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Transmission of Salmonella clones between different animal species in a horse and cattle breeding region in Japan
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  • Published: 06 March 2026

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

  • Nobuo Arai1,
  • Hidekazu Niwa2,
  • Eri Uchida-Fujii2,
  • Yuiko Sawa3,
  • Yukino Tamamura-Andoh1,
  • Yuta Kinoshita2,
  • Anna Momoki1,
  • Ayako Watanabe-Yanai1,
  • Taketoshi Iwata1,
  • Midori Kubo3 &
  • …
  • Masahiro Kusumoto1,4 

Scientific Reports , Article number:  (2026) Cite this article

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Subjects

  • Evolution
  • Genetics
  • Microbiology

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.

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Data availability

All data generated or analyzed in this study are included in this article with supplementary information. The sequence data used in this study are deposited in the DDBJ Sequence Read Archive, and the accession numbers are listed in Tables S1 and S2 in the supplementary information.

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Funding

This study was supported by JSPS KAKENHI Grant Number JP24K18035.

Author information

Authors and Affiliations

  1. Division of Zoonosis Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan

    Nobuo Arai, Yukino Tamamura-Andoh, Anna Momoki, Ayako Watanabe-Yanai, Taketoshi Iwata & Masahiro Kusumoto

  2. Division of Microbiology, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan

    Hidekazu Niwa, Eri Uchida-Fujii & Yuta Kinoshita

  3. Hokkaido Hidaka Livestock Hygiene Service Center, Hidaka, Hokkaido, Japan

    Yuiko Sawa & Midori Kubo

  4. Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan

    Masahiro Kusumoto

Authors
  1. Nobuo Arai
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  2. Hidekazu Niwa
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Contributions

Conceptualization: NA, HN & MK. Investigation: NA, HN, EU, YS, YT, YK, AM, AW, TI, & MK. Data analysis: NA, HN, EU, YS, & MK. Supervision: HS & MK. Writing-original draft: NA & MK. Writing-review and editing: NA, HN, EU, YS, YT, YK, AM, AW, TI, MK, & MK.

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Correspondence to Masahiro Kusumoto.

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Arai, N., Niwa, H., Uchida-Fujii, E. et al. Transmission of Salmonella clones between different animal species in a horse and cattle breeding region in Japan. Sci Rep (2026). https://doi.org/10.1038/s41598-026-39311-y

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  • Received: 21 October 2025

  • Accepted: 04 February 2026

  • Published: 06 March 2026

  • DOI: https://doi.org/10.1038/s41598-026-39311-y

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Keywords

  • Cattle
  • Cross-species transmission
  • Horse
  • Salmonella 4,[5],12:i:-
  • Sequence type 34
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