TEMPORAL ANALYSIS OF MICROBIAL COMMUNITY AND ANTIBIOTIC RESISTANCE DYNAMICS IN A PROPHYLACTICALLY-FED INTENSIVE AQUACULTURE SYSTEM

Excessive use of antibiotics in aquaculture may significantly impact microbial community structure and contribute to antibiotic resistance. In this study, we explored the scope and abundance of antibiotic resistance genes coupled to bacterial community composition in the water column of an intensive aquaculture over an 11-month fish fattening cycle. Fish in the system were prophylactically-treated for 10 days with sulfamethoxazole-trimethoprim, after which antibiotics were not amended. Microbial community composition was monitored at eight central stages of the fish fattening cycle using amplicon sequence of the 16S rRNA gene. In tandem, the resistomes of four representative samples were established by comparing water column metagenomes to the CARD antibiotic resistance gene database. Subsequentally, qPCR was applied to assess the relative abundance of selected antibiotic resistance genes (sul1, sul2, sul3, dfrA1, tetA and blaTEM) and class 1 integrons. Collectively, Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Cyanobacteria and Planctomycetes were the dominant phyla in the water column. Planctomycetes and Cyanobacteria abundance decreased in winter, whereas the relative abundance of several genera associated with pathogens such as Aeromonas, Flavobacterium, Mycobacterium, Clostridium and Acinetobacter increased in late phase of the fish fattening cycle. The relative abundances of trimethoprim, sulfonamide and tetracycline resitance genes and class 1 integrons were highin all of the tested profiles, but increased during the fish fattening cycle relative to the fallow water column. In contrast the abundance of the betalactamase blaTEM decreased.. Resistome analysis revealed elevated levels of dfrE, sul1, sul2 and tet family genes in later profiles. Collectively, this study indicates significant temporal shifts in water column microbiomes and resistomes that are impacted by seasonal factors and fish growth and potentially also by antibiotic amendment.