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

Abstract

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 genenormalized) 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 macrolidelincosamide-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.

Population-level impacts of antibiotic usage on the human gut microbiome

“…Previous studies have shown a higher abundance of ARGs in microbiomes from individuals deriving from countries with higher antibiotic consumption 21,24 , but we have demonstrated a direct correlation between consumption rates and ARG levels in the microbiome at a global scale for healthy antibiotic free individuals. This is in contrast to global wastewater metagenome surveys of ARGs, which failed to find a clear link between antibiotic consumption and ARG abundance 44,45 . This highlights the importance of sampling microbiomes directly from individuals rather than from waste streams where additional factors may be impacting abundance.…”

Metatranscriptomic analysis of wastewater sites reveals a high abundance of antimicrobial resistance genes from hospital wastewater

“…Sulfonamide ARGs have been detected in wastewater effluents at varying concentrations independent of the environmental conditions [28,29]. The identified core ARGs have also been previously reported when assessing the global resistosome [30]. The presence of these core ARGs, such as sul1, sul2 , aph(6)-ld, and aph(’3’)-lb, could be linked to prolonged clinical use of sulfonamides and aminoglycosides both within and outside clinical settings.…”

Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens

“…The viral taxa were dominated by bacteriophage sequences with a minor nonbacteriophage viral component. Among bacteriophages detected, the families associated with enteric bacteria ( 23 ) were the most abundant, Podoviridae , Myoviridae , and Siphoviridae ( Fig. 2a ).…”

“…Shotgun MGS can help mitigate some of the drawbacks of other approaches, including low cultivability of most WWTP microbes, low primer efficiencies and PCR bias of amplicon approaches, and the difficulty of taxonomic identification using microscopy ( 19 , 21 ). MGS can help better understand the processes within WWTPs, providing information on the relationships and interactions between microflora and physicochemical factors ( 22 , 23 ). Shotgun MGS studies have also led to the identification of uncultured WWTP microbes that are of environmental, biotechnological, and pharmaceutical importance ( 21 , 22 ).…”