Stay informed with the latest updates on coronavirus (COVID-19). Find out more >>

Sexually transmitted infection STI screening

  • Background

    Common sexually transmitted infections (STI) include gonorrhoea (Neisseria gonorrhoeae), chlamydia (Chlamydia trachomatis), syphilis (Treponema pallidum), Mycoplasma genitalium, and Trichomonas vaginalis. Most of these are easily treatable with antibiotics, but can cause significant morbidity if left untreated, including infertility, miscarriage, ectopic pregnancy, and neonatal/infant infections [1]. Blood borne infections (that are also STIs) include HIV, hepatitis C and hepatitis B.   

    Rates of STI infection vary according to country of origin and are not well quantified. Two recent Australian studies have found very low rates of STIs in newly arrived refugees – a study of 2610 refugees aged 15 years and older in Western Australia found a prevalence of 0.8% for chlamydia and no episodes of gonorrhoea infection [2] and a study of 1136 Karen refugees in Melbourne found a prevalence of 0.3% for chlamydia, and no cases of HIV, gonorrhoea or syphilis infection [3]. Other Australian studies have found the prevalence of syphilis was 0-5% in adult, predominantly African, cohorts[4-7] although there were no paediatric cases in two cohorts.[8, 9] There have been very few people with HIV, although HIV does not necessarily preclude a visa being granted, and changes to the health waiver for humanitarian entrants in 2012 mean there may be increasing numbers of people with HIV arriving. 

    A high proportion of female (and some male) refugees and asylum seekers have experienced sexual violence/assault [1]. A UK study of unaccompanied child refugees found that one quarter of African girls reported having been sexually assaulted or raped [10], and unaccompanied minors are at highest risk of sexual assault [11]. Most asylum seekers and refugees will not have had adequate medical care or testing for sexually transmitted infections (STIs) after the assault. It is important to be aware that adolescents/adults are also at risk of acquiring STIs after arrival in their new country [11].

    Pre-migration STI screening is limited. All permanent migrants to Australia have a visa health assessment before travel – this includes[12]:

    • HIV testing in people ≥15 yrs, unaccompanied humanitarian minors, international adoptees, and if HCV is identified; also in children <15 years where infection is suspected or risk factors are present. 
    • Hepatitis B screening in pregnant women, unaccompanied humanitarian minors, international adoptees, those aged ≥15 years intending to work as a doctor, dentist, nurse or paramedic, and applicants considered high risk by the assessing doctor; those aged ≥15 years applying for an onshore protection visa.
    • Syphilis screening in those ≥15 years applying for offshore or onshore protection visa (previously - refugee entrants from refugee camp-like conditions, or where infection is suspected)

    There is no routine testing for other STIs as part of the pre-migration screen. Asylum seekers in detention aged ≥15 years have screening for HIV, Hepatitis B, HCV and syphilis as part of detention health screening.

    Given limited pre-migration screening and possible exposure, including through sexual violence, STI screening should be considered in the post-arrival refugee health assessment, although universal screening is not supported by current evidence ( 2016 ASID guidelines). Early diagnosis can allow appropriate treatment to prevent long-term complications. People may be reluctant to disclose a history of sexual assault and the issue needs to be addressed specifically in a sensitive manner.


    Many STIs are asymptomatic and will only be picked up on routine screening tests. Common presentation for STIs include:

    • Vaginal discharge - usually due to candidiasis, bacterial vaginosis (BV), or trichomoniasis (note: candidiasis and BV are not classified as STIs), however it may be secondary to cervicitis caused by Neisseria gonorrhoeaeChlamydia trachomatis or Mycoplasma genitalium
    • Skin lesions on the external genitalia - Common pathogens include Pthirus pubis (genital louse), Molluscum contagiosum and human papillomavirus (HPV, causing genital warts)
    • Genital ulcers - pathogens include herpes simplex virus (HSV), primary syphilis (Treponema pallidum) and rarely Haemophilus ducreyi (chancroid) or donovanosis (caused by Klebsiella granulomatosis).


    Initial post arrival refugee health screening includes:

    • Considering STI risk factors
    • STI screen for people (adults, adolescents, children) with risk factors, or on request (self-collected swab or first pass urine nucleic acid amplification (NAAT) test and consideration of throat and rectal swabs for Chlamydia and Gonorrhoea, and serology for HIV, syphilis and hepatitis B)
    • Syphilis serology in unaccompanied or separated children <15 years - see syphilis guideline
    • Hepatitis B and Hepatitis C infection, both of which may be vertically acquired – see  hepatitis B guideline
    • HIV serology in unaccompanied or separated children <15 years. The prevalence of HIV in recently arrived children of a refugee background is very low (<<1%), and universal HIV screening is no longer recommended [13]. HIV testing should always be completed in sexually active adolescents, if there is a history of sexual violence, where parents are deceased/missing/known to be HIV positive, or where there are clinical symptoms/signs.

    If there is a history of sexual activity complete additional testing:

    • (HIV serology, syphilis, hepatitis B as above) 
    • Urine- N. gonorrhoeae and C. trachomatis (by PCR)
    • Pregnancy testing if relevant

    If vaginal discharge is present also test for: 

    • Trichomonas vaginalis
    • Mycoplasma genitalium
    • Bacterial vaginosis
    • Candidiasis

    If ulcers/ skin lesions are present consider taking a swab and testing for: 

    • Syphilis PCR
    • HSV PCR
    • HPV nucleic acid testing (NAT) 

    For information on appropriate specimen collection and treatment, see table 1. 
    Note: In a child/adolescent, particularly one who is not usually sexually active, it is usually appropriate to test for STIs using urine rather than high vaginal swab. 

    If a remote history of sexual violence against a child is disclosed, consider referral to a service experienced in managing child sexual abuse [1] (e.g. Gatehouse centre at RCH). If there is recent sexual assault follow usual procedures via  Victorian Forensic Paediatric Medical Service (VFPMS). 

    Table 1: Common STIs - appropriate specimens for initial testing and first line therapy 


    Appropriate specimen

    1st line therapy (adult doses)

    Neisseria gonorrheae

    High vaginal swab for culture and PCR or Urine for PCR

    Ceftriaxone 500mg IM AND Azithromycin 1g orally

    Chlamydia trachomatis

    Urine for PCR

    Azithromycin 1g orally

    Syphilis (T. pallidum)

    Serology (usually EIA, with confirmatory testing as required), Swab of primary chancre for PCR if indicated

    See Syphilis guideline

    Mycoplasma genitalium

    High vaginal swab or Urine for PCR

    Azithromycin 1g orally

    Trichomonas vaginalis

    High vaginal swab PCR

    Metronidazole 2g orally

    Blood-borne viruses


    Serology (HIV Ab) with confirmatory testing

    Seek expert advice

    Hepatitis B

    Serology (HepB sAg, cAb, sAb)

    Seek expert advice

    Hepatitis C

    Serology (Hep C Ab)

    Seek expert advice



      Immigrant health resources. Authors: Vanessa Clifford and Georgie Paxton, January 2014. Last review May 2017. Contact