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Scientific reports2026; doi: 10.1038/s41598-026-39311-y

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

Abstract: 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.
© 2026. The Author(s).
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Publication Date: 2026-03-06 PubMed ID: 41792274DOI: 10.1038/s41598-026-39311-yGoogle Scholar: Lookup
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Summary

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Transmission of Salmonella enterica ST34 clones occurs between horses and cattle in a breeding region in Japan, with genetic evidence showing both local Japanese epidemic lineages and global lineages circulating among these animals.

Background and Importance

  • Salmonella enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are widespread clones causing infections in humans and animals worldwide, including Japan.
  • Understanding transmission dynamics of these clones, especially across different animal species, is critical for controlling outbreaks in agriculture and preventing zoonotic transmission to humans.
  • Although prior studies suggested cross-species transmission might occur, the mechanisms and patterns of spread, especially between horses and cattle in the same area, had not been fully elucidated.

Study Objective and Region

  • The study focused on a horse and cattle breeding district in Japan to investigate whether cross-species transmission of ST34 Salmonella clones happens between these animals.
  • The goal was to use high-resolution genomic methods to analyze the genetic relationships among Salmonella isolates from these species.

Methodology

  • Whole-genome sequencing was performed on Salmonella Typhimurium and 4,[5],12:i:- isolates collected from horses and cattle in the region.
  • Genetic variation was analyzed using core genome single-nucleotide polymorphisms (cgSNPs) to classify the isolates into distinct clusters (cgSNP clusters 1-5) based on their genetic distance.
  • A broader phylogenetic analysis was conducted including 496 ST34 strains from Japan and other countries to contextualize the local isolates within global diversity.
  • Hierarchical clustering through the rhierBAPS tool was used to define major clades (genetically related groups) within the ST34 population.

Key Findings

  • The isolates from the horse and cattle breeding region grouped into five distinct cgSNP clusters, suggesting multiple independent transmission events or sources.
  • CgSNP clusters 1-3 were primarily found in two major clades (clades 1 and 3), defined as Japanese epidemic lineages, indicating these are well-established local strains circulating within Japan.
  • CgSNP cluster 5 belonged to clade 2, which corresponds to a global lineage, suggesting that international or external strains have also entered the Japanese breeding region.
  • The presence of multiple clusters across clades and the detection of the same clones in both horses and cattle confirmed cross-species transmission in the breeding district.
  • Findings indicate that ST34 Salmonella entered Japan through multiple routes rather than a single introduction and that interspecies transmission contributes to local epidemiology.

Implications and Conclusions

  • This study highlights the risk of Salmonella transmission between different livestock species, which can complicate disease control and eradication efforts in animal breeding areas.
  • Understanding the genetic background and transmission routes of ST34 clones can inform targeted surveillance, biosecurity, and intervention strategies for both animal and public health.
  • The detection of both local Japanese epidemic strains and global lineages suggests that international trade or movement of animals or animal products may play a role in introducing Salmonella variants.
  • Overall, the research demonstrates the power of whole-genome sequencing and phylogenetic analysis for unraveling complex epidemiological patterns and guiding effective management of zoonotic pathogens.

Cite This Article

APA
Arai N, Niwa H, Uchida-Fujii E, Sawa Y, Tamamura-Andoh Y, Kinoshita Y, Momoki A, Watanabe-Yanai A, Iwata T, Kubo M, Kusumoto M. (2026). Transmission of Salmonella clones between different animal species in a horse and cattle breeding region in Japan. Sci Rep. https://doi.org/10.1038/s41598-026-39311-y

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English

Researcher Affiliations

Arai, Nobuo
  • Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Niwa, Hidekazu
  • Division of Microbiology, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan.
Uchida-Fujii, Eri
  • Division of Microbiology, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan.
Sawa, Yuiko
  • Hokkaido Hidaka Livestock Hygiene Service Center, Hidaka, Hokkaido, Japan.
Tamamura-Andoh, Yukino
  • Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Kinoshita, Yuta
  • Division of Microbiology, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan.
Momoki, Anna
  • Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Watanabe-Yanai, Ayako
  • Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Iwata, Taketoshi
  • Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Kubo, Midori
  • Hokkaido Hidaka Livestock Hygiene Service Center, Hidaka, Hokkaido, Japan.
Kusumoto, Masahiro
  • Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan. kusumoto.masahiro645@naro.go.jp.
  • Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan. kusumoto.masahiro645@naro.go.jp.

Grant Funding

  • JP24K18035 / Japan Society for the Promotion of Science

Conflict of Interest Statement

Declarations. Competing interests: The authors declare no competing interests.

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