One Health genomic surveillance identifies potential genetic links of antimicrobial-resistant foodborne pathogens across sectors
Foodborne pathogens and antimicrobial resistance are major global health concerns. The integration and analysis of genomic surveillance data across human, animal, and environmental sectors remain a critical challenge in the study of foodborne bacteria. Here we investigate potential cross-sector genetic links between antimicrobial-resistant isolates from food (mainly chicken meat), animals (mainly cecal and rectal samples), and humans (clinical cases) by comparing whole-genome sequences of non-typhoidal Salmonella (n = 1,613), Campylobacter (n = 682), and Enterococcus (n = 72) collected from these sectors across Japan. For Salmonella, we identify closely related human- and food-derived S. Blockley isolates carrying blaCTX-M-15, with pairwise SNP distances of 6–10 SNPs, as well as S. Agona isolates carrying fosA7.2, with pairwise SNP distances of 13–15 SNPs, suggesting that resistant Salmonella strains are shared between human and food sectors. For Campylobacter, we identified closely related human- and food-derived ST-22 isolates carrying a tetracycline resistance gene and a fluoroquinolone resistance-conferring gyrA mutation, with a pairwise SNP distance of 4 SNPs. These findings highlight potential genetic links of antimicrobial-resistant foodborne bacteria between food and humans. In this study, the authors use nationwide genomic data collected across sectors in Japan to identify closely related antimicrobial-resistant Salmonella and Campylobacter isolates in food and humans, highlighting the value of integrated One Health surveillance.
Authors
- Yusuke Hashimoto (ORCID: https://orcid.org/0000-0002-1886-9332)
- Chizuko Sato
- Koji Yokoyama (ORCID: https://orcid.org/0000-0002-7794-7249)
- 末永朱美
- Koji Yahara (ORCID: https://orcid.org/0000-0003-4289-1115)
- 岩崎直昭
- 暁洋 永田
- Hideaki Kariya
- Yuta Kawakami (ORCID: https://orcid.org/0000-0003-0260-2040)
- Tomohiro Kajihara
- Manao Ozawa (ORCID: https://orcid.org/0000-0003-1234-6634)
- Chiemi Fukuda
- Emi Maenishi
- Yuka Otsuka (ORCID: https://orcid.org/0000-0003-3739-5790)
- Miyuki Saeki
- Junko Sakata
- 蔵田和正
- Yo Sugawara (ORCID: https://orcid.org/0000-0002-9897-3905)
- Satoko Yamaya
- Motoyuki Sugai (ORCID: https://orcid.org/0000-0001-9252-7739)
- Hiromi FUKUDA
- Haruyoshi Tomita (ORCID: https://orcid.org/0000-0001-9969-2235)
- Miho Toho
- Yukiko Asano (ORCID: https://orcid.org/0000-0001-5643-0710)
- Takahiro Nomura (ORCID: https://orcid.org/0000-0002-5733-332X)
- 治樹 石森
- Kenji Ohya (ORCID: https://orcid.org/0000-0002-8867-3618)
- Keiko Kimata (ORCID: https://orcid.org/0009-0006-8468-2329)
- Kanako Ishihara (ORCID: https://orcid.org/0000-0001-5881-6078)
- Chieko Goto (ORCID: https://orcid.org/0000-0002-0604-3760)
- Naoshi Ando (ORCID: https://orcid.org/0000-0002-6009-1712)
- Noriko Konishi
- Etsuko Saito
- Miyuki Suzuki (ORCID: https://orcid.org/0000-0003-4360-6478)
- Norikazu Kitamura (ORCID: https://orcid.org/0009-0006-3738-3545)
- Ichiro Furukawa
- Ryoji Nomura
- Keita Yanagimoto (ORCID: https://orcid.org/0000-0003-0574-3164)
- Kenichi Ogita
- Hiroto Shinomiya
- Yui Tsukiyama
- Jun Kurushima (ORCID: https://orcid.org/0000-0002-8573-6169)
- Tomoka Masaoka
- 紀子 青木
- Yuki Wakabayashi (ORCID: https://orcid.org/0000-0001-9786-9121)
- Chizuko Kimura
- Tetsuo Asai (ORCID: https://orcid.org/0000-0002-6556-9674)
- Yuka Fukuguchi
- Hiroki Hayashi (ORCID: https://orcid.org/0009-0005-0894-6102)
- Yoko Kimura
- Kazumi Seki
- Hideto Sekiguchi
- Hisahiro Kawai
- Yuko Mizuno Matsumoto
- Michiko Kawanishi (ORCID: https://orcid.org/0009-0004-8973-2140)
- Koichi Tanimoto
- Kaho Ikeda
- Haruo Watanabe
- Katsunori Nakano
- Yamagami Takeshi
- Junko Isobe
- Yoko Iwashita
- Shunya Nishijima (ORCID: https://orcid.org/0009-0004-7470-6302)
- Miwako Yamamoto
- Nobuyo Ikeda
- Nobushige Sakai
- Kaori Sato
- Shihomi Osanai
- Kyoko Meguro
- Kanako Ueno
- Takahito Tano
- Natsuki Ueda
- Yukie Ohara
- Mitsumasa Koizumi
- Shiho Tajima
- Shintaro Hirai
- Chinami Hakataya
- Mai Shiina
- Michiko Fujisaki
- Etsuko Nakamura
- Ayaka Chigami
- Yohei Takahashi
- Tomoko Yazaki
- Yukina Hashimoto
- Takashi Iwama
- Hironobu Ooba
- Satomi Iwasaki
- Kazumi Ikeda
Institutions
- Ministry of Agriculture, Forestry and Fisheries (JP)
- Gunma University (JP)
- National Institute of Infectious Diseases (JP)
- Chiba Prefectural Institute of Public Health (JP)
- Toyama Institute of Health (JP)
- Tokyo Metropolitan Institute of Public Health (JP)
- Kanagawa Prefectural Institute of Public Health (JP)
- Shimane Prefectural Institute of Public Health and Environmental Sciences (JP)
- National Institute of Health Sciences (JP)
- Hyogo Prefectural Institute of Environmental Sciences (JP)
- Nara Prefectural Institute of Public Health Research Center (JP)
- Gifu University (JP)
- Sakai City Institute of Public Health (JP)
- Yamanashi Institute for Public Health and Environment (JP)
- Hiroshima City Institute of Public Health (JP)
- Yokohama City Institute of Public Health (JP)
- Okayama Prefectural Institute for Environmental Science and Public Health (JP)
- Kitakyushu City Institute of Health and Environmental Sciences (JP)
- Kagawa Prefectural Research Institute for Environmental Sciences and Public Health (JP)
- Miyagi Prefectural Institute of Public Health and Environment (JP)
- Ehime Prefectural Institute of Public Health and Environmental Science (JP)
- Fukui Prefectural Institute of Public Health and Environmental Science (JP)
- Osaka Institute of Public Health (JP)
- Japan Institute for Health Security (JP)
- National Veterinary Assay Laboratory (JP)
- Tokyo University of Agriculture and Technology (JP)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-10-30
- DOI
- https://doi.org/10.1038/s41467-026-78530-9
- Primary Topic
- Salmonella and Campylobacter epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Ministry of Health, Labour and Welfare