Tackling Soil ARG‐Carrying Pathogens with Global‐Scale Metagenomics

Author:

Wang Binhao1ORCID,Xu Jianming1,Wang Yiling12,Stirling Erinne34,Zhao Kankan12,Lu Caiyu12,Tan Xiangfeng56,Kong Dedong56,Yan Qingyun7,He Zhili7,Ruan Yunjie89,Ma Bin12ORCID

Affiliation:

1. Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment Institute of Soil and Water Resources and Environmental Science College of Environmental and Resource Sciences Zhejiang University Hangzhou 310058 P. R. China

2. Hangzhou Global Scientific and Technological Innovation Center Zhejiang University Hangzhou 310058 P. R. China

3. Agriculture and Food Commonwealth Scientific and Industrial Research Organization Adelaide 5064 Australia

4. School of Biological Sciences The University of Adelaide Adelaide 5005 Australia

5. Institute of Digital Agriculture Zhejiang Academy of Agricultural Sciences Hangzhou 310021 P. R. China

6. Xianghu Laboratory Hangzhou Zhejiang 311200 P. R. China

7. Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Zhuhai 519080 P. R. China

8. Institute of Agricultural Bio‐Environmental Engineering College of Bio‐Systems Engineering and Food Science Zhejiang University Hangzhou 310058 P. R. China

9. The Rural Development Academy Zhejiang University Hangzhou 310058 P. R. China

Abstract

AbstractAntibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG‐carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non‐agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.

Funder

National Natural Science Foundation of China

Publisher

Wiley

Subject

General Physics and Astronomy,General Engineering,Biochemistry, Genetics and Molecular Biology (miscellaneous),General Materials Science,General Chemical Engineering,Medicine (miscellaneous)

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