Transmission of Salmonella clones between different animal species in a horse and cattle breeding region in Japan

Sequence type 34 (ST34) Salmonella enterica serovar Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are the most prevalent clones among humans and animals worldwide, including in Japan. Although cross-species transmission may have occurred in the background of global spread, the matter remains unresolved. Here, we conducted high-resolution phylogenetic analysis using whole-genome sequencing data of Salmonella Typhimurium and 4,[5],12:i:- obtained from a horse and cattle breeding district in Japan and identified cases of cross-species transmission of ST34 Salmonella 4,[5],12:i:- between horses and cattle. These isolates were classified into five clusters, core genome single-nucleotide polymorphism (cgSNP) clusters 1-5, based on the SNP distance. To elucidate the genetic background of each cgSNP cluster, we also conducted a phylogenetic analysis of 496 ST34 strains obtained from Japan and other countries. Hierarchical clustering using rhierBAPS revealed three clades. The past ST34 epidemic strains in Japan and cgSNP clusters 1-3 were concentrated in clades 1 and 3, which should be referred to as the Japanese epidemic lineages, whereas cgSNP cluster 5 belonged to clade 2, which should be referred to as the global lineage. These results suggest that ST34 Salmonella may have entered Japan through multiple routes and was transmitted between horses and cattle.