Antimicrobial Resistance in Water Systems: From Environmental Drivers to Detection and Mitigation

Background

Antimicrobial resistance (AMR) is a defining global health crisis, with waterborne transmission representing a critical dissemination pathway. Aquatic environments receive AMR inputs from agricultural runoff, wastewater effluents, pharmaceutical discharge, and hospital waste. Resistant microorganisms and antibiotic resistance genes (ARGs) persist and spread through horizontal gene transfer, biofilm formation, and selective pressure from residual antibiotics and co-selective agents, including potentially toxic elements. Interactions between microbial kingdoms, particularly protists and bacteria, create protected niches that amplify AMR persistence and dissemination across environmental and engineered water systems. Existing monitoring frameworks are not yet equipped to capture the full diversity and clinical relevance of waterborne AMR threats. The convergence of environmental microbiology, advanced biosensing, and wastewater-based epidemiology offers transformative opportunities to characterize, detect, and mitigate AMR across the water cycle.


Goals

Despite growing recognition of water systems as key conduits for AMR dissemination, critical gaps persist across the detection-to-mitigation pipeline. Field-deployable diagnostic platforms capable of rapid, specific, and sensitive detection of ARGs and resistant pathogens in complex water matrices remain limited in accessibility and validation. Population-level surveillance of AMR through wastewater-based epidemiology is advancing rapidly but lacks standardized methods and integrated frameworks that connect environmental signals to public health outcomes. Mechanistic understanding of how abiotic and biotic factors in aquatic environments modulate AMR gene transfer, persistence, and evolution remains incomplete. This Research Topic aims to bridge these gaps by uniting three complementary scientific communities: environmental microbiologists characterizing AMR mechanisms and ecological drivers; engineers and analytical scientists developing biosensor and diagnostic platforms for field-deployable AMR detection; and epidemiologists and water quality scientists applying wastewater-based surveillance to track AMR at the community and population scale. Together, these contributions will define a rigorous, translational knowledge base to inform evidence-based water management, public health policy, and One Health frameworks for AMR mitigation globally.



Scope and Information for Authors

This Research Topic welcomes original research, reviews, methods papers, perspectives, and hypothesis and theory articles addressing AMR in freshwater, wastewater, drinking water, aquaculture systems, and aquatic ecosystems. Specific themes of interest include:

• Molecular epidemiology of ARGs and mobile genetic elements in water environments

• Environmental reservoirs of AMR including free-living protists, biofilms, and sediments

• Emerging detection and diagnostic technologies for AMR surveillance in water matrices, including CRISPR-based diagnostics, digital PCR, sequencing-based approaches (metagenomics, amplicon sequencing, and targeted nanopore sequencing), electrochemical biosensors, optical and colorimetric platforms, lateral flow assays, and portable or field-deployable sensor systems

• Wastewater-based epidemiology as a surveillance tool for community-level AMR monitoring

• Fate and removal of resistant microorganisms and ARGs in water and aquaculture treatment systems

• One Health approaches integrating human, animal, and environmental AMR data

• Policy-relevant frameworks for AMR surveillance in low-resource and aquaculture settings

Studies combining novel detection technologies with environmental validation are particularly encouraged. Purely descriptive resistome surveys without clear mechanistic hypotheses or experimental validation fall outside the scope of this collection.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Community Case Study
• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Community Case Study
• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Original Research
• Perspective
• Systematic Review
• Technology and Code

Keywords: Antimicrobial resistance, antibiotic resistance genes, water-based surveillance, CRISPR diagnostics, wastewater-based epidemiology, environmental reservoirs, biosensors, One Health

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.