Compartment-specific host association and mobility shape ARG risk in aquaculture systems

Area of Science:

• Environmental microbiology
• Aquatic ecology
• Antimicrobial resistance

Background:

• Antimicrobial resistance genes (ARGs) in aquaculture pose significant environmental and public health risks.
• Assessing ARG risk solely by abundance is insufficient; host association and mobility potential are critical factors.
• Understanding how ecological compartments influence ARG characteristics is vital for risk assessment in aquaculture.

Purpose of the Study:

• To investigate the influence of ecological compartments (water vs. sediment) on ARG host background, mobility, and risk in aquaculture systems.
• To identify key environmental factors predicting ARG mobility.
• To develop a risk-oriented framework for prioritizing surveillance and intervention strategies.

Main Methods:

• Analysis of 437 metagenomes from freshwater and marine aquaculture water and sediment samples.
• Resistome profiling, host assignment, genetic localization, and ARG-MGE co-occurrence analysis.
• Application of a four-tier risk framework and machine learning (LightGBM) for risk and mobility prediction.

Main Results:

• Detected 1413 nonredundant ARG subtypes across 28 classes.
• Water compartments exhibited higher ARG diversity, stronger associations with opportunistic pathogens, and greater mobility signals compared to sediment.
• High-risk ARGs were predominantly found in water, with Rank I ARGs exclusive to this compartment and significant water-specific Rank II ARGs.
• Salinity, temperature, and pH were identified as key predictors of ARG mobility.

Conclusions:

• ARG risk in aquaculture is a complex interplay of ecological compartment, host association, and mobility potential.
• Aquatic environments, specifically water, serve as the primary high-risk interface for ARGs.
• The developed risk-oriented framework offers a transferable approach for targeted surveillance and intervention in aquaculture.