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Background <p>Wastewater occupies a critical nexus at the confluence of human activity, environmental change, and microbial evolution. This review synthesizes the emerging role of wastewater as a mirror of community health and a driver of microbial and resistome restructuring across environmental compartments. Wastewater systems harbor diverse biological and chemical markers, including pathogens, antimicrobial resistance genes (ARGs), pharmaceuticals, and nutrients, reflecting dynamic population health, agricultural practices, and socioeconomic activities. Advanced metagenomic approaches reveal that wastewater treatment plants (WWTPs) are global hotspots for the selection and spread of resistant bacteria, mobile genetic elements, and opportunistic pathogens, even after secondary or tertiary treatment.</p> Main body <p>The reuse of treated wastewater for irrigation and other applications enhances water security and can support soil fertility and crop production, but it also distributes dense microbial communities and antimicrobial resistance determinants into soils, crops, and food animal microbiomes. These resistome shifts create interconnected One Health consequences by influencing food safety, livestock health, and human infection risk, with knock‑on effects on agricultural productivity and trade. Metagenomic wastewater surveillance offers a pooled, early‑warning view of antimicrobial resistance trends that complement conventional clinical monitoring and reveal environmental transmission pathways that are otherwise difficult to capture. However, current policies and reuse guidelines only partially integrate resistome information, leaving critical gaps in risk management for reclaimed water, agricultural systems, and downstream populations.</p> Conclusion <p>This review advocates multi-faceted actions: optimizing WWTP operations and effluent quality; guiding agricultural and livestock practices using reclaimed-water profiles; implementing robust microbiome and resistome surveillance; and harmonizing policy frameworks at local and global scales. Collaborative efforts are needed to transform wastewater from a source of risk into a strategic resource for resilient agriculture, sustainable water management, and global public health in the face of escalating water scarcity and antimicrobial resistance. By bringing together mechanistic microbiome insights, evidence from risk‑assessment studies, and policy‑oriented analyses, this synthesis highlights wastewater’s pivotal role in shaping environmental microbiomes and resilience within rapidly changing socioecological systems.</p>

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Wastewater Metagenomics and Resistomics Surveillance: A One Health Framework for Policy and Agricultural Sustainability

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年7月24日

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  • Aya G. Atalla,
  • Shaymaa Abdelmalek

摘要

Background

Wastewater occupies a critical nexus at the confluence of human activity, environmental change, and microbial evolution. This review synthesizes the emerging role of wastewater as a mirror of community health and a driver of microbial and resistome restructuring across environmental compartments. Wastewater systems harbor diverse biological and chemical markers, including pathogens, antimicrobial resistance genes (ARGs), pharmaceuticals, and nutrients, reflecting dynamic population health, agricultural practices, and socioeconomic activities. Advanced metagenomic approaches reveal that wastewater treatment plants (WWTPs) are global hotspots for the selection and spread of resistant bacteria, mobile genetic elements, and opportunistic pathogens, even after secondary or tertiary treatment.

Main body

The reuse of treated wastewater for irrigation and other applications enhances water security and can support soil fertility and crop production, but it also distributes dense microbial communities and antimicrobial resistance determinants into soils, crops, and food animal microbiomes. These resistome shifts create interconnected One Health consequences by influencing food safety, livestock health, and human infection risk, with knock‑on effects on agricultural productivity and trade. Metagenomic wastewater surveillance offers a pooled, early‑warning view of antimicrobial resistance trends that complement conventional clinical monitoring and reveal environmental transmission pathways that are otherwise difficult to capture. However, current policies and reuse guidelines only partially integrate resistome information, leaving critical gaps in risk management for reclaimed water, agricultural systems, and downstream populations.

Conclusion

This review advocates multi-faceted actions: optimizing WWTP operations and effluent quality; guiding agricultural and livestock practices using reclaimed-water profiles; implementing robust microbiome and resistome surveillance; and harmonizing policy frameworks at local and global scales. Collaborative efforts are needed to transform wastewater from a source of risk into a strategic resource for resilient agriculture, sustainable water management, and global public health in the face of escalating water scarcity and antimicrobial resistance. By bringing together mechanistic microbiome insights, evidence from risk‑assessment studies, and policy‑oriented analyses, this synthesis highlights wastewater’s pivotal role in shaping environmental microbiomes and resilience within rapidly changing socioecological systems.