Supplementary Material 6

Identifying single nucleotide polymorphisms (SNPs) in Escherichia coli is crucial in understanding genetic variations, antimicrobial resistance, and evolutionary relationships among strains. SNP detection involves sequencing the bacterial genome using next-generation sequencing (NGS) technologies and comparing it to a reference genome. Bioinformatics tools such as Snippy, GATK, and SAMtools are commonly used to align sequencing reads, call SNPs, and filter out low-quality variants. SNP analysis helps track bacterial evolution, identify outbreak strains, and understand genomic adaptations, including antibiotic resistance mechanisms and virulence factors. In epidemiological studies, SNP-based phylogenetic analysis provides high-resolution strain differentiation, making it a powerful approach for studying E. coli diversity and transmission dynamics in clinical and environmental settings.