Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes

Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent method-ologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparabyility and sensitivity to local/regional factors.

Automated summary

This study presents a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage. The results show that there are shared antibiotic resistance genes (ARGs) across different regions/communities, and certain ARGs can be used as discriminatory markers to differentiate Asian and European/US resistomes. The study also reveals discrepancies between measured antibiotic concentrations and public sales data, suggesting that wastewater-based surveillance (WBS) can capture additional antibiotic uses that are not accounted for. The WBS approach demonstrated in this study is sensitive to local/regional factors and can provide comparable results across different sites.