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Despite increasingly routine use of WGS and SNP subtyping in outbreak and source tracking investigations, whether and how MGEs affect SNP subtyping has not been thoroughly investigated. Besides chromosomal MGEs, plasmids are frequently entangled in draft genome assemblies and yet to be assessed for their impact on SNP subtyping. This study provides evidence-based guidance on the treatment of MGEs in SNP analysis forSalmonella to infer phylogenetic relationship and SNP distance between isolates.

Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations