Whole genome sequencing of Salmonella enterica serovar Typhimurium and its monophasic variant isolated from food animals in Japan

Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and the monophasic variant (Salmonella 4,[5],12:i:-) are the major cause of gastroenteritis for both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods of this pathogens in the molecular epidemiological analyses, however the results do not reflect the phylogenetic information precisely. In this study, we performed phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine clades to be discriminated each other as genotypes.