STI screening and management: the AU general practice guide

Sexually transmitted infections are common, often asymptomatic, and disproportionately affect younger Australians and specific communities. Chlamydia is the most notified infectious disease in Australia — around 100,000 cases per year — and most are detected opportunistically in general practice because infection is asymptomatic in up to 70% of women and 50% of men. Syphilis notifications are rising sharply, with congenital cases appearing for the first time in decades. Gonorrhoea is rising with antimicrobial resistance emerging. The GP’s role is central: opportunistic screening, targeted risk-based testing, treatment, partner notification, and prevention counselling all sit in general practice.

The clinical framework is the Australian STI Management Guidelines (ASHM) and eTG Antibiotic: Genital infections. These are updated annually and are the authoritative references for pathogen-specific treatment.

A. Core clinical — the AU general practice framework

Taking the sexual history

The 5 Ps framework — Partners, Practices, Protection, Past STI history, Pregnancy intentions — provides a structured, non-judgemental approach to sexual history:

• Partners — number of partners in the past three to six months; gender of partners; whether partners have had STI testing
• Practices — penetrative vaginal, anal (insertive/receptive), oral (giving/receiving); use of toys; chemsex context (drug use during sex, elevated risk)
• Protection — condom use: always, sometimes, never; PrEP use (see HIV below)
• Past STI — prior STIs are the single strongest predictor of current infection; prior gonorrhoea suggests ongoing risk
• Pregnancy — current plans, contraception, last menstrual period if relevant

Additional relevant history: vaccination status (HPV, hepatitis B, mpox), migration or travel (tropical STIs, areas of endemic syphilis), sexual assault history, ATSI or refugee status (higher STI burden in some communities), and mental health.

Who to screen and how

Sexually active people under 30: annual chlamydia and gonorrhoea by PCR — first-pass urine for men, self-collected vulvovaginal swab for women. These can be patient-collected in the clinic or at home, increasing acceptance and convenience.

Men who have sex with men (MSM) and women who have sex with women (WSW): multi-site sampling is essential — genital only misses extragenital infection in around 70% of MSM. Throat and anal swabs must be collected alongside genital samples. Comprehensive screen (HIV, syphilis, hepatitis B/C, chlamydia/gonorrhoea all sites) every three months for higher-risk MSM; annually as minimum.

Pre-PrEP baseline and ongoing PrEP monitoring: HIV antigen/antibody, renal function, hepatitis B/C, comprehensive STI screen at initiation and three-monthly.

Pregnancy: chlamydia, syphilis, HIV, and hepatitis B/C at booking; gonorrhoea selectively (per ASHM risk assessment); repeat syphilis and HIV in the third trimester for women at risk.

Symptomatic patients: urethral discharge, dysuria, genital ulcer, pelvic pain, vaginal discharge, anal symptoms — all warrant targeted testing plus comprehensive screen.

Routine with any new STI diagnosis: offer HIV testing. Co-infection is common and HIV affects management, partner notification priorities, and treatment.

Investigations

Standard screen:

• Chlamydia + gonorrhoea NAAT — first-pass urine (men), self-collected vulvovaginal swab (women), throat and anal swabs for MSM/WSW
• Syphilis serology — treponemal test (TPPA or EIA) plus non-treponemal quantitative titre (RPR or VDRL)
• HIV 4th-generation antigen/antibody (with RNA if seroconversion suspected — fever, rash, lymphadenopathy in high-risk person)
• Hepatitis B serology (HBsAg, anti-HBs, anti-HBc)
• Hepatitis C antibody ± RNA PCR

Add selectively:

• Mycoplasma genitalium PCR with macrolide resistance testing — for persistent or recurrent urethritis or cervicitis, or after contact with confirmed Mg
• Trichomonas vaginalis NAAT — symptomatic vaginal discharge or partner with trichomonas
• HSV PCR swab from lesion — genital ulcer, vesicles
• Mpox PCR — characteristic lesions in appropriate epidemiological context

eTG provides specific guidance on specimen handling and which NAAT platforms perform well for extragenital sites.

B. Treatment — pathogen-specific

Chlamydia (Chlamydia trachomatis)

Per ASHM guidelines:

• Doxycycline 100 mg twice daily × 7 days — first-line; superior rectal/pharyngeal clearance over single-dose azithromycin
• Azithromycin 1 g single dose — alternative for uncomplicated urogenital infection only; pregnancy (preferred in first trimester along with amoxicillin option)
• Test of cure at 4 weeks post-treatment
• Contact tracing window: 6 months prior to diagnosis

Gonorrhoea (Neisseria gonorrhoeae)

Antimicrobial resistance is evolving — ASHM and eTG guidance should be checked for current first-line:

• Ceftriaxone 500 mg IM single dose — current recommended first-line (confirm culture and sensitivities where possible)
• Previously ceftriaxone 500 mg IM + azithromycin 1 g PO was standard (to delay resistance); check ASHM for any update
• Test of cure 2 weeks post-treatment
• Contact tracing window: 2 months
• Disseminated gonococcal infection (DGI — septic arthritis, dermatitis-arthritis syndrome) requires IV ceftriaxone and hospital admission

Syphilis (Treponema pallidum)

• Primary, secondary, early latent (≤2 years): benzathine penicillin G 1.8 g IM single dose
• Late latent / latent unknown duration: benzathine penicillin G 1.8 g IM × 3 doses, one week apart
• Neurosyphilis: IV benzathine penicillin G or procaine penicillin — specialist care
• Penicillin allergy: doxycycline 100 mg twice daily × 14 days (early) or 28 days (late); penicillin is the only option in pregnancy — desensitise
• Syphilis is notifiable to state public health; partner notification window 3 months (primary), 6 months (secondary), 1 year (early latent)

Mycoplasma genitalium

Macrolide resistance is now ~60% in Australian isolates. ASHM recommends macrolide resistance testing before azithromycin. Treat sequentially:

1. Doxycycline 100 mg twice daily × 7 days (reduces load, improves azithromycin success)
2. Then azithromycin 1 g day 1, then 500 mg daily × 4 days (if macrolide-sensitive)
3. If macrolide-resistant: moxifloxacin 400 mg daily × 10 days (specialist guidance advised)

Pelvic inflammatory disease (PID)

Empirical treatment for PID (after gonorrhoea/chlamydia swabs taken):

• Ceftriaxone 500 mg IM single dose + doxycycline 100 mg twice daily × 14 days + metronidazole 400 mg twice daily × 14 days
• Hospitalise for severe PID, suspected TOA, pregnancy, or failure to improve with outpatient treatment
• Counsel about long-term risks: tubal factor infertility, ectopic pregnancy, chronic pelvic pain

Hepatitis C (HCV)

PBS-listed direct-acting antivirals are prescribable by appropriately trained GPs:

• Glecaprevir/pibrentasvir (Maviret) — pangenotypic, 8 weeks for treatment-naive without cirrhosis; requires PBS Authority (Streamlined)
• Sofosbuvir/velpatasvir (Epclusa) — pangenotypic, 12 weeks; PBS Authority (Streamlined)
• Both achieve sustained virological response (SVR12 — effective elimination of virus) in approximately 95% of patients

Pre-treatment: screen for significant drug interactions; check hepatitis B (risk of HBV reactivation if HBsAg positive — specialist input); assess for cirrhosis (FIB-4 score or liver imaging).

C. Prevention — vaccination, PrEP, and partner notification

Vaccination

• HPV (Gardasil 9): National Immunisation Program (NIP) for all students aged 12–13; catch-up for MSM up to age 26 via NIP; over-26 by private prescription. Covers 9 HPV types including oncogenic strains and those causing genital warts. Discuss with all unvaccinated adolescent and young adult patients.
• Hepatitis B: NIP for infants; catch-up adults. Vaccinate all hepatitis-B non-immune contacts of STI patients and all MSM, people who inject drugs, and sex workers.
• Mpox (JYNNEOS/IMVAMUNE): NIP for eligible groups including MSM with risk factors and sex workers; discuss eligibility per Australian Immunisation Handbook.

HIV pre-exposure prophylaxis (PrEP)

PrEP (emtricitabine/tenofovir disoproxil, Truvada and generics) is PBS Authority (Streamlined) for HIV-negative people at substantial ongoing risk. It reduces HIV acquisition by >99% when taken as prescribed. Baseline: HIV test (must be negative), renal function, hepatitis B/C, STI screen. Monitor three-monthly: HIV, renal, and STI screening. GPs are well-positioned to initiate and maintain PrEP prescribing.

Partner notification

After any bacterial STI diagnosis, partner notification is a core obligation — epidemiological, ethical, and increasingly medico-legal. Let Them Know is a free anonymous online notification service. State sexual health units provide contract tracing officers for complex cases and notifiable conditions. Document the notification discussion in the medical record.

D. Australian operations

MBS pathways

Standard consultations MBS items 23, 36, 44 cover STI consultations. Pathology items for STI screening are within the 69384 range (serology) and 69405 range (NAAT). Mental Health Care Plan (items 2700, 2715, 2717) is appropriate for the psychological impact of STI diagnosis, HIV diagnosis, or relationship distress.

Chronic HIV and chronic hepatitis C/B with comorbidity qualifies for GPCCMP (items 965/967). ATSI Health Assessment (item 715) is an opportunity for opportunistic STI screening in eligible patients.

PBS

• Doxycycline, azithromycin, metronidazole — general schedule
• Ceftriaxone IM — Authority Required
• Benzathine penicillin G — Authority Required
• Aciclovir / valaciclovir / famciclovir — general schedule
• Hepatitis C DAAs (Maviret, Epclusa) — Authority Required (Streamlined); GP-prescribable with training
• HIV ART — Section 100 Authority (specialist-initiated)
• HIV PrEP (emtricitabine/tenofovir) — Authority Required (Streamlined); GP-prescribable
• Imiquimod, podophyllotoxin for anogenital warts — Authority Required
• Mpox vaccine (JYNNEOS) — NIP for eligible groups

Notifiable diseases

Chlamydia, gonorrhoea, syphilis, HIV, hepatitis B, hepatitis C, and mpox are notifiable to state and territory public health under relevant legislation. Notification is the prescribing clinician’s responsibility. State health departments provide instructions for notification — most can be completed online or via pathology laboratory pathways.

Medico-legal obligations

Child sexual abuse with STI — mandatory child protection notification regardless of clinical setting. Sexual assault cases — dedicated sexual assault service referral; PEP within 72 hours; emergency contraception; forensic documentation. Document HIV test offer at any new STI diagnosis. Document partner notification discussion.

E. Special populations

Pregnant women. Congenital syphilis causes devastating outcomes and is entirely preventable with adequate ante-natal treatment. Missed syphilis diagnoses in pregnancy are a sentinel clinical event. T3 repeat syphilis testing for all women in areas of ongoing outbreak (most of Australia currently). HSV first episode in third trimester warrants specialist obstetrics input. HIV-positive pregnant women require specialist-managed ART; vertical transmission is near-zero with appropriate treatment.

Young people under 18. Fraser guidelines (in most states) permit confidential sexual health consultations without parental consent for competent young people. Creating a safe, confidential space is necessary for effective STI care in this group. Mandatory reporting applies to sexual abuse but not consensual adolescent sexual activity.

People who inject drugs. Hepatitis C is highly prevalent in this group, and HCV treatment access through general practice is transformative. Needle and syringe programs reduce transmission; many GPs can facilitate referral.

ATSI Australians. STI prevalence, including syphilis, is disproportionately elevated in some Aboriginal and Torres Strait Islander communities, particularly in rural and remote settings. Point-of-care testing (POCT) for gonorrhoea, chlamydia, syphilis, trichomonas, and HIV is available and deployed through some community-controlled health services — transforming STI management in remote settings. NACCHO guidelines and ASHM provide specific resources.

When to escalate

Refer urgently or seek specialist input:

• Disseminated gonococcal infection — IV antibiotics, hospital admission
• Severe PID or suspected tubo-ovarian abscess — hospital
• Syphilis in pregnancy — specialist obstetrics and sexual health
• Neurosyphilis — IV penicillin, neurologist, ID specialist
• HIV diagnosis — HIV specialist for ART initiation; ongoing co-management with GP appropriate
• Sexual assault — dedicated sexual assault service (same-day)
• Macrolide-resistant Mycoplasma genitalium — ASHM guidance; consider ID/sexual health input
• Child sexual abuse with STI — mandatory notification and child protection services

What this article is and is not

This is general health information drawn from the ASHM Australian STI Management Guidelines, eTG Antibiotic: Genital infections, AMH, and the Australian Immunisation Handbook. It does not constitute personal medical advice and does not replace discussion with your GP or sexual health clinician.

For Australian consumer resources: HealthDirect — STIs, Let Them Know, Better Health Channel — STIs, ASHM.

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Sources cited

1. ASHM — Australian STI Management Guidelines
2. Therapeutic Guidelines (eTG) — Antibiotic: Genital infections
3. Australian Medicines Handbook
4. Department of Health — National STI Strategy
5. Let Them Know — partner notification
6. Australian Immunisation Handbook
7. PBS — DAAs, HIV ART, PrEP, mpox vaccine
8. HealthDirect — STIs
9. Better Health Channel — STIs