Decoding resistance: a genomic and clinical overview of multidrug-resistant Escherichia coli in catheter-associated urinary infections

Catheter-associated urinary tract infections (CAUTIs) continue to be one of the most prevalent healthcare-associated infections (HAIs) globally. Among the causative agents, Escherichia coli , particularly multidrug-resistant (MDR) strains, plays a major role and presents increasing challenges in clinical management because of restricted therapeutic options. Important resistance genes such as blaCTX-M-15 , blaNDM-5 , and rmtB are commonly linked to high-risk clonal lineages, including ST131, ST410, and ST167. These determinants are often carried on mobile genetic elements, especially IncF and IncX3 plasmids, facilitating their rapid spread. This review outlines the key molecular mechanisms responsible for antimicrobial resistance (AMR) in MDR E. coli , focusing on β-lactamase production, carbapenemase activity, and 16S rRNA methyltransferase-mediated resistance. It further discusses the application of next-generation sequencing (NGS) in detecting resistance genes, analyzing plasmid structures, identifying virulence factors, and understanding phylogenetic relationships. In addition, widely used bioinformatics tools, including ResFinder, AMRFinderPlus, CARD, and ARG-ANNOT, are evaluated for their role in resistome profiling. A clearer understanding of the genomic characteristics and epidemiological patterns of AMR in E. coli is essential for improving diagnostic approaches, optimizing antimicrobial use, and enhancing infection control strategies in CAUTIs.