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Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Author

Listed:
  • Patrick Munk

    (Technical University of Denmark, Kgs)

  • Christian Brinch

    (Technical University of Denmark, Kgs)

  • Frederik Duus Møller

    (Technical University of Denmark, Kgs)

  • Thomas N. Petersen

    (Technical University of Denmark, Kgs)

  • Rene S. Hendriksen

    (Technical University of Denmark, Kgs)

  • Anne Mette Seyfarth

    (Technical University of Denmark, Kgs)

  • Jette S. Kjeldgaard

    (Technical University of Denmark, Kgs)

  • Christina Aaby Svendsen

    (Technical University of Denmark, Kgs)

  • Bram Bunnik

    (University of Edinburgh)

  • Fanny Berglund

    (University of Gothenburg)

  • D. G. Joakim Larsson

    (University of Gothenburg)

  • Marion Koopmans

    (Department of Viroscience, Erasmus MC)

  • Mark Woolhouse

    (University of Edinburgh)

  • Frank M. Aarestrup

    (Technical University of Denmark, Kgs)

Abstract

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Suggested Citation

  • Patrick Munk & Christian Brinch & Frederik Duus Møller & Thomas N. Petersen & Rene S. Hendriksen & Anne Mette Seyfarth & Jette S. Kjeldgaard & Christina Aaby Svendsen & Bram Bunnik & Fanny Berglund & , 2022. "Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34312-7
    DOI: 10.1038/s41467-022-34312-7
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    Cited by:

    1. Ágnes Becsei & Alessandro Fuschi & Saria Otani & Ravi Kant & Ilja Weinstein & Patricia Alba & József Stéger & Dávid Visontai & Christian Brinch & Miranda Graaf & Claudia M. E. Schapendonk & Antonio Ba, 2024. "Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Claas Kirchhelle, 2023. "The Antibiocene – towards an eco-social analysis of humanity’s antimicrobial footprint," Palgrave Communications, Palgrave Macmillan, vol. 10(1), pages 1-12, December.
    3. Peter J. Diebold & Matthew W. Rhee & Qiaojuan Shi & Nguyen Vinh Trung & Fayaz Umrani & Sheraz Ahmed & Vandana Kulkarni & Prasad Deshpande & Mallika Alexander & Ngo Hoa & Nicholas A. Christakis & Najee, 2023. "Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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