Characterization of Antibiotic Resistance and Prevalence of Diarrheagenic E. coli Strains Isolated from Stool Samples in a Hospital Setting in Mali

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Introduction: Antibiotic resistance is a major global health challenge that disproportionately affects low-resource countries, particularly those in West Africa. E. coli, a major pathogen in childhood diarrhea, is both a prominent infectious agent and a reservoir of resistance genes, including resistance to last-resort antibiotics, such as carbapenems. Methodology: The study focused on 98 clinical E. coli isolates collected from stool samples of patients in a hospital setting in Bamako. The analyses included screening for DEC-specific virulence genes, detection of resistance genes across various classes of antibiotics (e.g., beta-lactams, carbapenems, fluoroquinolones), and identification of class 1, 2, and 3 integrons. The blaNDM gene was sequenced to identify mutations associated with carbapenem resistance. Results: Among the isolates, 85.7% carried at least one virulence gene. Of these, half involved co-infections, commonly combining EPEC, EAEC, and ETEC strains. Regarding antibiotic resistance, 94.9% of isolates harbored at least one resistance gene, and 50% were multidrug-resistant. The most frequently detected genes were blaTEM, qnrS1, and aphA3. Class 2 integrons were significantly associated with multidrug resistance (p = 0.01). Sequencing of the blaNDM gene revealed point mutations likely to affect protein function, suggesting an evolution toward increased resistance to carbapenems. Conclusion: The high prevalence of multidrug-resistant diarrheagenic E. coli strains in this study highlights the local antibiotic pressure and the serious health threat it represents. This study shows that the new β-lactamase blaNDM gene has disseminated in the hospital environment of Bamako. It should be noted that this will become a major challenge for clinicians.