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Nat Commun. 2019 Mar 8;10(1):1124. doi: 10.1038/s41467-019-08853-3.

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

Author information

1
National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
2
Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK.
3
Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK.
4
Viroscience, Erasmus Medical Center, Rotterdam, 3015, The Netherlands.
5
RIKILT Wageningen University and Research, Wageningen, 6708, The Netherlands.
6
National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands.
7
Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
8
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK.
9
Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, 08100, Malaysia.
10
World Health Organization, Geneva, 1202, Switzerland.
11
National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark. fmaa@food.dtu.dk.

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.

PMID:
30850636
PMCID:
PMC6408512
DOI:
10.1038/s41467-019-08853-3
[Indexed for MEDLINE]
Free PMC Article

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