Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture

Shrimp aquaculture environments are a natural reservoir of multiple antibiotic resistance genes (ARGs) due to the overuse antibiotics. Nowadays, prevalence these kinds emerging contaminants in shrimp is still unclear. In this study, high-throughput sequencing techniques were used analyze distribution ARGs and mobile genetic elements (MGEs), bacterial communities, their correlations water sediment samples two types typical (Procambarus clarkii Macrobrachium rosenbergii) freshwater environments. A total 318 ARG subtypes within 19 detected all samples. The biodiversity relative abundance showed much higher levels compared from ponds study area. Bacitracin (17.44–82.82%) multidrug (8.57–49.70%) dominant P. ponds, while sulfonamide (26.33–39.59%) bacitracin (12.75–37.11%) M. rosenbergii ponds. Network analysis underlined complex co-occurrence patterns between communities ARGs. Proteobacteria, Cyanobacteria, Actinobacteria exhibited high samples, which C39 (OTU25355) Hydrogenophaga (OTU162961) played important roles dissemination variation based on strong connections communities. Furthermore, pathogens (e.g., Aeromonadaceae (OTU195200) Microbacteriaceae (OTU16033)), potential hosts for various ARGs, may accelerate propagation be harmful human health via horizontal gene transfer mediated by MGEs. Variation partitioning further confirmed that MGEs most crucial contributor (74.76%) driving resistome alteration. This help us understand non-ignorable among diversity,