Antimicrobial Resistance Trends in Urinary Tract Infections in 6 African Countries

Importance Escherichia coli and Klebsiella pneumoniae are major causes of urinary tract infections. While antibiotic resistance in these critical pathogens is a global concern, data from Africa remain sparse, cover short time frames, and aggregate multiple specimen types. Objective To model antimicrobial resistance trends in urinary E coli and K pneumoniae isolates from 6 African countries between 2010 and 2022 and to project future resistance patterns. Design, Setting, and Participants Data for this retrospective cross-sectional study were obtained from Pasteur Network clinical laboratories located in the capital cities of 5 African countries (Cameroon, Central African Republic [CAR], Madagascar, Morocco, and Senegal) and from 1 university hospital in Benin. Urine samples yielding E coli or K pneumoniae collected during routine clinical care were included. Data collection spanned 2008 to 2023, with a shared observation period from October 2014 to December 2021. Data were analyzed from March through December 2025. Main Outcomes and Measures The primary outcome was resistance in E coli and K pneumoniae urinary isolates, measured as nonsusceptibility to aminopenicillins (for E coli ), fluoroquinolones, third- and fourth-generation cephalosporins, β-lactam and β-lactamase inhibitor combinations, aminoglycosides, and carbapenems. Resistance trends were analyzed using logistic regression with generalized estimating equations. Results A total of 44 367 urinary isolates (mean [SD] age of patients, 35.8 [30.2] years; 26 935 isolates from women among 42 839 samples with sex data [62.9%]) were included. Mean (SD) age ranged from 29.1 (30.5) years among patients with K pneumoniae –positive samples in Cameroon to 54.3 (23.4) years among patients with E coli –positive samples in Morocco. E coli –positive samples were more common in women, with the highest proportions in Madagascar (11 948 women among 16 137 patients [74.0%]) and CAR (1329 women among 1893 patients [70.2%]), whereas K pneumoniae positive samples showed no clear sex pattern. At study end, amoxicillin resistance in E coli exceeded 85% across sites (eg, 96.0% [95% CI, 93.5%-97.6%] in Morocco), and amoxicillin-clavulanate resistance surpassed 50% for E coli (eg, 84.9% [95% CI, 77.7%-90.1%] in Morocco) and K pneumoniae (eg, 96.1% [95% CI, 89.4%-98.7%] in Morocco) in most countries. E coli resistance to third-generation cephalosporins (3GCs) and fluoroquinolones surpassed 35% at study end, with increasing trends in most countries (eg, 34.5% [95% CI, 27.3%-42.6%] to 59.8% [95% CI, 55.7%-63.8%] for cefotaxime in Benin and 32.4% [95% CI, 25.1%-40.7%] to 75.9% [95% CI, 72.4%-79.1%] for norfloxacin in Senegal). For K pneumoniae , resistance to 3GCs increased in Cameroon, Madagascar, CAR, and Senegal, exceeding 50% in most settings (eg, 50.7% [95% CI, 45.6%-55.9%] to 76.6% [95% CI, 71.7%-80.9%] for cefotaxime in Madagascar). Rates remained stable in Benin and Morocco. Fluoroquinolone resistance increased in Cameroon, Senegal, and CAR (eg, 38.5% [95% CI, 25.7%-53.0%] to 65.8% [95% CI, 58.8%-72.2%] for ciprofloxacin in Senegal); remained high in Benin and Morocco; and decreased in Madagascar but remained elevated (eg, 63.7% [95% CI, 58.7%-68.3%] to 59.9% [95% CI, 54.1%-65.4%] for norfloxacin). For both bacteria, carbapenem resistance remained less than 18% (eg, 17.2% [95% CI, 11.8%-24.3%] for K pneumoniae resistance to ertapenem in Senegal), but resistance to ertapenem reached 28.0% (95% CI, 25.7%-30.5%) for E coli and 27.8% (95% CI, 22.0%-34.5%] for K pneumoniae in Madagascar. Projections suggest that 3GC and carbapenem resistance could exceed 90% by 2050 in most countries (eg, 2037 [95% CI, 2032-2053] for E coli resistance to imipenem in Benin). Conclusions and Relevance In this study, elevated and increasing resistance levels were observed, underlining the urgent need for improved measures against antimicrobial resistance in Africa.