Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

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, Philip Thomas Lanken Conradsen Clausen, Josef Korbinian Vogt, Pimlapas Leekitcharoenphon, Milou G. M. Schans, Tina Zuidema, Ana Maria Roda Husman, Simon Rasmussen, Bent Petersen, Clara Amid, Guy Cochrane, Thomas Sicheritz-Ponten, Heike Schmitt, Jorge Raul Matheu Alvarez, Awa Aidara-Kane, Sünje J. Pamp, Ole Lund, Tine Hald, Mark Woolhouse, Marion P. Koopmans, Håkan Vigre, Thomas Nordahl Petersen and Frank M. Aarestrup ()
Additional contact information
Rene S. Hendriksen: Technical University of Denmark
Patrick Munk: Technical University of Denmark
Patrick Njage: Technical University of Denmark
Bram Bunnik: University of Edinburgh
Luke McNally: University of Edinburgh
Oksana Lukjancenko: Technical University of Denmark
Timo Röder: Technical University of Denmark
David Nieuwenhuijse: Viroscience, Erasmus Medical Center
Susanne Karlsmose Pedersen: Technical University of Denmark
Jette Kjeldgaard: Technical University of Denmark
Rolf S. Kaas: Technical University of Denmark
Philip Thomas Lanken Conradsen Clausen: Technical University of Denmark
Josef Korbinian Vogt: Technical University of Denmark
Pimlapas Leekitcharoenphon: Technical University of Denmark
Milou G. M. Schans: RIKILT Wageningen University and Research
Tina Zuidema: RIKILT Wageningen University and Research
Ana Maria Roda Husman: National Institute for Public Health and the Environment (RIVM)
Simon Rasmussen: Technical University of Denmark
Bent Petersen: Technical University of Denmark
Clara Amid: European Bioinformatics Institute
Guy Cochrane: European Bioinformatics Institute
Thomas Sicheritz-Ponten: AIMST University
Heike Schmitt: National Institute for Public Health and the Environment (RIVM)
Jorge Raul Matheu Alvarez: World Health Organization
Awa Aidara-Kane: World Health Organization
Sünje J. Pamp: Technical University of Denmark
Ole Lund: Technical University of Denmark
Tine Hald: Technical University of Denmark
Mark Woolhouse: University of Edinburgh
Marion P. Koopmans: Viroscience, Erasmus Medical Center
Håkan Vigre: Technical University of Denmark
Thomas Nordahl Petersen: Technical University of Denmark
Frank M. Aarestrup: Technical University of Denmark

Nature Communications, 2019, vol. 10, issue 1, 1-12

Abstract: Abstract Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.

Date: 2019
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-08853-3

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DOI: 10.1038/s41467-019-08853-3

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