A global atlas and drivers of antimicrobial resistance in Salmonella during 1900-2023

Yanan Wang (), Xuebin Xu, Shulei Jia, Mengqi Qu, Yuhang Pei, Shaofu Qiu, Jianmin Zhang, Yue Liu, Sufang Ma, Na Lyu, Yongfei Hu, Jianli Li, Erqin Zhang, Bo Wan, Baoli Zhu and George F. Gao ()
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Yanan Wang: Henan Agricultural University
Xuebin Xu: Shanghai Municipal Center for Disease Control and Prevention
Shulei Jia: Tianjin Medical University
Mengqi Qu: Henan Agricultural University
Yuhang Pei: Henan Agricultural University
Shaofu Qiu: Center for Disease Control and Prevention of Chinese PLA
Jianmin Zhang: South China Agricultural University
Yue Liu: Shanghai Municipal Center for Disease Control and Prevention
Sufang Ma: Chinese Academy of Sciences (CAS)
Na Lyu: Chinese Academy of Sciences (CAS)
Yongfei Hu: China Agricultural University
Jianli Li: Henan Agricultural University
Erqin Zhang: Henan Agricultural University
Bo Wan: Henan Agricultural University
Baoli Zhu: Chinese Academy of Sciences (CAS)
George F. Gao: Chinese Academy of Sciences (CAS)

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Although previous studies using phenotypic or/and genomic approaches monitoring have revealed the spatiotemporal distribution of antimicrobial resistance (AMR) in Salmonella in local areas, their geographical patterns and driving factors remain largely unknown at a global scale. Here, we performed an analysis of publicly available data of 208,233 Salmonella genomes in 148 countries/regions between 1900 and 2023 and explored driving indicators of AMR. Overall, we found that the geographic distribution of AMR varied depending on the location, source, and serovar. The proportion of AMR levels increased across six continents, especially in serovars Agona, Dublin, I 1,4,[5],12:i:-, Muenchen, Senftenberg, Mbandaka mainly from chickens, food, wild animals, and the environment, while decreased in Schwarzengrund and Saintpaul mainly from cattle, pigs, and turkeys. We also found that S. Typhimurium exhibiting macro, red, dry, and rough was detected as early as 1992 in the USA, earlier than in China. Moreover, we identified that antibiotic consumption, agriculture, climate, urban, health, and socioeconomic factors contribute to the development of AMR in Salmonella. We present a globally high-resolution genetic atlas of Salmonella and also identify some factors driving the rise of AMR, which can provide valuable information for understanding the transmission dynamics and evolutionary trajectories of Salmonella.

Date: 2025
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DOI: 10.1038/s41467-025-59758-3

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