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

• Published in: Environmental science & technology 2022-11, Vol.56 (21), p.14982-14993
• Main Authors: Prieto Riquelme, Maria Virginia, Garner, Emily, Gupta, Suraj, Metch, Jake, Zhu, Ni, Blair, Matthew F., Arango-Argoty, Gustavo, Maile-Moskowitz, Ayella, Li, An-dong, Flach, Carl-Fredrik, Aga, Diana S., Nambi, Indumathi M., Larsson, D. G. Joakim, Bürgmann, Helmut, Zhang, Tong, Pruden, Amy, Vikesland, Peter J.
• Format: Article
• Language: English
• Subjects: Antibiotic resistance; antibiotic-resistance genes; Antibiotics; antimicrobial resistance; bacterial; Contaminants in Aquatic and Terrestrial Environments; curation; diversity; Drug resistance; Engineering; environment; Environmental Sciences & Ecology; Genes; Infectious Medicine; Infektionsmedicin; Metagenomics; Metal concentrations; microbiome; Multidrug resistance; prevalence; resistome; rRNA 16S; Sales; Sewage; Surveillance; treatment-plant; Trends; Wastewater; wastewater-based surveillance (WBS)
• ISSN: 0013-936X; 1520-5851; 1520-5851
• DOI: 10.1021/acs.est.1c08673

Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies 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 comparability and sensitivity to local/regional factors.