From Clinical guidelines — Diagnosis and treatment manual › Chapter 9: Genito-urinary diseases · Médecins Sans Frontières, Current online edition (updated July 2021)
MSF guidance on diagnosis and treatment of major sexually transmitted and genital infections for clinicians in resource-limited settings.
- Issuer
- Médecins Sans Frontières
- Edition
- Current online edition (updated July 2021)
- Audience
- Clinicians in resource-limited settings
- Evidence
- Expert consensus based on field experience
- Reviewed
- 21 Oct 2026 · GMJ
What this guideline says
GMJ summary
This MSF clinical guideline provides a comprehensive summary of the diagnosis and treatment of nine major genital infections: gonorrhoea, chlamydia, trichomoniasis, bacterial vaginosis, candidiasis, genital herpes, syphilis, chancroid, and genital warts. For each pathogen, the guideline details clinical features in men and women, recommended investigations, and first-line treatment regimens with specific doses.
The guideline emphasises syndromic management principles, noting the high frequency of asymptomatic infections (50% for gonorrhoea in women, >50% for chlamydia, up to 90% in men for chlamydia) and recommending co-treatment for gonorrhoea and chlamydia when either is suspected. PCR (Xpert) is identified as the best diagnostic method when available, though clinical diagnosis and basic microscopy remain valuable in resource-limited settings.
Treatment recommendations prioritise single-dose regimens where possible (e.g., ceftriaxone 500 mg IM for gonorrhoea, azithromycin 1 g for chlamydia, tinidazole or metronidazole 2 g for trichomoniasis) to improve adherence. Alternative regimens are provided for settings where first-line drugs are unavailable, with specific contraindications noted for pregnant and breastfeeding women.
Key points
For clinicians — doses and thresholds as stated in the guideline
- Gonorrhoea: ceftriaxone IM 500 mg single dose (or cefixime PO 400 mg single dose); always co-treat for chlamydia
- Chlamydia: azithromycin PO 1 g single dose or doxycycline PO 200 mg daily for 7 days; co-treat for gonorrhoea except when excluded by Gram stain or PCR
- Trichomoniasis: tinidazole or metronidazole PO 2 g single dose
- Bacterial vaginosis: diagnosed when 3 of 4 criteria present (grey-white discharge, pH >4.5, fishy odour with KOH, clue cells); treat with tinidazole or metronidazole PO 2 g single dose
- Syphilis: benzathine benzylpenicillin IM 2.4 MIU single dose (<12 months duration) or weekly for 3 weeks (>12 months or unknown duration); always co-treat for chancroid
- Chancroid: azithromycin PO 1 g single dose or ceftriaxone IM 250 mg single dose; always co-treat for syphilis
- Genital herpes: aciclovir PO 1200 mg daily for 7 days (primary episode, started within 5 days) or 5 days (recurrence, started within 24 hours)
- Doxycycline is contraindicated in pregnant women and should not exceed 7 days in breastfeeding women; ciprofloxacin should be avoided in pregnancy
Major genital infections: pathogens, clinical features, investigations and treatment
Table extracted from the guideline
| Pathogens/Infections | Clinical features | Investigations | Treatment |
|---|---|---|---|
| Neisseria gonorrhoeae (gonorrhoea) | Women: vaginal discharge, cervicitis, dysuria (50% asymptomatic); UGTI. Men: purulent urethral discharge, dysuria (5–50% asymptomatic) | PCR (Xpert) best; Gram/methylene blue stain in men: intracellular diplococci, >4 PMN/field | Ceftriaxone IM 500 mg single dose or cefixime PO 400 mg single dose; treat also for chlamydia |
| Chlamydia trachomatis (chlamydia) | Women: vaginal discharge, cervicitis, dysuria (>50% asymptomatic); UGTI. Men: mild discharge, dysuria (up to 90% asymptomatic) | PCR (Xpert) best | Azithromycin PO 1 g single dose or doxycycline PO 200 mg daily × 7 days; treat also for gonorrhoea (except when excluded) |
| Trichomonas vaginalis (trichomoniasis) | Women: yellow-green discharge, vulvar irritation (10–50% asymptomatic). Men: mostly asymptomatic; balanitis, urethritis | Wet mount shows motile trichomonas; pH >4.5 | Tinidazole or metronidazole PO 2 g single dose |
| Bacterial vaginosis | Grey-white discharge, pH >4.5, fishy odour with KOH, clue cells (3 of 4 for diagnosis) | Clinical criteria | Tinidazole or metronidazole PO 2 g single dose |
| Candida albicans (candidiasis) | Women: pruritus, vulvovaginitis, creamy-white discharge. Men: balanitis, erythema, white pustules | Wet mount shows budding yeast cells, pseudohyphae; normal pH | Women: clotrimazole 500 mg vaginal tablet single dose. Men: miconazole 2% cream twice daily × 7 days |
| Herpes simplex virus type 2 | Multiple vesicles → painful ulcers; fever (30%), lymphadenopathy (50%) in primary episodes; recurrences in 1/3 | Culture, serology, PCR at reference laboratory | Analgesics, local disinfection. Aciclovir PO 1200 mg daily × 7 days (primary) or × 5 days (recurrence) |
| Treponema pallidum (syphilis) | Single firm painless genital ulcer | Treponemal tests (TPHA, FTA-ABS, rapid tests) more sensitive/specific than RPR/VDRL | Benzathine benzylpenicillin IM 2.4 MIU single dose (<12 months) or weekly × 3 weeks (>12 months); alternatives: azithromycin 2 g, erythromycin 2 g daily × 14 days, doxycycline 200 mg daily × 14 days; treat also for chancroid |
| Haemophilus ducreyi (chancroid) | Painful genital ulcer(s), bleeds easily; painful inguinal lymphadenitis (50%), fistulae (25%) | Difficult to identify by microscopy/culture | Azithromycin PO 1 g or ceftriaxone IM 250 mg single dose, or ciprofloxacin PO 1 g daily × 3 days, or erythromycin PO 2 g daily × 7 days; treat also for syphilis |
| Human papillomavirus (genital warts) | Soft, raised, painless growths; acuminate or flat; external/internal | Clinical diagnosis; screen for cervical pre-cancer in women | External warts <3 cm, vaginal warts: podophyllotoxin 0.5%; larger/internal/pregnant: surgical excision, cryotherapy or electrocoagulation |
Source: Médecins Sans Frontières, Major genital infections (summary) — Clinical guidelines — Diagnosis and treatment manual — MSF Clinical guidelines. Reproduced in summary form.
From the guideline
Verbatim
“Treat also for gonococcal infection (except when a Gram stain in males or PCR shows no N. gonorrhoeae).”
Editor’s perspective
Why this matters for Georgia and the region
Prof. Giorgi Pkhakadze, MD, MPH, PhD
Editor-in-Chief, Georgian Medical Journal · Chair, Public Health Institute of Georgia · WHO consultant, health and migration
As Editor-in-Chief of the Georgian Medical Journal and WHO consultant, I recognise that sexually transmitted infections remain a significant challenge across Georgia and the South Caucasus, where stigma often delays diagnosis and laboratory capacity varies markedly between Tbilisi and regional areas. The MSF emphasis on single-dose regimens and syndromic co-treatment for gonorrhoea and chlamydia is particularly valuable for Georgian primary care, where patient follow-up can be challenging and where many infections remain asymptomatic until complications develop. I would stress to Georgian clinicians the importance of presumptive co-treatment even without definitive laboratory diagnosis, given our limited PCR capacity outside major centres. The realistic implementation caveat is ensuring reliable supply chains for ceftriaxone and azithromycin through our essential medicines programme, as stock-outs of these first-line agents would force reliance on less effective alternatives and potentially compromise antimicrobial stewardship efforts.
ORCID 0000-0001-7609-4515 · Perspective written for the GMJ Guidelines Library, 21 Oct 2026
Applicability
Georgia and the South Caucasus
This guidance is directly applicable to clinical practice in Georgia and the South Caucasus, where sexually transmitted infections remain a public health concern and laboratory capacity varies between urban and rural settings. Georgian clinicians should note that whilst PCR diagnostics are increasingly available in tertiary centres in Tbilisi and regional capitals, many primary care facilities still rely on syndromic management and basic microscopy, making the alternative diagnostic approaches outlined here particularly relevant. National STI programmes should consider the high asymptomatic infection rates (50–90% for chlamydia and gonorrhoea) when designing screening strategies for key populations, and ensure availability of single-dose treatments to improve adherence in settings with potential follow-up challenges.
Questions this guideline answers
Quick answers
Why should I treat for both gonorrhoea and chlamydia together?
Co-infection is common, and both infections are frequently asymptomatic (50% of gonorrhoea in women, up to 90% of chlamydia in men are asymptomatic). Treating both presumptively prevents treatment failure and reduces complications like upper genital tract infection.
What is the best diagnostic method for gonorrhoea and chlamydia?
PCR (Xpert) is the best method when available. In men only, Gram or methylene blue stain showing intracellular diplococci and more than 4 polymorphonuclear leukocytes per field can diagnose gonorrhoea, but this method is not sensitive enough in women.
How do I diagnose bacterial vaginosis?
Diagnosis requires 3 of 4 criteria: homogenous grey-white adherent vaginal discharge, vaginal pH >4.5, fishy amine odour especially with 10% KOH, and presence of clue cells on wet mount or Gram stain.
Can I use doxycycline for chlamydia in pregnant or breastfeeding women?
No. Doxycycline is contraindicated in pregnant women and should not be given to breastfeeding women if treatment exceeds 7 days. Use erythromycin as an alternative in these situations.
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Same guideline
- Venereal warts — MSF Clinical guidelinesChapter 9: Genito-urinary diseases
- Upper genital tract infections (UGTI) — MSF Clinical guidelinesChapter 9: Genito-urinary diseases
- Genital ulcers — MSF Clinical guidelinesChapter 9: Genito-urinary diseases
- Abnormal vaginal discharge — MSF Clinical guidelinesChapter 9: Genito-urinary diseases
- Urethral discharge — Clinical guidelines — Diagnosis and treatment manual — MSF Clinical guidelinesChapter 9: Genito-urinary diseases
- Genital infections — Clinical guidelines — MSF Clinical guidelinesChapter 9: Genito-urinary diseases
- Issuer
- Médecins Sans Frontières
- Guideline
- Clinical guidelines — Diagnosis and treatment manual
- Chapter
- Chapter 9: Genito-urinary diseases
- Type
- Clinical guideline (chapter)
- Edition
- Current online edition (updated July 2021)
- Status
- Current
- Published
- 2026-10-14
- Languages
- English, French
- Scope
- Major genital infections
- Audience
- Clinicians in resource-limited settings
- Evidence
- Expert consensus based on field experience
- Record history
- Created 21 Oct 2026 · updated 21 Oct 2026 · next check Apr 2027
Médecins Sans Frontières. Major genital infections (summary). In: Clinical guidelines — Diagnosis and treatment manual [Internet]. Paris: MSF; 2021 [updated 2021 Jul; cited 2026 Oct 14]. Available from: https://medicalguidelines.msf.org/GMJ Guidelines Library records are original summaries written by the GMJ editorial team from the issuer’s published document and reviewed by a physician. They do not replace the full guideline. The document is the copyright of its issuer and is linked, not hosted. Spotted an error or a newer edition? Tell the Guidelines Desk.
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