Sexually transmissible infections (STIs)

Aesen Thambiran, Mitchell Smith, Vanessa Clifford
(For other STIs – HIV, HBV, HCV).


  • A sexual health history should be completed sensitively, with awareness of gender issues, and with reassurance and careful explanations.
  • Offer an STI screen to people with a risk factor for acquiring an STI or on request (see text). Universal post-arrival screening for STIs for people from refugee-like backgrounds is not supported by current available evidence.
    • Syphilis serology should be offered to unaccompanied and separated children <15 years.
    • Children <15 years should be offered screening for other STIs including HIV and syphilis if there are clinical concerns (see text for details).
  • A complete STI screen includes a self-collected swab or first pass urine Nucleic Acid Amplification Test (NAAT) and consideration of throat and rectal swabs for chlamydia and gonorrhoea, and serology for syphilis, HIV and hepatitis B.
  • Asymptomatic patients with positive syphilis serology should be treated, unless there is documented prior treatment of treponemal infection. Treat syphilis with parenteral penicillin in consultation with a sexual health or ID unit.
  • Specimens for Neisseria gonorrhoea microscopy and culture should be taken before treatment is instituted. Treat gonorrhoea with ceftriaxone 500mg in 2mL of 1% lignocaine IMI, plus azithromycin 1g orally.76 Repeat NAAT and culture for test of cure of gonorrhoea two weeks after treatment.
  • Treat chlamydia with azithromycin 1g orally as a single dose, or, alternatively, doxycycline 100mg orally 12 hourly for 7 days.76
  • Treat anorectal chlamydia with doxycycline 100mg orally 12 hourly for 7 days or azithromycin 1g orally as a single dose with a repeat dose a week later.205
  • Offer women a pregnancy test and contraception, as appropriate (see Women’s Health).
  • An STI screen provides an opportunity for education about safer sex and condom use.
* Chlamydia testing is consistent with the current National STI Strategy206 and Australasian Sexual Health Alliance (ASHA) guidelines.205

The potential health impacts of STIs include multi-organ damage and congenital effects from syphilis, while chlamydia and gonorrhoea can cause infertility and a risk of ectopic pregnancy. Maternal gonorrhoea and chlamydia can lead to severe neonatal conjunctivitis. There are personal health and public health reasons to detect these infections in individuals regardless of background and to limit their transmission in the community.

Gender-based violence is common in women and girls in conflict zones and refugee camps,207,208 although men may also experience sexual violence, and also face barriers to disclosing this information. Once settled in Australia women may be at increased risk of sexual violence22 and sexual assaults have been reported in both onshore and offshore immigration detention centres.209,210

People may not be aware of STIs or their partners’ STI status or may be unable to negotiate a monogamous relationship with their partner and may be unaware of their risk of acquiring STIs. This can occur in any relationship, including new or longstanding relationships, where people have returned from overseas having married a new partner, and in adolescents. It is important to be aware of situations that may have led to an STI acquisition, such as sexual assault, and that these circumstances may not be disclosed. In addition, due to limited access to health education, both adolescents and adults may have poor understanding of sexual health and limited knowledge of contraception or safe sex practices.

The previous ASID guidelines recommended universal screening in adults for chlamydia and gonorrhoea;14 however, since this time, there have been more published data on STI prevalence in resettled refugee populations. Despite the apparent risks, there is a low reported prevalence of chlamydia (0.8-2.0%)43,48,159,211 and gonorrhoea (0%)43,48,159,211 infections in newly arrived refugees settling in Australia and in other developed countries.48,159,211–214 Therefore, the current available evidence does not support universal screening of newly arrived people from refugee-like backgrounds for chlamydia and gonorrhoea, and favours a risk-based approach to screening.a

Syphilis infection has a higher incidence in many parts of Africa and Asia and has been diagnosed in refugees settling in Australia (prevalence 1.5-8%).41,108 Until 2014, only a proportion of refugee applicants had syphilis screening overseas as part of their visa medical examination, which was recommended for those living in ‘camp-like conditions.’17 Routine syphilis screening is now part of the Australian immigration medical examination for humanitarian entrants aged 15 years and over.18 Additionally, asylum seekers aged 15 years and older are screened and treated for syphilis in immigration detention facilities after arrival.

a. Some members of the EAG recommended offering universal STI screening in adolescents and adult because of the sensitivities of obtaining a sexual history in people from refugee-like backgrounds, particularly at an initial visit, and the difficulties in ensuring that previous syphilis has been adequately screened and treated. However, given available prevalence data, the panel did not consider that this was indicated. Furthermore, STI testing should be performed with informed consent, and hence universal screening does not obviate the need to discuss STI risks with the patient.

History and Examination

Discussion of sexual health and STIs can be challenging where there is low English proficiency and low health literacy. Furthermore in some cultures, open discussions about sexuality and sexual health are discouraged and there are demarcations between men’s and women’s issues. Individuals may feel deeply embarrassed to discuss sexual health with a health practitioner. Feelings of shame, guilt and fear may decrease the likelihood of patients asking for STI testing. People who identify as lesbian, gay, bisexual, transgender or intersex (LGBTI) may be reluctant to disclose/discuss this with health providers, especially if they experienced persecution in their country of origin.

Questions about sexual health should be asked sensitively, and reassuring the patient that health professionals understand these questions may be culturally unfamiliar can be helpful. It is important to explain need for screening, obtain informed consent, clarify that results will have no impact on residency status, and that confidential treatment, care and counselling is available if needed.215 Recognise the potential sensitivities around gender differences between doctor and patient – the best advice is to ask the patient about what is acceptable to them. Pelvic examination in women should be undertaken only if clinically necessary, ensuring that the woman feels comfortable with the provider and that time has been taken to build rapport and trust. Offer a chaperone and to also consider the gender of the interpreter whether onsite or via telephone.

STIs are often asymptomatic. Women may have local symptoms such as dysuria, urethritis, vaginal discharge, pelvic pain, dyspareunia, inter-menstrual or post-coital bleeding, or they may present with sequelae such as complaints of infertility. Men may have dysuria, urethral discharge or testicular pain. Anorectal symptoms include discharge, irritation, painful defecation and disturbed bowel function. Gonorrhoea or chlamydia can also present with purulent conjunctivitis.

Syphilis is usually asymptomatic; however, symptoms can range from the chancre of primary infection, to the generalised rash of secondary syphilis, to signs of tertiary disease such as aortic pathology and neurological manifestations.

Taking a sexual history from a person from a refugee-like background is an opportunity to build trust and create a safe environment in which the person may disclose an experience of sexual violence. However, most patients will not volunteer violence, in particular if family members or friends are accompanying clients. The patient needs not only to feel assured that what will be shared will remain confidential, but also that in risking the discussion about violence, there will be resources and opportunities to obtain help for this. Interpreter confidentiality and privacy is a further issue to consider, and offering a telephone interpreter is useful to preserve anonymity.

There may be cultural pressures affecting disclosure of family violence, and additional vulnerabilities related to migration status. Asylum seekers on bridging visas and those in community detention sign a code of conduct, potentially acting as a powerful negative disincentive to disclose family violence. Consider intimate partner violence in all relationships, including for those who identify as LGBTI.


People from refugee-like backgrounds should be offered individualised STI screening which takes into account past screening and risk assessment.

Offer STI testing to:205,206

  • Anyone with symptoms or a recent history of STI symptoms.
  • Individuals who have had more than one recent partner or who have recently changed partners (this may not always be volunteered).
  • Pregnant women.
  • People living with HIV.
  • People who inject drugs.
  • Sex workers, and people who are clients of sex workers.
  • Men who have sex with men (MSM) and those who identify as LGBTI.
  • Adults and adolescents with a history of being incarcerated, including in immigration detention centres.
  • Anyone who is interested in, or who would like an STI screen.
  • Woman who present opportunistically for a well women’s check or PAP smear.
  • Anyone disclosing a history of sexual assault or gender-based violence.

In addition any sexually active person aged 15–29 years should be offered chlamydia screening in accordance with the National STI Strategy.206

The most significant risk factor for HIV and syphilis infection in minors is maternal infection. Therefore unaccompanied or separated children should be tested for HIV and syphilis.

Tests to offer in an STI screen:

  • First pass urine for Chlamydia trachomatis and Neisseria gonorrhoea nucleic acid amplification test (NAAT). This is non-invasive and highly sensitive.
  • Self-obtained Lower Vaginal Swabs (SOLVS) is the optimal sampling method in women for Chlamydia trachomatis and Neisseria gonorrhoea. While it should be offered, this method may not be culturally acceptable to women from refugee-like backgrounds and first void urine should be offered if patient declines SOLVS. See link below for instructions on how client can self-obtain samples.205
  • Rectal and throat swab for NAAT if at risk of infection at those sites. Offer test to all MSM, following sexual assault (at those sites) or to anyone with symptoms suggestive of infection. Gonococcal throat infections can occur in the setting of unprotected oral sex and patients may be unaware of this risk.
  • Swab for microscopy, culture and sensitivity for Neisseria gonorrhoea from any site with pus.
  • Syphilis serology

Consider offering tests for other sexually transmissible infections including: hepatitis B, HIV, hepatitis C.

Management and Referral


Venereal syphilis, when found through screening of asymptomatic recent arrivals, is usually late latent disease of low infectivity. Ask if there is a history of previous treatment with parenteral penicillin.

Interpretation of serological tests for treponemal infection can be quite complex. Seek advice from a sexual health or ID physician whenever there is any concern or doubt. Infection with various subspecies of Treponema can also cause yaws, bejel or pinta. As it is rarely possible to determine with certainty which type of treponemal infection has resulted in positive serology in an asymptomatic patient, such patients should always be treated, unless there is documented prior treatment of treponemal infection. Treatment is with parenteral penicillin (pregnancy category A) and is usually best done in the context of a specialised sexual health or ID unit. The sexual health service will monitor treatment response with the RPR serological test at 3, 6 and (if necessary) at 12 months.205 Note that the specific treponemal tests (e.g. TPHA) tend to remain positive lifelong, even after successful treatment.


Wherever possible, patients with a positive NAAT test for N. gonorrhoea should have microscopy and culture of genital (cervical, vaginal, urethral) and/or throat swabs if discharge is present, and/or first pass urine, before treatment is instituted.

Treatment is generally with ceftriaxone 500mg in 2mL of 1% lignocaine IMI, plus azithromycin 1g orally as a single dose.76,205 For pharyngeal, anal or cervical infection, test of cure (NAAT) should be performed two weeks after treatment is completed.205 Microscopy and culture should also be repeated to assess for antibiotic resistance. These samples can be collected at the time of NAAT test of cure sample collection to save the patient having to return again.


Current treatment is with azithromycin 1g orally as a single dose, or doxycycline 100mg orally 12 hourly for 7 days.76,205 Treat anorectal chlamydia with doxycycline 100mg orally 12 hourly for 7 days or azithromycin 1g orally as a single dose with a repeat dose a week later.205

Test of cure is not routinely recommended, except for pregnant women or those with rectal chlamydia. In these situations, NAAT should be done at least four weeks after treatment.205

Other STIs

Detailed guidance on the conditions above and on other STIs is available from the Australasian STI Management Guidelines for Use in Primary Care205 and the Australian Therapeutic Guidelines.76 Advice can also be sought from a sexual health service or physician.

Contact tracing of sexual partners (and children in the case of syphilis), where relevant and appropriate, should be discussed with the patient and attempted by the treating clinician. Seek specialist advice if unsure or in complex cases e.g. new HIV diagnosis. The Australasian Contact Tracing Manual 216 offers comprehensive assistance. If working with a telephone interpreter, offer to keep your patient’s name confidential.

HIV testing should be performed in all people diagnosed with an STI (see HIV).

Regular review during therapy provides an opportunity to confirm adherence with treatment, to review contact history and to give further sexual health education. If indicated, further testing may need to be undertaken for HIV after the three-month window period (see HIV) and for other STIs at the three-month visit if not undertaken at first presentation.

Consider offering immunisation for human papilloma virus for women, girls and boys in appropriate age or risk groups (see immunisation).

Consider offering cervical cancer screening, pregnancy testing and assess for contraceptive needs (see Women’s Health).

Consider referral for follow up of trauma associated with a history of sexual assault or gender- based violence.

An STI screen provides an opportunity for education about safer sex and condom use. It is important to inform individuals that an STI screen is not comprehensive, infections such as herpes simplex and HPV are not routinely screened for and thus the need for barrier contraception should be emphasised to minimise future risk.

Gonorrhoea, chlamydia and syphilis are notifiable diseases.

Considerations in Pregnancy and Breastfeeding

Doxycycline (Pregnancy category D) should not be used in pregnancy or during breastfeeding. Azithromycin (Pregnancy category B1) can be used for treatment of chlamydia and gonorrhoea.

Syphilis detected during antenatal screening should always be managed by a specialist; treatment is with penicillin (Pregnancy category A). Infants should be referred to a paediatrician for testing and follow-up.

Considerations for Children and Adolescents

Although children and adolescents from refugee-like backgrounds are at risk of having experienced sexual abuse and/or assault, families rarely volunteer this information. However, if such information is disclosed, or if an STI is suspected for other reasons, e.g. vaginal discharge, genital ulcers or undiagnosed chronic lower abdominal pain, seek advice from a service experienced in managing child sexual abuse, and consider mandatory reporting obligations. Other non-STI causes of genital symptoms in girls need to be considered, including pinworm infection and, occasionally, female genital mutilation/cutting (FGM/C, see Women’s health).

Unlike adults, children under 15 years are not routinely tested for HIV as part of the pre-migration or detention screen unless they are unaccompanied or separated minors; and they are not tested for syphilis.

Adolescent sexual health is frequently missed, but should be included in a post-arrival assessment. Adolescents should be seen alone for part of the consultation once rapport is established. Explaining this is routine in the Australian healthcare system and seeking permission from both the adolescent and their parent/carers is helpful in facilitating this process. Adolescent sexual health is often approached using the HEADDS framework;217 and adolescents frequently value the opportunity to ask questions of health providers.218 This form of consultation is also an opportunity for health promotion and to improve sexual health literacy.

Most adolescents can be treated for common STIs using standard adult doses. Seek specialist advice (including for assessment of child protection issues for younger children). Child and adolescent refugees who have a positive treponemal serology result should be discussed with or referred to a paediatric ID physician. If the patient is a child and the biological mother’s treponemal test is negative, congenital syphilis can usually be excluded.

Doxycycline should not be used in children less than 8 years of age. Seek specialist advice.

Produced by

in consultation with

                  Refugee Health Network of Australia

Endorsed by

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The Australian Refugee Health Practice Guide was produced with funds from the Australian Government Department of Health.


The information set out in the Australian Refugee Health Practice Guide (“the Guide”) is current at the date of first publication and is intended for use as a guide of a general nature only and may or may not be relevant to particular patients or circumstances. Nor is the Guide exhaustive of the subject matter. Persons implementing any recommendations contained in the Guide must exercise their own independent skill or judgement or seek appropriate professional advice relevant to their own particular circumstances when so doing. The statements or opinions that are expressed in the Guide reflect the views of the contributing authors and do not necessarily represent the views of the editors or Foundation House. Compliance with any recommendations cannot of itself guarantee discharge of the duty of care owed to patients and others coming into contact with the health professional and the premises from which the health professional operates.

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