Antibiotics-Induced Transfer of Resistance Genes and Emergence of New Resistant Bacteria in Red Swamp Crayfish Guts and Culture Sediments

Abstract Background Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, which could lead to treatment failure of bacterial infections. The aquaculture, which is polluted by current and past over-used antibiotics, is considered as a notorious reservoir of ARGs. However, the fact on the mobilization of ARGs in aquaculture systems, and their contributions to the emergence and dissemination of antibiotic resistant bacteria (ARB) remain elusive. Results We used crayfish as an aquatic animal model to analyze longitudinal changes of bacterial communities, ARGs and mobile gene elements (MGEs) in the gut and sediment samples in response to enrofloxacin administration. Our metagenomic analysis revealed significant perturbations of the microbiota and ARGs compositions in the gut compared to those in sediments, which is characterized by a obviously delayed recovery after antibiotic administration. The significantly positive correlation between the total abundance of ARGs and MGEs was observed and MGEs were frequently located close to ARGs in genomes of the bacteria from Enterobacteriaceae. These mobile ARGs had high intracellular and intercellular transferred potential by transposon-mediated recombination in gut and sediment samples in the pressure of antibiotics. In addition, multiple antibiotic resistant pathogens of Enterobacteriaceae and other new ARBs had emerged and proliferating under the pressure of antibiotic. Conclusion Our findings showed that MGEs facilitated the diffuse of ARGs through horizontal gene transfer mainly in the bacteria from Enterobacteriaceae family in gut and sediment environments. Especially, the transposase-mediated recombination was the major driver of the transfer for ARGs in the pressure of antibiotics. Simultaneously, the changes in community composition as the emerged and proliferating of the multiple resistant pathogenic bacteria played a crucial role in the augment of various ARGs.