Prevalence, multidrug resistance patterns, and carbapenemase-encoding genes of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from clinical and non-clinical samples in Ethiopia: Systematic review and meta-analysis

Abstract

Background Carbapenems are considered the last resort to treat life-threatening bacterial infections. However, their efficacy is increasingly compromised by carbapenemase-producing K. pneumoniae (CPKP) and Escherichia coli (CPEC). Although these organisms have been reported in Ethiopia, the overall burden and distribution of carbapenemase-encoding genes remain unclear. This study aims to determine the pooled prevalence of CPKP and CPEC from both clinical and non-clinical samples in Ethiopia and to identify the most common carbapenemase-encoding genes. Methods A systematic search was conducted in electronic databases for studies published in English up to June 30, 2025. The review followed PRISMA guidelines and included 44 eligible studies. Quality assessment was performed using the Joanna Briggs Institute (JBI) checklist. The meta-analysis was performed using Comprehensive Meta-Analysis (CMA) software version 2, applying a random-effects model to estimate pooled prevalence. Heterogeneity and publication bias were evaluated using the I2 statistic, funnel plot, and Egger’s test. Results The pooled prevalence of CPKP and/or CPEC in Ethiopia was 8.3% (95% CI: 6.3–10.9; I2 = 86.41, p < 0.001), with a higher prevalence in non-clinical samples (13.3%) than in clinical ones (8%). Six studies reported 60 carbapenemase-encoding genes in 51 K. pneumoniae isolates. The most dominant resistant gene was the blaNDM metallo-β-lactamase type, accounting for 85%. The pooled prevalence of multidrug-resistant E. coli and/or K. pneumoniae reported by studies included in the review was 78.4% (95% CI = 71-84.2, I2 = 96.10, p< 0.001). Conclusions This study reveals a high pooled prevalence of CPKP and CPEC in Ethiopia and high dominance of the blaNDM carbapenemase gene. These findings underscore the need for enhanced antimicrobial resistance surveillance, infection prevention strategies, and stewardship interventions across both clinical and environmental settings.