid extremes of temperature. Do not place samples in the freezer section of the refrigerator and avoid direct contact with freezer blocks during transport.
Specimen collection men
Discharge present: Milk discharge forward to collect specimens for antimicrobial sensitivity testing using swab with charcoal (black) or non-charcoal (clear) agar gel transport medium and glass slide; and collect 20 mL of first void urine (FVU) for chlamydia and gonorrhoea NAAT. If GeneXpert point-of-care test is available, test specimen/s with point-of-care test and collect additional swabs and urine samples for sending to the laboratory for antibiotic susceptibility testing; one for microscopy, culture and sensitivity (MC&S) and another for NAAT testing.

No discharge: Collect 20 mL of FVU for chlamydia and gonorrhoea NAAT (if no urine available, provide the patient with a specimen jar and ask him to wait until he can void or return an FVU at his earliest convenience). A urethral NAAT swab could be used if the patient prefers not to wait. If GeneXpert point-of-care test is available, test specimen/s with point-of-care test and collect an additional swab and urine sample for sending to the laboratory for NAAT testing.

Step 1

Anal and throat swabs

History or receptive anal sex, oro-anal sex, rimming or fingering and no anal symptoms: Patients can be instructed how to take blind anal swabs themselves for NAAT (no transport medium). Please refer to the STI self testing card (PDF 346KB).

History of receptive anal sex, anal-oral sex or fingering, and anal symptoms present: A proctoscope needs to be inserted if possible and the swabs obtained under direct vision. If the patient declines or proctoscope not available, patients can be instructed how to take blind anal swabs themselves.

Also collect two throat swabs (one for culture and sensitivity [charcoal or non-charcoal agar gel transport medium], and one for NAAT [no transport medium]) if there is a history of receptive oral sex. No slide is necessary for microscopy. 

Step 2

Collect blood for serological tests: syphilis, HIV and hepatitis B. Also test for hepatitis A if symptomatic or if there is a history of male to male and/or oro-anal sex and there is an intention to vaccinate if negative; and hepatitis C if there is a history of injecting drug use.

Step 3

Order the tests for the laboratory: label all specimens clearly and prepare for transport.

Step 4

Consider treatment: if there is any doubt about follow-up, start treatment based upon clinical diagnosis.
Vaginal pH testing

Vaginal pH testing should be carried out as part of a full examination using narrow range pH paper (range pH 4 – 6).

Performing the test

The test should be performed on vaginal secretions, which are taken from near the opening of the vagina. Secretions taken higher up may be contaminated by cervical secretion, which has a higher pH and will give a falsely elevated vaginal pH reading. The test should not be performed if the patient is menstruating or has had unprotected sex in the last 24 hours or is pre-pubertal or post-menopausal.

Either:

  • use a loop or swab, and press some vaginal secretion on to the paper allowing the moisture to adsorb onto the pH paper

        or

  • press some pH paper on to the walls of the vagina

        or

  • hold the pH paper at the opening of the vagina and press the moist lips of the vulva onto the paper (no speculum is needed for this latter method).

Wait 30 seconds and then compare the colour change on the paper with the colour range given on the pH paper container. Holding the paper with a bright light behind it assists with interpretation of the colour change.

Interpreting the test

A vaginal pH reading of >4.5 is abnormal unless the woman is post-menopausal and not on hormone replacement therapy.

Elevated readings are found in the following circumstances:

  • bacterial vaginosis
  • trichomoniasis
  • desquamative inflammatory vaginitis
  • post-menopausal not on hormone replacement therapy.

False high readings are found in the following situations:

  • cervical secretion is sampled instead of vaginal secretion
  • sexual intercourse in the last 24 hours
  • examining glove touches the paper
  • patient menstruating.

Elevated vaginal pH and HIV

  • Low vaginal pH is hostile for HIV and infected lymphocytes.
  • High pH (>5) may contribute to increased susceptibility to HIV.
GeneXpert point of care NAAT for chlamydia and gonorrhoea
The GeneXpert point-of-care test can be performed on urine, vaginal or cervical swabs (clinician or self-collected). Please see the GeneXpert point-of-care manuals/posters for specimen collection guidelines.
Essential communication

Mutual trust and respect, counselling and patient education are essential parts of STI management.

On presentation

Ask: am I the right person to examine this patient? If not, find an alternative service provider.

Otherwise:

  • take a medical/sexual/drug history
  • explain confidentiality of patient records
  • explain the examination and specimen collection you are about to do
  • obtain consent for all investigations.

Counselling with examination

  • Talk about prevention and safe sex practices.
  • Talk about what a positive test result would mean.
  • Explain the notification requirements for STIs, emphasising their importance to public health, and reassuring the patient that their privacy will be respected.

Interpreting the test result

  • Test results are usually reported as either positive or negative.
  • If you are unclear about the significance of a test result, discuss it and your patient's history and clinical findings with a clinical microbiologist at the laboratory.
  • Remember the test results do not have perfect sensitivity or specificity.
  • Use your clinical judgement to treat the patient – not just laboratory results.

On confirming an STI diagnosis

  • Explain the diagnosis.
  • Explain the treatment.
  • Emphasise the need for sexual abstinence during treatment.
  • Emphasise the importance of returning for follow-up.

Contract tracing

  • Inform the patient of the importance of contact tracing.
  • Explain that their identity will not be disclosed.
  • Discuss possible contacts over the past three months.
  • Consider who is the appropriate person to follow up contacts.
  • Obtain permission to follow up contacts.

For more information about contact tracing, see Contract tracing (managing sex partners)

Follow-up

Repeat messages about prevention and safe sex.

Nucleic acid amplification tests

Tests that detect specific sequences of deoxyribonucleic acid (DNA) are now available to detect gonorrhoea, chlamydia and to a limited extent, other STIs.

These tests are nucleic acid amplification tests (NAAT), a generic term which includes polymerase chain reaction (PCR). The choice of test depends on the laboratory.

The NAAT process identifies DNA sequences found only in the organism being tested, making it a highly specific test. NAAT also amplifies very low amounts of DNA so that they are easily detected, making the technique highly sensitive. These two properties of the test make it much more accurate than the older technique of microscopy and culture. NAAT can identify chlamydia and gonorrhoea in a urine sample. As NAAT does not rely on live organisms it will also detect the DNA from dead organisms. Recently, studies have suggested that, in a woman, the sensitivity of NAAT testing in self-obtained vaginal swabs is better than that of urine, particularly for the detection of gonorrhoea. As a general rule in these guidelines we recommend the use of a self-obtained low vaginal swab (SOLVS) as the primary single specimen collection method of choice for women.

NAAT point-of-care testing using the GeneXpert test is available at health services in WA that have been selected to participate in a research project funded by the National Health and Medical Council Research Council.

Gonorrhoea culture is still required where there is urethral or cervical discharge. Current methods with NAAT do not allow antibiotic susceptibility testing and therefore, it is still important that, when patients present with a discharge, swabs are sent for culture.

NAAT may also be used to detect other STI pathogens, including herpes simplex virus (HSV), mycoplasma, ureaplasma, donovanosis, trichomoniasis and chancroid. Providers should discuss the appropriate testing options with their local laboratory service.

Sample test pack for diagnostic testing

A ready-to-use test pack will simplify STI consultations and save time. Note: additional swabs may be required should you need to do throat or rectal tests.

Such kits can be provided by the laboratory that supplies testing services. The composition of the pack will depend on the range of tests that the referral laboratory can conduct.

Male kit

A. Swab with charcoal (black) or non charcoal (clear) agar gel transport medium for collecting urethral discharge (if present) and making a smear and sending for culture (charcoal transport media is preferred if longer delays are anticipated).
B. Glass slide in slide holder for making a smear of urethral discharge.
C. Urine container for first void urine for chlamydia and gonorrhoea NAAT (shaded area equals 20 mL).
D. Clotted blood tube for serological tests.
E. Wire/plastic shaft fine swab for urethral swab (if required) for chlamydia and gonorrhoea NAAT (no transport medium)
F. Wire/plastic shaft fine swab for genital ulcer multiplex NAAT (no transport medium).

Sample male test kit                                     

                                                           Note: colours of tubes and lids may vary

Female kit

A. Swab with charcoal (black) or non charcoal (clear) agar gel transport medium for collecting a high vaginal specimen for a smear and culture.
B. Glass slide in a slide holder for making a smear of the high vaginal specimen.
C. Swab with charcoal or non-charcoal agar gel transport medium for collecting cervical discharge (if present) and making a smear to send for culture.
D. Glass slide in slide holder for making an endocervical swab (ECS) smear.
E. Wire/plastic shaft fine swab for collection of an ECS sample for chlamydia and gonorrhoea NAAT (no transport medium)
F. Urine container for first void urine for chlamydia and gonorrhoea NAAT (shaded area equals 20 mL).
G. Clotted blood tube for serological tests.
H. Wire/plastic shaft fine swab for collection for genital ulcer multiplex NAAT (no transport medium).

Sample female test kit

                                                                   Note: colours of tubes and lids may vary


Sample protocol for chlamydia and gonorrhoea diagnosis

For men

When a urethral discharge is present

  • Milk discharge forward.
  • To make a smear, pick up discharge on a standard plastic-shafted dacron or nylon swab and roll it onto a glass slide. Allow to air dry and label. This should be placed in a slide holder and the slide holder labelled with the patient's name and date of birth or medical record number, and the site, date and time of collection.
  • The swab is then placed in charcoal (black) or non-charcoal (clear) agar gel transport medium. The swab should be labelled with the patient's name and date of birth or medical record number, and the site, date and time of collection. This can remain at room temperature.
  • Ask the patient to pass 20 mL of first void urine (FVU) into a yellow-topped urine container labelled with the patient's name and date of birth or medical record number, and the site, date and time of collection. Store and keep cool during transport, preferably at about 4 ° C.

If GeneXpert point-of-care test is available, test specimen/s with point-of-care test and collect additional swabs and urine samples for sending to the laboratory for antibiotic susceptibility testing; one for microscopy, culture and sensitivity (MC&S) and another for NAAT testing.

No discharge present

  • Ask the patient to pass 20 mL of FVU into a yellow-topped urine container labelled with the patient's name and date of birth or medical record number, and the site, date and time of collection. Store and keep cool during transport, preferably at about 4 °C.
  • If the patient is unable to pass urine, get him to wait until he can void. A urethral swab could be used if the patient prefers not to wait.
  • If GeneXpert point-of-care test is available, test specimen/s with point-of-care test and collect an additional swab and urine sample for sending to the laboratory for NAAT testing.

For women

  • Pass a speculum.
  • Take a high vaginal swab and smear to exclude other pathogens.
  • Take vaginal pH.
  • Take a HPV test first if indicated.
  • Clean mucus off the cervix.
  • Collect an endocervical swab for NAAT and place it back into the container provided. No transport medium is required. The swab should be labelled with the patient's name and date of birth or medical record number, and the site, date and time of collection.
    • The NAAT swab can be stored at either room temperature or in the fridge but the culture should not be refrigerated.
  • If pus is present or the cervix is inflamed, also collect an endocervical swab for microscopy, culture and sensitivity testing (MC&S) using glass slide and swab in charcoal (black) or non-charcoal (clear) agar gel transport medium.
  • Ask the patient to pass 20 mL of FVU into a yellow-topped urine container labelled with the patient's name and date of birth or medical record number, and the site, date and time of collection. Store and keep cool during transport, preferably at about 4 °C.
  • If GeneXpert point-of-care test is available, test specimen/s with point-of-care test. If patient has no discharge from the cervix and the cervix is not inflamed, collect an additional swab and urine sample for sending to the laboratory for NAAT testing. If patient has discharge from the cervix and/or the cervix is inflamed, collect two endocervical swabs for sending to the laboratory for antibiotic susceptibility testing; one for microscopy, culture and sensitivity (MC&S) and another for NAAT testing.
Specimen collection in women who are examined

Symptomatic

Step 1

Urine available: Collect 20 mL first void urine for chlamydia and gonorrhoea NAAT (collect after swabs).

Step 2

Measure vaginal pH. Pass speculum and visualise cervix. Collect high vaginal swab for MC&S using swab, glass slide and charcoal (black) or non-charcoal (clear) agar gel transport medium.

Step 3

HPV test required:
  • collect specimen from cervix for HPV test.

Pap smear not required:

  • collect endocervical smear for NAAT, using swab (no transport medium).

Step 4

If pus present or cervix is inflamed:
  • collect endocervical smear for MC&S using swab, glass slide and charcoal (black) or non-charcoal (clear) agar gel transport medium.
  • if GeneXpert point-of-care test is available, test specimen/s with point-of-care test and collect two endocervical swabs for sending to the laboratory for antibiotic susceptibility testing; one for microscopy, culture and sensitivity (MC&S) and another for NAAT testing.

Step 5

Collect blood for serological tests: syphilis, HIV and hepatitis B. Also test for hepatitis A if symptomatic or if there is a history of oro-anal sex and there is an intention to vaccinate if negative; and hepatitis C if there is a history of injecting drug use.

Step 6

History of receptive anal intercourse and no anal symptoms: Take blind anal swab for NAAT (no transport medium). 

History of receptive anal intercourse and anal symptoms present: A proctoscope needs to be inserted if possible and swabs obtained under direct vision. If the patient declines or proctoscope not available, patients can be instructed on how to take blind anal swabs themselves. Also collect two throat swabs (one for culture and sensitivity [charcoal or non-charcoal agar gel transport medium], and one for NAAT [no transport medium]) if there is a history of receptive oral sex. No slide is necessary for microscopy. 

Step 7

Order the tests for the laboratory: label all specimens clearly and prepare for transport.

Step 8

Consider treatment: if there is any doubt about follow-up, start treatment based upon clinical diagnosis.

Asymptomatic

Step 1

Urine available: Collect 20 mL first void urine for chlamydia and gonorrhoea NAAT (collect after swabs).

Step 2

Measure vaginal pH. Pass speculum and visualise cervix. Collect high vaginal swab for MC&S using swab, glass slide and charcoal (black) or non-charcoal (clear) transport medium. This should only be done if symptomatic and/or abnormal vaginal discharge is present - not usually done as part of opportunistic testing of asymptomatic patients.

Step 3

HPV test required:
  • collect specimen from cervix for HPV test. 

Pap smear not required:

  • collect endocervical smear for NAAT, using swab.

Step 4

If pus present or cervix is inflamed:
  • collect endocervical smear for MC&S using swab, glass slide and charcoal medium.
  • if GeneXpert point-of-care test is available, test specimen/s with point-of-care test and collect two endocervical swabs for sending to the laboratory for antibiotic susceptibility testing; one for microscopy, culture and sensitivity (MC&S) and another for NAAT testing.

Step 5

Collect blood for serological tests: syphilis, HIV and hepatitis B. Also test for hepatitis A if symptomatic or if there is a history of oro-anal sex and there is an intention to vaccinate if negative; and hepatitis C if there is a history of injecting drug use.

Step 6

History of receptive anal intercourse and no anal symptoms: Take blind anal swab for NAAT (no transport medium). 

History of receptive anal intercourse and anal symptoms present: A proctoscope needs to be inserted if possible and swabs obtained under direct vision. If the patient declines or proctoscope not available, patients can be instructed on how to take blind anal swabs themselves. Also collect two throat swabs (one for culture and sensitivity [charcoal or non-charcoal agar gel transport medium], and one for NAAT [no transport medium]) if there is a history of receptive oral sex. No slide is necessary for microscopy. 

Step 7

Order the tests for the laboratory: label all specimens clearly and prepare for transport.

Step 8

Consider treatment: if there is any doubt about follow-up, start treatment based upon clinical diagnosis.