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Continental-scale pollution of estuaries with antibiotic resistance genes

Nature Microbiology volume 2, Article number: 16270 (2017) | Download Citation

Abstract

Antibiotic resistance genes (ARGs) have moved from the environmental resistome into human commensals and pathogens, driven by human selection with antimicrobial agents. These genes have increased in abundance in humans and domestic animals, to become common components of waste streams. Estuarine habitats lie between terrestrial/freshwater and marine ecosystems, acting as natural filtering points for pollutants. Here, we have profiled ARGs in sediments from 18 estuaries over 4,000 km of coastal China using high-throughput quantitative polymerase chain reaction, and investigated their relationship with bacterial communities, antibiotic residues and socio-economic factors. ARGs in estuarine sediments were diverse and abundant, with over 200 different resistance genes being detected, 18 of which were found in all 90 sediment samples. The strong correlations of identified resistance genes with known mobile elements, network analyses and partial redundancy analysis all led to the conclusion that human activity is responsible for the abundance and dissemination of these ARGs. Such widespread pollution with xenogenetic elements has environmental, agricultural and medical consequences.

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Acknowledgements

The authors thank H. Li and Y.-W. Hong for help with sample collection. This study was supported financially by the National Key Research and Development Plan (2016YFD0800205), the Natural Science Foundation of China (21210008), the Knowledge Innovation Program of the Chinese Academy of Sciences (IUEQN201504), the International Science & Technology Cooperation Program of China (2011DFB91710) and Youth Innovation Promotion Association CAS.

Author information

Author notes

    • Yong-Guan Zhu
    •  & Yi Zhao

    These authors contributed equally to this work.

Affiliations

  1. Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China

    • Yong-Guan Zhu
    • , Yi Zhao
    • , Chu-Long Huang
    • , Shen Yu
    • , Yong-Shan Chen
    •  & Jian-Qiang Su
  2. State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China

    • Yong-Guan Zhu
    •  & Si-Yu Zhang
  3. Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China

    • Bing Li
  4. Environmental Biotechnology Laboratory, Department of Civil Engineering, University of Hong Kong, Hong Kong SAR, China

    • Tong Zhang
  5. Department of Biological Sciences, Genes to Geoscience Research Centre, Macquarie University, Sydney, New South Wales 2109, Australia

    • Michael R. Gillings

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Contributions

Y.-G.Z. and J.-Q.S. designed the project. S.Y. and Y.-S.C. performed sediment sampling. Y.Z. performed ARGs quantification and data analysis with J.Q.S. B.L. conducted network analysis. S.-Y.Z. conducted distance-decay analysis. C.-L.H. and Y.Z. collected the socio-economic data. Y.-G.Z. and Y.Z. wrote the manuscript with contributions from M.R.G. Y.-G.Z., J.-Q.S. and T.Z. provided conceptual advice. J.-Q.S. and M.R.G. revised the paper. All authors discussed and interpreted the results and contributed to the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Yong-Guan Zhu or Jian-Qiang Su.

Supplementary information

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    Supplementary Information

    Supplementary Tables 1–11; Supplementary Figures 1–15; Supplementary Discussion and Tables.

Excel files

  1. 1.

    Supplementary Data 1

    Normalized gene copy numbers (copies per 4,000 bacterial cells). The data are the ratio of gene copy numbers to 16S gene copy numbers subsequently multiplied by 4,000.

  2. 2.

    Supplementary Data 2

    Primer sets (296) used in this study.

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DOI

https://doi.org/10.1038/nmicrobiol.2016.270

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