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Source-Resolved Wastewater Metagenomics Reveals Distinct Resistome and Virulome Landscapes Across an Urban Wastewater Continuum
Journal article   Open access   Peer reviewed

Source-Resolved Wastewater Metagenomics Reveals Distinct Resistome and Virulome Landscapes Across an Urban Wastewater Continuum

Douha Shouqair, Subham Verma, Rashed Alghafri, Rania Nassar, Lobna Mohamed, Fatima Al Dhaheri, Dean Everett, Ahmed A. Shibl, Jorge Rodríguez, Danesh Moradigaravand, …
Antibiotics (Basel), Vol.15(9), 817
2026
DOI: https://doi.org/10.3390/antibiotics15090817
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Published (Version of Record) Open Access CC BY V4.0

Abstract

antimicrobial resistance wastewater shotgun metagenomics One Health WWTP resistome virulome
Background/Objectives Wastewater-based antimicrobial resistance (AMR) surveillance typically relies on treatment plant influent as a single integrated matrix, obscuring source-specific signals. In arid settings where treated effluent is reused, understanding how resistomes and virulomes are structured across wastewater compartments is essential for One Health monitoring. Methods Shotgun metagenomic sequencing was applied to 57 wastewater samples collected in Dubai, United Arab Emirates, between October 2024 and January 2025. Samples represented nine community sewer nodes, two tertiary-care hospital outflows, and influent and effluent from two wastewater treatment plants (WWTP). Datasets were used for taxonomic, resistome, and virulome profiling. Alpha diversity was compared using Wilcoxon rank-sum tests, beta-diversity differences were assessed using permutational multivariate analysis of variance, and source-associated AMR genes were identified using linear discriminant analysis effect size analysis. Results A total of 1470 bacterial species, 822 antimicrobial resistance genes (ARGs), and 1554 virulence factor genes were identified. Bacterial diversity was significantly lower in WWTP effluent than in other compartments. Hospital wastewater was enriched for class D β-lactamases, including multiple blaOXA variants, whereas community wastewater and WWTP influent shared dominant macrolide and aminoglycoside resistance genes including msr(E), mph(E), strB and aadA1. Despite marked reductions in bacterial diversity after treatment, no significant difference in ARG diversity was observed between WWTP influent and WWTP effluent (p = 0.558), with resistance genes such as blaVEB, msr(E), mph(E) detected in the latter. Virulome profiles shifted from fimbrial gene dominance in untreated sources toward biofilm- and persistence-associated genes in WWTP effluent. ARG alpha diversity varied over time, whereas taxonomic and virulome diversity remained stable. Conclusions Community and influent wastewater capture population-level AMR carriage, hospital outflows concentrate clinically relevant resistance determinants, and WWTP effluent retains resistance markers despite microbial biomass reduction. Compartment-resolved metagenomic surveillance provides a practical One Health framework for identifying high-value monitoring points.

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UN Sustainable Development Goals (SDGs)

This output has contributed to the advancement of the following goals:

#6 Clean Water and Sanitation

Source: SDGs in the Output

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