Supplementary Material 7

ResFinder, CARD (Comprehensive Antibiotic Resistance Database), and MegARes are essential databases for analyzing antibiotic resistance genes in <i>Escherichia coli</i>, helping researchers identify resistance mechanisms and assess the threat of multidrug-resistant strains.<b>ResFinder</b> is a web-based tool that detects acquired antibiotic resistance genes in bacterial genomes by comparing sequences against a curated database. It is widely used for identifying resistance genes in <i>E. coli</i>, providing insights into the presence of β-lactamases, aminoglycoside-modifying enzymes, and other resistance determinants.<b>CARD (Comprehensive Antibiotic Resistance Database)</b> is a high-quality, manually curated database that categorizes resistance genes, mutations, and mechanisms based on molecular models. It utilizes the Resistance Gene Identifier (RGI) tool to detect resistance genes and SNPs linked to resistance, making it valuable for studying both acquired and intrinsic resistance mechanisms in <i>E. coli</i>.<b>MegARes</b> is a specialized database for metagenomic analysis of antimicrobial resistance (AMR). It provides structured annotations of resistance genes and their associated antimicrobial classes, allowing researchers to study AMR profiles in complex microbial communities, including clinical and environmental <i>E. coli</i> isolates.By leveraging these databases, researchers can comprehensively assess antibiotic resistance in <i>E. coli</i>, track the emergence of resistant strains, and develop strategies for combating antimicrobial resistance in clinical and public health settings.