Figure 1.

Core gene–based phylogenetic analysis of the global Salmonella Oranienburg strain set, which includes 37 Japanese strains sequenced in this study and 1622 strains whose genome sequences were obtained from the EnteroBase website. Single-nucleotide polymorphisms (SNPs) were identified using the finished genome sequence of strain 0250 as a reference. Based on the 106 958 SNPs identified in 2660 core genes, a maximum-likelihood tree was constructed using IQ-TREE with a model inferred by ModelTest and 5000 bootstrap replicates. Bars represented the number of substitutions per site. Salmonella enterica serotype O8 strain 11556 was used as an outlier. Abbreviations: CC, continent or country; DI, detailed information of human sources; SC, sources.