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

Patrick Munk*, Christian Brinch, Global Sewage Surveillance Consortium, Frederik Duus Møller, Thomas N. Petersen, Rene S. Hendriksen, Anne Mette Seyfarth, Jette S. Kjeldgaard, Christina Aaby Svendsen, Bram van Bunnik, Fanny Berglund, D. G.Joakim Larsson, Marion Koopmans, Mark Woolhouse, Frank M. Aarestrup

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

58 Citations (Scopus)
14 Downloads (Pure)

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.

Original languageEnglish
Article number7251
Pages (from-to)7251
Number of pages1
JournalNature Communications
Volume13
Issue number1
DOIs
Publication statusPublished - 1 Dec 2022

Bibliographical note

Funding Information:
We would like to thank everyone who has helped with sampling, shipping, and the logistics of transporting sewage to Denmark since the beginning of the pilot project including the Drainage Services Department, The Government of the Hong Kong Special Administrative Region. We also want to thank the system administrators of Computerome, for troubleshooting, guidance, and compute resources. A special thanks to the laboratory technicians at DTU who worked hard to receive and treat the incoming sewage and Elena Lavinia Diaconu (IZSLT). Lastly, we would like to acknowledge the Novo Nordisk Foundation (Grant: NNF16OC0021856: Global Surveillance of Antimicrobial Resistance) and the European Union’s Horizon 2020 research and innovation programme (Grant: 874735) for funding the work.

Funding Information:
We would like to thank everyone who has helped with sampling, shipping, and the logistics of transporting sewage to Denmark since the beginning of the pilot project including the Drainage Services Department, The Government of the Hong Kong Special Administrative Region. We also want to thank the system administrators of Computerome, for troubleshooting, guidance, and compute resources. A special thanks to the laboratory technicians at DTU who worked hard to receive and treat the incoming sewage and Elena Lavinia Diaconu (IZSLT). Lastly, we would like to acknowledge the Novo Nordisk Foundation (Grant: NNF16OC0021856: Global Surveillance of Antimicrobial Resistance) and the European Union’s Horizon 2020 research and innovation programme (Grant: 874735) for funding the work.

Publisher Copyright:
© 2022, The Author(s).

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