Supplementary Material 6

Identifying single nucleotide polymorphisms (SNPs) in <i>Escherichia coli</i> 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 <i>E. coli</i> diversity and transmission dynamics in clinical and environmental settings.

识别大肠杆菌（<i>Escherichia coli</i>）中的单核苷酸多态性（single nucleotide polymorphisms, SNPs）对于理解菌株间的遗传变异、抗菌药物耐药性（antimicrobial resistance）及进化关系至关重要。SNP检测涉及利用下一代测序（next-generation sequencing, NGS）技术对细菌基因组进行测序，并将其与参考基因组比对。Snippy、GATK和SAMtools等生物信息学工具常用于比对测序读段、识别SNP及过滤低质量变异。SNP分析有助于追踪细菌进化、识别暴发菌株，并理解基因组适应性，包括抗生素耐药机制和毒力因子。在流行病学研究中，基于SNP的系统发育分析可提供高分辨率的菌株区分能力，使其成为研究临床与环境场景下大肠杆菌（<i>E. coli</i>）多样性及传播动态的强大方法。