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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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    1. Alyssa G. Kent & Albert C. Vill & Qiaojuan Shi & Michael J. Satlin & Ilana Lauren Brito, 2020. "Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    2. Jinxin Liu & Diana H. Taft & Maria X. Maldonado-Gomez & Daisy Johnson & Michelle L. Treiber & Danielle G. Lemay & Edward J. DePeters & David A. Mills, 2019. "The fecal resistome of dairy cattle is associated with diet during nursing," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    3. Erik Volz & Swapnil Mishra & Meera Chand & Jeffrey C. Barrett & Robert Johnson & Lily Geidelberg & Wes R. Hinsley & Daniel J. Laydon & Gavin Dabrera & Áine O’Toole & Robert Amato & Manon Ragonnet-Cron, 2021. "Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England," Nature, Nature, vol. 593(7858), pages 266-269, May.
    4. Rene S. Hendriksen & Patrick Munk & Patrick Njage & Bram Bunnik & Luke McNally & Oksana Lukjancenko & Timo Röder & David Nieuwenhuijse & Susanne Karlsmose Pedersen & Jette Kjeldgaard & Rolf S. Kaas & , 2019. "Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    5. Sheetal R. Modi & Henry H. Lee & Catherine S. Spina & James J. Collins, 2013. "Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome," Nature, Nature, vol. 499(7457), pages 219-222, July.
    6. Chris S. Smillie & Mark B. Smith & Jonathan Friedman & Otto X. Cordero & Lawrence A. David & Eric J. Alm, 2011. "Ecology drives a global network of gene exchange connecting the human microbiome," Nature, Nature, vol. 480(7376), pages 241-244, December.
    7. Mohammad Bahram & Falk Hildebrand & Sofia K. Forslund & Jennifer L. Anderson & Nadejda A. Soudzilovskaia & Peter M. Bodegom & Johan Bengtsson-Palme & Sten Anslan & Luis Pedro Coelho & Helery Harend & , 2018. "Structure and function of the global topsoil microbiome," Nature, Nature, vol. 560(7717), pages 233-237, August.
    8. Erica C. Pehrsson & Pablo Tsukayama & Sanket Patel & Melissa Mejía-Bautista & Giordano Sosa-Soto & Karla M. Navarrete & Maritza Calderon & Lilia Cabrera & William Hoyos-Arango & M. Teresita Bertoli & , 2016. "Interconnected microbiomes and resistomes in low-income human habitats," Nature, Nature, vol. 533(7602), pages 212-216, May.
    9. Zhenyan Zhang & Qi Zhang & Tingzhang Wang & Nuohan Xu & Tao Lu & Wenjie Hong & Josep Penuelas & Michael Gillings & Meixia Wang & Wenwen Gao & Haifeng Qian, 2022. "Assessment of global health risk of antibiotic resistance genes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
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    Cited by:

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    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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