Metagenomic analysis revealed the prevalence of antibiotic resistance genes in the gut and living environment of freshwater shrimp.

Antibiotic resistance disseminating from animals and their environments is a public issue that poses significant threats to human health. In the present study, the diversity and abundance of antibiotic resistance genes (ARGs) in 15 samples from the guts and related aquaculture environments (water and sediment) of shrimp were investigated. In total, 60 ARGs, 102 ARGs and 67 ARGs primarily belonging to 13, 15 and 15 different types were detected in the shrimp gut, pond water and sediment samples, respectively. Efflux pump and target modification were the predominant resistance mechanisms in all samples. It was found that Aeromonas, Yersinia and Clostridium XlVb were significantly correlated with the distribution of the ARGs. Besides, the relative abundance of ARGs was positively correlated with the levels of mobile genetic elements (MGEs). Moreover, variation partitioning analysis showed that MGEs, contributing to 74.46% of the resistome variation, played an important role in the affecting of the antibiotic resistome than the bacterial communities and their joint effects. Collectively, this study provides comprehensive information to better understand the ARG dissemination in aquaculture environments and to improve the ecological management of aquatic ecosystems.