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.

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Rene S. Hendriksen1, Patrick Munk 1, Patrick Njage1, Bram van Bunnik 2, Luke McNally3, Oksana Lukjancenko1, Timo Röder1, David Nieuwenhuijse4, Susanne Karlsmose Pedersen1
, Jette Kjeldgaard1, Rolf S. Kaas1, Philip Thomas Lanken Conradsen Clausen1, Josef Korbinian Vogt1, Pimlapas Leekitcharoenphon1,Milou G.M. van de Schans5, Tina Zuidema5, Ana Maria de Roda Husman6, Simon Rasmussen 7,Bent Petersen7, The Global Sewage Surveillance project consortium#, Clara Amid8, Guy Cochrane8,Thomas Sicheritz-Ponten9, Heike Schmitt6, Jorge Raul Matheu Alvarez10, Awa Aidara-Kane10, Sünje J. Pamp1, Ole Lund7, Tine Hald1, Mark Woolhouse2, Marion P. Koopmans4, Håkan Vigre1, Thomas Nordahl Petersen1 &Frank M. Aarestrup 1