From Clinical guidelines — Diagnosis and treatment manual › Chapter 9: Genito-urinary diseases · Médecins Sans Frontières, Current online edition (section last updated July 2021)
Evidence-based antibiotic treatment protocols for acute cystitis in girls, non-pregnant women, and pregnant/lactating women.
- Issuer
- Médecins Sans Frontières
- Edition
- Current online edition (section last updated July 2021)
- Audience
- Clinicians working in primary care and humanitarian 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 systematic approach to diagnosing and treating acute cystitis, a bladder and urethral infection predominantly affecting women and girls from 2 years of age. Escherichia coli accounts for at least 70% of cases, with other pathogens including Proteus mirabilis, Enterococcus sp, Klebsiella sp, and Staphylococcus saprophyticus in young women.
Diagnosis relies on characteristic clinical features (burning pain on urination, urinary urgency and frequency, absence of fever or flank pain) combined with urine dipstick testing for nitrites and leukocytes. The guideline emphasizes the critical importance of ruling out pyelonephritis and notes that burning pain on urination alone is insufficient for diagnosis. Microscopy and culture are recommended when dipstick is positive, particularly in children and pregnant women.
Treatment protocols are stratified by patient population: girls aged 2 years and older receive cefixime or amoxicillin/clavulanic acid for 3 days; young non-pregnant women receive fosfomycin-trometamol single dose or nitrofurantoin for 5 days; and pregnant/lactating women receive fosfomycin, nitrofurantoin (contraindicated in the last month of pregnancy), or cefixime. Ciprofloxacin is reserved for treatment failure or recurrent cystitis (>3-4 episodes per year).
Key points
For clinicians — doses and thresholds as stated in the guideline
- Girls ≥2 years: cefixime PO 8 mg/kg once daily for 3 days or amoxicillin/clavulanic acid PO 12.5 mg/kg twice daily for 3 days
- Young non-pregnant women with positive nitrites and leukocytes: fosfomycin-trometamol PO 3 g single dose or nitrofurantoin PO 100 mg 3 times daily for 5 days
- If dipstick is negative for nitrites but positive for leukocytes, use nitrofurantoin (not fosfomycin) as S. saprophyticus may be the causative pathogen
- Pregnant/lactating women: fosfomycin-trometamol PO 3 g single dose, or nitrofurantoin PO 100 mg 3 times daily for 7 days (contraindicated in last month of pregnancy), or cefixime PO 200 mg twice daily for 5 days
- Treatment failure or recurrent cystitis (>3-4 episodes/year): ciprofloxacin PO 500 mg twice daily for 3 days
- Urine dipstick positive for nitrites and/or leukocytes indicates likely urinary infection; in women, negative dipstick for both excludes urinary infection
- Symptoms may persist for 2-3 days despite adequate treatment; recurrent cystitis warrants investigation for bladder stones, urinary schistosomiasis, urinary tuberculosis or gonorrhoea
- In schistosomiasis-endemic areas, consider concomitant schistosomiasis in patients with haematuria, especially children aged 5-15 years
Antibiotic treatment protocols for acute cystitis by patient population
Table extracted from the guideline
| Population | First-line treatment | Alternatives/Notes |
|---|---|---|
| Girls ≥2 years | Cefixime PO 8 mg/kg once daily × 3 days | Amoxicillin/clavulanic acid PO 12.5 mg/kg twice daily × 3 days |
| Young non-pregnant women (nitrites + leukocytes +) | Fosfomycin-trometamol PO 3 g single dose | Nitrofurantoin PO 100 mg 3 times daily × 5 days |
| Young non-pregnant women (nitrites −, leukocytes +) | Nitrofurantoin PO 100 mg 3 times daily × 5 days | Fosfomycin not active against S. saprophyticus |
| Pregnant/lactating women | Fosfomycin-trometamol PO 3 g single dose | Nitrofurantoin PO 100 mg 3 times daily × 7 days (contraindicated last month of pregnancy); cefixime PO 200 mg twice daily × 5 days |
| Treatment failure/recurrent (>3-4/year) | Ciprofloxacin PO 500 mg twice daily × 3 days | Investigate for bladder stones, schistosomiasis, TB, gonorrhoea |
Source: Médecins Sans Frontières, Acute cystitis — MSF Clinical guidelines. Reproduced in summary form.
From the guideline
Verbatim
“It is essential to rule out pyelonephritis. The symptom 'burning pain on urination' alone is insufficient to make the diagnosis.”
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 a clinician who has worked extensively in primary healthcare settings across Georgia, I recognise that acute cystitis represents one of the most frequent presentations in our ambulatory care facilities, and this MSF guideline offers a pragmatic, evidence-based approach well-suited to resource-variable contexts. The stratified treatment protocols are particularly valuable, though I would emphasise to Georgian colleagues the critical importance of local antimicrobial susceptibility surveillance—our National Centre for Disease Control data suggests E. coli resistance patterns to common oral antibiotics may differ from global averages, particularly for fluoroquinolones. The guideline's emphasis on dipstick-based diagnosis aligns well with Georgia's primary healthcare capacity, though the recommendation for microscopy and culture in children and pregnant women may be challenging in rural facilities where laboratory access remains limited. For implementation in Georgia, I would stress the need to integrate these protocols with our national antimicrobial stewardship framework and ensure that fosfomycin and nitrofurantoin are consistently available through our essential medicines supply chain, as stock-outs of second-line antibiotics remain an operational reality in peripheral health facilities.
ORCID 0000-0001-7609-4515 · Perspective written for the GMJ Guidelines Library, 21 Oct 2026
Applicability
Georgia and the South Caucasus
This guideline is highly relevant for Georgia and the South Caucasus, where urinary tract infections are common primary care presentations. Georgian clinicians should note that antimicrobial resistance patterns may differ from MSF’s global field experience, and local antibiotic susceptibility data should inform empirical treatment choices where available. The diagnostic approach using dipstick testing is appropriate for Georgian primary healthcare settings, though access to urine microscopy and culture varies between urban and rural facilities. National antimicrobial stewardship programmes should consider adapting these protocols to local resistance patterns, particularly for E. coli susceptibility to oral antibiotics. Urinary schistosomiasis is not endemic in Georgia, but the differential diagnostic approach for recurrent cystitis (including tuberculosis screening) remains relevant given the regional TB burden.
Questions this guideline answers
Quick answers
When can I exclude urinary tract infection based on dipstick testing alone?
In women, if dipstick analysis is negative for both nitrites and leukocytes, a urinary infection is excluded. However, in children and pregnant women, microscopy/culture is recommended when dipstick is positive to confirm infection and identify the causative pathogen.
Why should I avoid fosfomycin when the dipstick shows only leukocytes without nitrites?
When dipstick is negative for nitrites but positive for leukocytes, the infection may be due to Staphylococcus saprophyticus, against which fosfomycin is not active. Use nitrofurantoin 100 mg 3 times daily for 5 days instead.
How long should symptoms persist before I consider treatment failure?
Whatever the antibiotic used, symptoms may persist for 2 to 3 days despite adequate treatment. Only after this period, if symptoms continue, should treatment failure be considered and ciprofloxacin 500 mg twice daily for 3 days be prescribed.
What should I investigate in patients with recurrent cystitis?
Recurrent cystitis (>3-4 episodes per year) warrants investigation for bladder stones, urinary schistosomiasis, urinary tuberculosis, or gonorrhoea (examine the partner). POCUS with FAST views can evaluate for signs of urinary tract pathologies in recurrent cases.
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- 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 (section last updated July 2021)
- Status
- Current
- Published
- 2026-10-14
- Scope
- Acute cystitis in girls ≥2 years, non-pregnant women, and pregnant/lactating women
- Audience
- Clinicians working in primary care and humanitarian 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. Acute cystitis. In: Clinical guidelines — Diagnosis and treatment manual. Chapter 9: Genito-urinary diseases. Paris: MSF; 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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