Comparative evaluation of ERIC-PCR and (GTG)₅-PCR for genetic diversity analysis of multidrug-resistant Escherichia coli from clinical, environmental, and food sources

Abstract Objectives The emergence and dissemination of multidrug-resistant (MDR) Escherichia coli across clinical, environmental, and food sources pose a major public health challenge within the One Health framework. This study compared the antimicrobial resistance, genetic diversity, and molecular relatedness of E. coli isolates from these ecological niches using ERIC-PCR and (GTG)₅-PCR fingerprinting. Materials and methods A total of 120 E. coli isolates were recovered, of which 68 MDR isolates clinical ( n = 21), environmental ( n = 23), and food ( n = 24) were selected for antimicrobial susceptibility testing, multiple antibiotic resistance (MAR) index determination, PCR detection of β-lactamase and carbapenemase genes, and molecular fingerprinting using ERIC-PCR and (GTG)₅-PCR. Genetic relationships were analysed by dendrogram construction and principal component analysis. Results High levels of multidrug resistance were observed across all sources, with MDR prevalence of 100% in clinical, 91.3% in environmental, and 79.2% in food isolates. The bla NDM gene was the predominant resistance determinant. Both fingerprinting methods revealed substantial genetic diversity, while several isolate clusters exhibited moderate genetic similarity across different sample sources. The (GTG)₅-PCR method demonstrated higher discriminatory performance for environmental and food isolates, whereas both methods showed comparable discriminatory ability among clinical isolates. Conclusion The widespread occurrence of MDR E. coli and the presence of similar resistance gene profiles across the studied sources, together with the absence of clear source-specific clustering, suggest possible genetic relatedness among isolates from different sources. These findings support the application of molecular fingerprinting for antimicrobial resistance surveillance within a One Health framework.