Genomic Tracing of Transmission Dynamics in Invasive Non-typhoidal Salmonella Outbreaks.

Whole-genome sequencing (WGS) provides high-resolution evidence for investigating bacterial transmission during outbreaks of invasive non-typhoidal Salmonella (iNTS). Here we describe a reproducible workflow for genomic tracing of transmission dynamics using short-read sequencing data. The protocol includes read quality assessment, genome assembly, reference-based single nucleotide polymorphism (SNP) calling, core-genome alignment, pairwise SNP distance analysis, phylogenetic reconstruction, and characterization of mobile genetic elements (MGEs) and antimicrobial resistance (AMR) determinants. Putative transmission links are defined using a rationally selected SNP threshold and are further interpreted together with isolate source metadata. This workflow enables the identification of transmission clusters, the classification of likely transmission patterns, and the comparative analysis of accessory genomic content across sources. The protocol is suitable for outbreak investigation, surveillance studies, and comparative genomic analysis of iNTS populations.