Carbapenem resistance in community-acquired urinary tract infections caused by Klebsiella pneumoniae and Escherichia coli in Morocco: a multicentre study (January 2022–December 2023)

Introduction Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are leading causes of urinary tract infections (UTIs). In Morocco, carbapenem resistance data are scarce and largely hospital-based. We investigated carbapenem-resistant E. coli and K. pneumoniae isolates from community settings in Morocco. Material and Methods In this prospective multicentre study, we analysed 1296 non-duplicate E. coli and K. pneumoniae isolates recovered from outpatients with community-acquired UTIs (CA-UTIs) across 12 Moroccan cities (January 2022–December 2023). Antimicrobial susceptibility testing was performed following EUCAST guidelines. All phenotypically carbapenem-resistant isolates (n = 54, 13 E. coli, et 41 K. pneumoniae) were subjected to whole-genome sequencing (WGS) using Illumina technology to identify resistance determinants, mobile genetic elements and clonal lineages. Results E. coli predominated [n = 1000, 77.2% (95% CI: 74.8–79.4)] while K. pneumoniae accounted for 22.8% [n = 296 (95% CI: 20.6–25.2)]. Carbapenem resistance rates were significantly higher in K. pneumoniae than in E. coli [ertapenem: 21.1% (95% CI: 16.6–26.4) versus 2.4% (95% CI: 1.6–3.6); imipenem: 15.0% (CI: 11.2–19.6) versus 1.9% (95% CI: 1.2–3.0)]. WGS revealed a high clonal diversity [eight sequence types (ST) in E. coli and 12 in K. pneumonnie]. Carbapenemase-mediated resistance was predominant in K. pneumoniae (notably blaNDM-14, blaNDM-7, blaNDM-5 and blaOXA-48). By contrast, E. coli primarily exhibited efflux and permeability defect mechanisms with sporadic carbapenemase-encoding gene carriage (blaNDM or blaOXA-48). The K. pneumoniae international high-risk clone ST147 producing NDM-14 was dominant (n = 23 isolates), followed by ST307 (n = 4), whereas ST410 was the most frequently identified among E. coli (n = 5). Conclusion Carbapenem-resistant E. coli and K. pneumoniae in community UTIs in Morocco, are driven by multiple clones. These findings underscore the urgent need to expand community-based AMR surveillance beyond hospital settings.