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

TLDR

AMR poses a serious global public health threat, yet representative data from healthy populations are difficult to obtain. The study proposes using sewage metagenomics as an ethical, cost‑effective method for continuous global AMR surveillance and prediction. The authors performed metagenomic sequencing of untreated sewage from 79 sites across 60 countries to profile the bacterial resistome. The analysis revealed regional differences in AMR gene abundance and diversity, with socio‑economic, health, and environmental factors strongly predicting AMR levels; antimicrobial use, bacterial taxonomy, cross‑selection, and air travel had limited influence, suggesting that improving sanitation and health could reduce the global AMR burden.

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.