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Continental-scale pollution of estuaries with antibiotic resistance genes

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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Figure 1: Distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in estuarine sediment samples along the coast of China.
Figure 2: ARG profiles in estuarine sediments.
Figure 3: Correlation of total absolute abundance of ARGs with total absolute abundance of transposases and that of the class 1 integron-integrase gene (intI1).
Figure 4: Network analysis depicting co-occurrence patterns among antibiotic resistance genes, transposases and the class 1 integron-integrase gene (intI1).
Figure 5: Partial redundancy analysis (pRDA) differentiating the effects of environmental factors, bacterial community and anthropogenic factors (including antibiotic concentration and socio-economic parameters) on ARG structures in Chinese estuary samples.

References

  1. Culliton, T. J. Population: distribution, density, and growth (State of the Coast Report, NOAA, 1998); http://oceanservice.noaa.gov/websites/retiredsites/sotc_pdf/POP.PDF.

  2. Lotze, H. K. et al. Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312, 1806–1809 (2006).

    Article  CAS  PubMed  Google Scholar 

  3. He, Q. et al. Economic development and coastal ecosystem change in China. Sci. Rep. 4, 5995 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Da, C., Liu, G. & Yuan, Z. Analysis of HCHs and DDTs in a sediment core from the Old Yellow River estuary, China. Ecotoxicol. Environ. Saf. 100, 171–177 (2014).

    Article  CAS  PubMed  Google Scholar 

  5. Wu, G., Shang, J., Pan, L. & Wang, Z. Heavy metals in surface sediments from nine estuaries along the coast of Bohai Bay, Northern China. Mar. Pollut. Bull.. 82, 194–200 (2014).

    Article  CAS  PubMed  Google Scholar 

  6. Pruden, A., Pei, R., Storteboom, H. & Carlson, K. H. Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environ. Sci. Technol. 40, 7445–7450 (2006).

    Article  CAS  PubMed  Google Scholar 

  7. Knapp, C. W., Dolfing, J., Ehlert, P. A. & Graham, D. W. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ. Sci. Technol. 44, 580–587 (2009).

    Article  CAS  Google Scholar 

  8. Segawa, T. et al. Distribution of antibiotic resistance genes in glacier environments. Environ. Microbiol. Rep. 5, 127–134 (2013).

    Article  CAS  PubMed  Google Scholar 

  9. Drudge, C. N. et al. Diversity of integron- and culture-associated antibiotic resistance genes in freshwater floc. Appl. Environ. Microbiol. 78, 4367–4372 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. McKinney, C. W. & Pruden, A. Ultraviolet disinfection of antibiotic resistant bacteria and their antibiotic resistance genes in water and wastewater. Environ. Sci. Technol. 46, 13393–13400 (2012).

    Article  CAS  PubMed  Google Scholar 

  11. Wang, F. H. et al. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. Environ Sci Technol. 48, 9079–9085 (2014).

    Article  CAS  PubMed  Google Scholar 

  12. Ouyang, W. Y., Huang, F. Y., Zhao, Y., Li, H. & Su, J. Q. Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China. Appl. Microbiol. Biotechnol. 99, 5697–5707 (2015).

    Article  CAS  PubMed  Google Scholar 

  13. Czekalski, N., Gascon Diez, E. & Burgmann, H. Wastewater as a point source of antibiotic-resistance genes in the sediment of a freshwater lake. ISME J. 8, 1381–1390 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Gaze, W. H. et al. Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment. ISME J. 5, 1253–1261 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Amos, G. C., Zhang, L., Hawkey, P. M., Gaze, W. H. & Wellington, E. M. Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes. Vet. Microbiol. 171, 441–447 (2014).

    Article  CAS  PubMed  Google Scholar 

  16. Khan, G. A., Berglund, B., Khan, K. M., Lindgren, P.-E. & Fick, J. Occurrence and abundance of antibiotics and resistance genes in rivers, canal and near drug formulation facilities—a study in Pakistan. PLoS ONE 8, e62712 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Zhang, Q. Q., Ying, G. G., Pan, C. G., Liu, Y. S. & Zhao, J. L. Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance. Environ. Sci. Technol. 49, 6772–6782 (2015).

    Article  CAS  PubMed  Google Scholar 

  18. Kolpin, D. W. et al. Pharmaceuticals, hormones, and other organic wastewater contaminants in US streams, 1999–2000: a national reconnaissance. Environ. Sci. Technol. 36, 1202–1211 (2002).

    Article  CAS  PubMed  Google Scholar 

  19. Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).

    Article  CAS  PubMed  Google Scholar 

  20. Chen, B., Liang, X., Huang, X., Zhang, T. & Li, X. Differentiating anthropogenic impacts on ARGs in the Pearl River estuary by using suitable gene indicators. Water Res. 47, 2811–2820 (2013).

    Article  CAS  PubMed  Google Scholar 

  21. Forsberg, K. J. et al. Bacterial phylogeny structures soil resistomes across habitats. Nature 509, 612–616 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Michael, I. et al. Urban wastewater treatment plants as hotspots for the release of antibiotics in the environment: a review. Water Res. 47, 957–995 (2013).

    Article  CAS  PubMed  Google Scholar 

  23. Cytryn, E. The soil resistome: the anthropogenic, the native, and the unknown. Soil Biol. Biochem. 63, 18–23 (2013).

    Article  CAS  Google Scholar 

  24. Partridge, S. R., Tsafnat, G., Coiera, E. & Iredell, J. R. Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol. Rev. 33, 757–784 (2009).

    Article  CAS  PubMed  Google Scholar 

  25. Newman, M. E. Modularity and community structure in networks. Proc. Natl Acad. Sci. USA 103, 8577–8582 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhu, Y. G. et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl Acad. Sci. USA 110, 3435–3440 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Oppegaard, H., Steinum, T. M. & Wasteson, Y. Horizontal transfer of a multi-drug resistance plasmid between coliform bacteria of human and bovine origin in a farm environment. Appl. Environ. Microbiol. 67, 3732–3734 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Zhang, R., Eggleston, K., Rotimi, V. & Zeckhauser, R. J. Antibiotic resistance as a global threat: evidence from China, Kuwait and the United States. Global. Health 2, 6 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  29. RUBIN, M. et al. Gram-positive infections and the use of vancomycin in 550 episodes of fever and neutropenia. Ann. Intern. Med. 108, 30–35 (1988).

    Article  CAS  PubMed  Google Scholar 

  30. D'Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Gilmore, M. S. & Hoch, J. A. Antibiotic resistance: a vancomycin surprise. Nature 399, 524–527 (1999).

    Article  CAS  PubMed  Google Scholar 

  32. Lauderdale, T. L. et al. Effect of banning vancomycin analogue avoparcin on vancomycin-resistant enterococci in chicken farms in Taiwan. Environ. Microbiol. 9, 819–823 (2007).

    Article  PubMed  Google Scholar 

  33. Perry, J. A., Westman, E. L. & Wright, G. D. The antibiotic resistome: what's new? Curr. Opin. Microbiol. 21, 45–50 (2014).

    Article  CAS  PubMed  Google Scholar 

  34. Gillings, M. R. et al. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9, 1269–1279 (2015).

    Article  CAS  PubMed  Google Scholar 

  35. Gillings, M. et al. The evolution of class 1 integrons and the rise of antibiotic resistance. J. Bacteriol. 190, 5095–5100 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Gillings, M. R. Integrons: past, present, and future. Microbiol. Mol. Biol. Rev. 78, 257–277 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Su, J. Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49, 7356–7363 (2015).

    Article  CAS  PubMed  Google Scholar 

  38. Dini-Andreote, F., Stegen, J. C., van Elsas, J. D. & Salles, J. F. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc. Natl Acad. Sci. USA 112, E1326–E1332 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Gillings, M. R. & Stokes, H. Are humans increasing bacterial evolvability? Trends Ecol. Evol. 27, 346–352 (2012).

    Article  PubMed  Google Scholar 

  40. Stokes, H. W. & Gillings, M. R. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS. Microbiol. Rev. 35, 790–819 (2011).

    Article  CAS  PubMed  Google Scholar 

  41. Liu, Y.-Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet. Infect. Dis. 16, 161–168 (2016).

    Article  PubMed  CAS  Google Scholar 

  42. Huang, Y. et al. Simultaneous extraction of four classes of antibiotics in soil, manure and sewage sludge and analysis by liquid chromatography-tandem mass spectrometry with the isotope-labelled internal standard method. Anal. Methods 5, 3721 (2013).

    Article  CAS  Google Scholar 

  43. Looft, T. et al. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl Acad. Sci. USA 109, 1691–1696 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Xu, H.-J. et al. Biochar impacts soil microbial community composition and nitrogen cycling in an acidic soil planted with rape. Environ. Sci. Technol. 48, 9391–9399 (2014).

    Article  CAS  PubMed  Google Scholar 

  45. Kuczynski, J. et al. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Bioinformatics 10, 10.7 (2011).

    Google Scholar 

  46. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    Article  CAS  PubMed  Google Scholar 

  47. Klappenbach, J. A., Saxman, P. R., Cole, J. R. & Schmidt, T. M. Rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 29, 181–184 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kolde, R. Pheatmap: pretty heatmaps, R package v. 16 (R Foundation for Statistical Computing, 2012).

  49. Li, B. et al. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 9, 2490–2502 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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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

Authors and Affiliations

Authors

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.

Corresponding authors

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

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Tables 1–11; Supplementary Figures 1–15; Supplementary Discussion and Tables. (PDF 1680 kb)

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. (XLSX 38 kb)

Supplementary Data 2

Primer sets (296) used in this study. (XLSX 27 kb)

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Zhu, YG., Zhao, Y., Li, B. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat Microbiol 2, 16270 (2017). https://doi.org/10.1038/nmicrobiol.2016.270

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

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