Urethritis and urethral discharge — the AU general practice approach

Urethritis in Australian general practice

Urethritis is inflammation of the urethra, almost always sexually acquired in adults. It is the most common symptomatic presentation of sexually transmitted infection (STI) in men and an important cause of non-specific pelvic discomfort in women. The cardinal presentations are urethral discharge (purulent or mucoid), dysuria, urethral itch or burning, and meatitis. However, approximately 50% of chlamydial infections — the most common notifiable bacterial STI in Australia — are entirely asymptomatic, so urethritis is also a diagnosis made through systematic STI screening, not symptom alone.

Australian STI Management Guidelines and Therapeutic Guidelines (eTG) divide urethritis into gonococcal (caused by Neisseria gonorrhoeae) and non-gonococcal (NGU), with Chlamydia trachomatis, Mycoplasma genitalium, and Trichomonas vaginalis as the principal NGU pathogens in Australia. The management landscape has shifted substantially in the past five years, driven by macrolide resistance in Mycoplasma genitalium and the move away from azithromycin as first-line therapy.

A. Core clinical — the AU general practice framework

History — the five Ps

Sexual history should be taken using the structured five Ps framework: Partners (number and gender), Practices (oral/vaginal/anal, insertive/receptive), Protection (condoms, PrEP), Past STI, and Pregnancy plans or current pregnancy. Additional key questions:

• Onset and incubation — gonococcal urethritis typically 2–7 days; NGU 1–5 weeks
• Character of discharge — purulent (gonococcal more likely) vs mucoid or clear (NGU more likely)
• Systemic features — fever, arthralgia, rash (disseminated gonococcal infection), skin lesions (mpox)
• Prior antibiotic exposure — recent antibiotics can suppress NAAT detection of gonorrhoea; note prior macrolide use (drives Mycoplasma genitalium resistance)
• HIV and PrEP status
• Hepatitis B vaccination status
• Mpox risk factors — MSM, high partner numbers, recent travel, festival or event exposure

Examination

Urethral examination is enhanced by milking the urethra if no discharge is visible — apply gentle proximal-to-distal pressure along the urethra and observe the meatus for 1–2 minutes. Document colour and consistency of any expressed discharge.

Additional examination points: anogenital skin (HSV, mpox lesions, syphilis chancre, condylomata), inguinal lymphadenopathy, oropharynx (gonococcal pharyngitis is often asymptomatic in MSM), joints (DGI presents as migratory septic monoarthritis), and skin (sparse pustular peripheral lesions in DGI).

Investigations

Investigation	Indication
First-pass urine NAAT — chlamydia + gonorrhoea + M. genitalium + macrolide resistance markers	All suspected urethritis; standard panel
Gonorrhoea culture + susceptibility	Any suspected GU; pharyngeal/rectal positive; resistance surveillance
Multi-site NAAT (throat + ano-rectal + genital)	MSM; oral or anal receptive practices
HIV 4th-gen Ag/Ab	All new STI diagnoses
Syphilis serology	All new STI diagnoses
Hepatitis B serology (HBsAg, anti-HBs, anti-HBc)	All; vaccinate if non-immune
Hepatitis C antibody ± RNA	All new STI diagnoses
Trichomonas NAAT	Refractory NGU, regional risk, female partner with TV
HSV PCR of lesion or urethral swab	Vesicles, ulcers, or severe dysuria with normal NAAT
Mpox PCR	MSM with proctitis, atypical lesions, or systemic features
Pregnancy test	All reproductive-age women

A critical pitfall flagged by Australian STI Guidelines: failing to test for Mycoplasma genitalium with macrolide-resistance markers means the resistance-guided sequential treatment algorithm cannot be applied, driving further macrolide resistance in the community.

Treatment — current guideline-aligned approach

Empirical treatment for symptomatic urethritis (Australian STI Guidelines; eTG):

• Doxycycline 100 mg orally twice daily for 7 days — covers chlamydia and most NGU. This replaced azithromycin 1 g single dose following Geisler NEJM 2015 and subsequent meta-analyses demonstrating superior rectal chlamydia cure and reduced macrolide selection pressure
• Plus ceftriaxone 500 mg IM single dose (reconstituted in 2 mL 1% lignocaine) if gonococcal features are present: purulent discharge, known contact with gonorrhoea, MSM in high-prevalence setting, or gram-negative intracellular diplococci on urethral smear

Confirmed chlamydia: doxycycline 100 mg twice daily for 7 days. Test of cure (TOC) is routine only in pregnancy, persistent symptoms, or rectal infection (repeat NAAT at 4 weeks).

Confirmed gonorrhoea: ceftriaxone 500 mg IM single dose plus azithromycin 1 g orally (AU dual therapy; some centres moving to ceftriaxone monotherapy — follow local sexual health centre algorithm). TOC at 2 weeks for pharyngeal infection or any deviation from first-line therapy.

Mycoplasma genitalium — resistance-guided sequential therapy (Australian STI Guidelines — MG; Read CID 2019):

• Macrolide-susceptible (MRes negative): doxycycline 100 mg twice daily × 7 days, then azithromycin 1 g day 1 + 500 mg days 2–4
• Macrolide-resistant (MRes positive) — >50% of AU isolates: doxycycline 100 mg twice daily × 7 days, then moxifloxacin 400 mg daily × 7 days
• TOC at 21–28 days is mandatory — first-void urine NAAT on completion

Moxifloxacin — TGA Boxed Warning. Document informed consent regarding tendinopathy, aortic aneurysm or dissection risk, peripheral neuropathy, dysglycaemia, and mental health effects before prescribing. Avoid in older patients, those with aortic disease or prior tendinopathy, or concurrent corticosteroid use.

Trichomonas: metronidazole 2 g single dose or 400 mg twice daily for 7 days (preferred in HIV-positive patients). Counsel regarding alcohol avoidance during and 48 hours post-treatment.

B. Evidence appraisal — the doxycycline-first shift and Mycoplasma genitalium resistance

The key evidence shifts in the management of urethritis over the past decade:

Doxycycline vs azithromycin for chlamydia and NGU. Geisler NEJM 2015 confirmed doxycycline superiority for rectal chlamydia cure in men who have sex with men. The subsequent Lau CID 2021 meta-analysis confirmed doxycycline is at least equivalent for urogenital chlamydia and superior for rectal infection. Both Australian and CDC 2021 guidelines consequently moved to doxycycline as first-line for all anatomical sites.

Macrolide resistance in Mycoplasma genitalium. By 2024, greater than 50% of M. genitalium isolates in Australia carry macrolide-resistance mutations (23S rRNA A2058G/A2059G). Using azithromycin empirically without resistance testing drives further resistance and produces treatment failure in the majority of MG cases. Resistance-guided sequential therapy with doxycycline followed by moxifloxacin (if resistant) achieves cure rates of 85–95% in Australian cohort data.

Doxy-PEP for STI prevention in MSM. Luetkemeyer NEJM 2023 demonstrated that 200 mg doxycycline taken within 72 hours of sexual exposure reduced chlamydia and syphilis by approximately 87% in MSM and transgender women on PrEP or living with HIV. ASHM is developing formal AU guidance. Note the negative result in heterosexual women (dPEP Kenya 2023 — different epidemiology). Doxy-PEP is not yet routinely PBS-funded or nationally endorsed in Australia, but informal use is growing among high-risk MSM.

Gonorrhoea dual therapy vs monotherapy. CDC 2021 moved to ceftriaxone monotherapy (1 g IM) for gonorrhoea, discontinuing azithromycin co-prescription because of macrolide resistance concerns. Australian guidelines retain dual therapy (ceftriaxone 500 mg IM + azithromycin 1 g) pending formal stewardship review, with some metropolitan sexual health centres aligning to the monotherapy approach. Follow your local sexual health centre algorithm.

C. Partner notification and mandatory reporting

Partner notification

Partner notification is both an ethical obligation and a clinical standard of care. It is also consistently the most common medico-legal failure point documented in STI management. Let Them Know provides a free anonymous SMS or email notification service that removes the patient’s burden of direct contact. In practice:

• Chlamydia and NGU: notify all partners from the past 6 months
• Gonorrhoea: notify all partners from the past 2 months
• Offer provider-assisted notification for complex situations (multiple anonymous partners, known contacts who are difficult to reach)
• Document that the notification offer was made and whether the patient accepted assistance

Mandatory disease notification

Chlamydia, gonorrhoea, and syphilis are notifiable conditions in every Australian jurisdiction. The treating laboratory automatically notifies the relevant state public health unit within the specified timeframe (typically 5 days). Mycoplasma genitalium is not currently notifiable in any Australian jurisdiction. Mpox is notifiable under CDNA national guidelines.

Child and adolescent presentations. Any STI diagnosed in a patient under the age of consent raises mandatory child protection notification obligations under state legislation. Engage the local child protection service and sexual assault service.

D. Australian operations

MBS. First-pass urine NAAT for chlamydia and gonorrhoea (69317/69319); STI multiplex panels including M. genitalium and resistance markers (69319 range — verify with pathology provider). Gonorrhoea culture and susceptibility (69300 range). HIV serology (69384 range). Syphilis serology (69384 range). Hepatitis B/C serology (69481 range). HSV PCR (69496). Pregnancy test serum βhCG (73529). Standard consultations 23/36/44. ATSI Health Assessment 715 — STI screening is embedded; post-1 March 2026 update allows individualised holistic assessment without age-based clinical activity restrictions per NACCHO 2026.

PBS. Doxycycline 100 mg — general schedule. Azithromycin 500 mg/1 g — general schedule. Ceftriaxone IM — typically supplied and administered in clinic; PBS Authority Required for serious bacterial infections. Moxifloxacin 400 mg — PBS Authority Streamlined (TGA Boxed Warning — document consent). Metronidazole 400 mg/2 g — general schedule. HIV PEP — PBS Section 100 (initiate within 72 hours). HIV PrEP (emtricitabine/tenofovir disoproxil) — Authority Streamlined. HPV vaccine, hepatitis B vaccine, and JYNNEOS mpox vaccine — National Immunisation Programme.

Telehealth. Results review, partner notification counselling, and TOC discussions are appropriate by telehealth. Examination for new symptomatic presentations requires in-person assessment.

E. Special populations

MSM. Multi-site sampling (throat, anorectal, urethral) is standard given high rates of asymptomatic extragenital infection. Consider mpox vaccine eligibility per ATAGI/ASHM criteria. Discuss doxy-PEP for very high-risk individuals using appropriate clinical judgement. PrEP discussion is routine.

Pregnancy. Vertical transmission of chlamydia (conjunctivitis, pneumonia) and gonorrhoea (ophthalmia neonatorum) make diagnosis and treatment urgent. Doxycycline is contraindicated; use azithromycin 1 g single dose or amoxicillin 500 mg three times daily for 7 days for chlamydia in pregnancy. Ceftriaxone for gonorrhoea is safe in pregnancy. TOC is routine in pregnancy regardless of anatomical site.

Aboriginal and Torres Strait Islander communities in outbreak regions. Enhanced partner notification, community testing, and engagement with Aboriginal Community Controlled Health Services and state outbreak coordinators is required for sustained gonorrhoea outbreaks in remote regions. ATSI Health Assessment and practice nurse follow-up items (10987) support systematic testing and treatment completion.

Transgender and gender-diverse patients. Anatomy-based sampling (based on what anatomy is present, not gender identity) avoids missed extragenital infections. Affirming, non-stigmatising language and clinical approach is standard of care.

When to escalate

Refer or escalate when:

• Disseminated gonococcal infection — fever, migratory arthritis, skin lesions: admit to hospital, commence IV ceftriaxone, infectious diseases input
• Persistent or recurrent urethritis after appropriate first-line treatment: sexual health clinic review, repeat resistance-guided testing, urethroscopy if structural cause suspected
• Mycoplasma genitalium failing moxifloxacin: pristinamycin (TGA Special Access Scheme) — specialist sexual health input mandatory
• Resistant gonorrhoea suspected
• HIV seroconversion illness
• Pregnancy with STI requiring urgent management
• Child or adolescent presentation — mandatory child protection notification
• Suspected mpox with systemic features: emergency review

What this article is and is not

This is general health information drawn from the Australian STI Management Guidelines, Therapeutic Guidelines (eTG), Australian Medicines Handbook, and ASHM resources. It is not personal medical advice and does not create a doctor–patient relationship. Specific antibiotic choices, resistance testing, and partner notification support are managed with your own GP or sexual health clinician.

For anonymous partner notification: Let Them Know. Consumer resources: HealthDirect — urethritis, Better Health Channel — STIs, Play Safe NSW, ACON, SHINE SA.

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Sources cited

1. Australian STI Management Guidelines — urethritis
2. Australian STI Management Guidelines — Mycoplasma genitalium
3. Australian STI Management Guidelines — chlamydia
4. Australian STI Management Guidelines — gonorrhoea
5. Therapeutic Guidelines (eTG) — Antibiotic: genital infections
6. Australian Medicines Handbook (AMH)
7. ASHM — Australasian Society for HIV, Viral Hepatitis and Sexual Health Medicine
8. TGA — Quinolone safety alert
9. NACCHO — MBS 1 March 2026 update, 715 restructuring
10. Geisler WM et al — Azithromycin vs doxycycline for chlamydia (NEJM 2015)
11. Read TRH et al — Resistance-guided M. genitalium therapy (CID 2019)
12. Luetkemeyer AF et al — Doxy-PEP in MSM (NEJM 2023)
13. Let Them Know — partner notification
14. HealthDirect — urethritis
15. Better Health Channel — sexually transmissible infections