Reducing antibiotic resistance gene risks in freshwater aquaculture: Comparative insights from rice-crayfish co-culture and traditional models in China

Antibiotic resistance genes (ARGs) in aquaculture ecosystems pose a threat to global public health under the “One Health” framework. However, mechanisms driving ARG dissemination across aquaculture models remain unclear. This study investigated ARG abundance, risks, and microbial communities in three typical freshwater aquaculture models of China—rice-crayfish coculture ponds (RCFPs), fish ponds (FPs), and crab-crayfish coculture ponds (CCFPs)—using high-throughput qPCR and 16S rRNA sequencing. RCFPs exhibited the lowest ARG abundance and risk in water compared to CCFPs and FPs. The rainy season showed significantly higher ARG levels ( P < 0.05), linked to elevated temperatures, nutrients, and antibiotics. Mobile genetic elements (MGEs) primarily shaped ARG profiles in water, while environmental factors (e.g., total phosphorus, ammonium nitrogen, oxidation‒reduction potential) and antibiotics (e.g., erythromycin, oxytetracycline, tetracycline, sulfamethoxazole, enrofloxacin) drove ARG profiles in sediment. Deterministic processes dominated bacterial community assembly (64.56% in water, 60.33% in sediment), with bacterial communities in water more sensitive to environmental changes. Pathogenic bacteria were potential hosts for a variety of ARGs. A novel risk assessment framework integrating ARG-related indicators (absolute abundance, detection frequency, mobility potential) and the pathogenicity risk of ARG hosts identified mexF , sul2 , ereA , aadA , and floR as high-risk subtypes. These findings highlight the role of RCFPs in mitigating ARG pollution in aquaculture, offering ecological insights and supporting sustainable aquaculture practices to combat antimicrobial resistance.