Introduction: Carbapenem-resistant Escherichia coli (CREC) poses a critical public health threat globally. High-risk clones ST131 and ST69 drive the pandemic, yet their epidemiology in sub-Saharan Africa remains poorly characterized. We investigated the genomic features and epidemiological patterns of E. coli from human, animal, and environmental sources in Zambia using a comprehensive One Health approach.

Methods: Whole-genome sequencing was performed on 97 E. coli isolates (57 clinical, 40 environmental) collected from Lusaka, Zambia. Antimicrobial susceptibility testing, MLST typing, phylogroup assignment, and identification of AMR genes, plasmid replicons, and virulence factors were conducted. Statistical analyses included chi-square tests, Fisher's exact test, and principal component analysis to identify significant associations.

Results: Overall, 82.5% of isolates were multidrug-resistant. Carbapenem resistance was detected in 16.5% of isolates, significantly higher in environmental (25.0%) than clinical (10.5%) sources. The carbapenemase blaNDM-5 was exclusively found in environmental isolates (7.2%). ST131 dominated clinical isolates (41.2%), while ST69 was predominant environmentally (45.0%). Phylogroup B2 was most common clinically (50.9%), whereas phylogroup D was more prevalent environmentally (32.5%). Significant associations existed between specific STs and AMR genes (blaTEM-1, blaOXA-1 with ST131; p<0.01).

Conclusions: Environmental reservoirs in Zambia harbor a significant and concerning CREC burden, particularly ST69 and blaNDM-5-producing isolates. The distinct distribution of ST131 and ST69 between clinical and environmental settings suggests separate epidemiological pathways and transmission routes. These findings highlight the environment as a critical hub for CREC evolution and transmission, emphasizing the urgent need for integrated One Health surveillance and infection control strategies in the region.