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全球土壤中的抗生素抗性基因与人类抗药基因组风险增加及关联性增强有关。

Global soil antibiotic resistance genes are associated with increasing risk and connectivity to human resistome.

作者信息

Zhao Yuxiang, Li Liguan, Huang Yue, Xu Xiaoqing, Liu Zishu, Li Shuxian, Zhu Lizhong, Hu Baolan, Zhang Tong

机构信息

Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.

College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.

出版信息

Nat Commun. 2025 Aug 4;16(1):7141. doi: 10.1038/s41467-025-61606-3.


DOI:10.1038/s41467-025-61606-3
PMID:40759899
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12322111/
Abstract

Soil is a reservoir of antibiotic resistance genes (ARGs), and understanding its connection to human antibiotic resistome is crucial for the One Health framework. Rank I ARGs appear key to deciphering this relationship, but their global distribution and attribution in soil remain unclear. To fill this gap, we analyze 3965 metagenomic data (12 habitats, including soil, feces, sewage) and 8388 genomes of Escherichia coli isolates. Results show that soil ARG risk has increased over time (from 2008 to 2021). We introduce a "connectivity" metric that evaluates cross-habitat ARGs connectivity through sequence similarity and phylogenetic analysis, and reveal higher genetic overlap with clinical E. coli genomes (1985-2023) over time suggesting an increasing link between soil and human resistome. A comparison of 45 million genome pairs suggests that cross-habitat horizontal gene transfer (HGT) is crucial for the connectivity of ARGs between humans and soil. Finally, we compile clinical antibiotic resistance datasets (covering 126 countries from 1998 to 2022) and find significant correlations between soil ARG risk, potential HGT events and clinical antibiotic resistance (R = 0.40-0.89, p < 0.001). Overall, our work provides insights into the ARGs connectivity between soil and humans, and could help identify strategies to prevent dissemination of antibiotic resistance.

摘要

土壤是抗生素抗性基因(ARGs)的储存库,了解其与人类抗生素抗性组的联系对于“同一个健康”框架至关重要。I类ARGs似乎是解读这种关系的关键,但它们在土壤中的全球分布和来源仍不清楚。为了填补这一空白,我们分析了3965个宏基因组数据(包括土壤、粪便、污水在内的12种生境)和8388个大肠杆菌分离株的基因组。结果表明,土壤ARG风险随时间(2008年至2021年)有所增加。我们引入了一种“连通性”指标,通过序列相似性和系统发育分析来评估跨生境ARGs的连通性,并发现随着时间的推移,与临床大肠杆菌基因组(1985年至2023年)的遗传重叠度更高,这表明土壤与人类抗性组之间的联系日益增加。对4500万个基因组对的比较表明,跨生境水平基因转移(HGT)对于人类与土壤之间ARGs的连通性至关重要。最后,我们汇编了临床抗生素抗性数据集(涵盖1998年至2022年的126个国家),并发现土壤ARG风险、潜在HGT事件与临床抗生素抗性之间存在显著相关性(R = 0.40 - 0.89,p < 0.001)。总体而言,我们的工作为土壤与人类之间ARGs的连通性提供了见解,并有助于确定预防抗生素抗性传播的策略。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/add5bbf2c5c4/41467_2025_61606_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/18b1583c2a90/41467_2025_61606_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/e49a7298ec9c/41467_2025_61606_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/d05fe56aa3f5/41467_2025_61606_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/136a88e54103/41467_2025_61606_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/525161aa4a9d/41467_2025_61606_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/add5bbf2c5c4/41467_2025_61606_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/18b1583c2a90/41467_2025_61606_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/e49a7298ec9c/41467_2025_61606_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/d05fe56aa3f5/41467_2025_61606_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/136a88e54103/41467_2025_61606_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/525161aa4a9d/41467_2025_61606_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e6bb/12322111/add5bbf2c5c4/41467_2025_61606_Fig6_HTML.jpg

相似文献

[1]
Global soil antibiotic resistance genes are associated with increasing risk and connectivity to human resistome.

Nat Commun. 2025-8-4

[2]
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[3]
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[4]
Hospital effluent in a low-resistance setting is responsible for dissemination of novel antibiotic resistance genes into the marine environment.

Ecotoxicol Environ Saf. 2025-8

[5]
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[6]
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BMC Microbiol. 2024-1-20

[7]
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J Hazard Mater. 2024-12-5

[8]
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Appl Environ Microbiol. 2025-6-18

[9]
Close interactions between prokaryotes and plasmids or viruses highlight a pivotal role of horizontal gene transfer in shaping antibiotic/metal(loid) resistome and their prokaryotic supercarriers in untreated hospital sewage.

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[10]
Antibiotic resistance patterns and cross-family ARG transfer in families Burkholderiaceae and Sphingomonadaceae: A large-scale genome-wide analysis of over 10 K genomes.

J Hazard Mater. 2025-8-15

本文引用的文献

[1]
Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally.

Nat Commun. 2024-4-29

[2]
Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils.

Proc Natl Acad Sci U S A. 2024-4-16

[3]
Mobile genetic elements mediate the cross-media transmission of antibiotic resistance genes from pig farms and their risks.

Sci Total Environ. 2024-5-20

[4]
Integrating global microbiome data into antibiotic resistance assessment in large rivers.

Water Res. 2024-2-15

[5]
Pathogenic Bacteria Are the Primary Determinants Shaping PM-Borne Resistomes in the Municipal Food Waste Treatment System.

Environ Sci Technol. 2023-12-5

[6]
Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.

Adv Sci (Weinh). 2023-11

[7]
Identification of mobile genetic elements with geNomad.

Nat Biotechnol. 2024-8

[8]
Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation.

Nat Commun. 2023-9-5

[9]
Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era.

Nat Rev Microbiol. 2024-1

[10]
Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.

Adv Sci (Weinh). 2023-9

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