Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment

Abstract

Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture

“…Therefore, significant effort has been invested in studying the aquatic microbiome in some aquaculture types, with the aim of using these measurements to understand fish health, to identify biomarkers/early markers of emerging diseases, or to explore the use of probiotics ( Dawood et al, 2019 ; Kuebutornye et al, 2019 ; Kolda et al, 2020 ; Zhang et al, 2020 ). In our dataset, we identify several bacterial lineages known as fish pathogens, including the genera Aeromonas , Vibrio , and Enterobacter , in agreement with previous studies from DARU ( Patil et al, 2016 , 2020 ). However, due to the limited phylogenetic resolution of partially sequenced 16S rRNA gene, it is usually not possible to identify whether the observed taxa are associated specifically with pathogenic strains.…”

“…Additionally, both Saprospiracae and another group enriched in the dry season, the genus Haliscomenobacter , has been suggested to be associated with the presence of both cyanobacterial blooms and antibiotic resistance genes in Lake Taihu ( Zhang et al, 2020 ). While antibiotics are not used directly in the three sampled water bodies, they are used prophylactically at DARU at the beginning of the fish fattening cycle (beginning of dry season), including in additional fishponds connected to the system ( Patil et al, 2016 , 2020 ).…”

“…As a result, aquaculture often supports fish health by using drugs and antibiotics, as well as algaecides in the case of algal blooms. However, despite the ubiquity of such aquaculture husbandry practices, and their potential impact on aquatic microbial populations, little is known about the temporal dynamics of the microbiome in fishponds, and how it responds to natural and anthropogenic perturbations ( Rodriguez-Brito et al, 2010 ; Patil et al, 2020 ).…”

Infection by the Parasite Myxobolus bejeranoi (Cnidaria: Myxozoa) Suppresses the Immune System of Hybrid Tilapia

“…Thus, as most of the fish defense mechanisms are down, the parasite renders its host more susceptible to other opportunistic pathogens. Aquaculture earthen ponds are home to highly dynamic microbial communities [ 97 ]. These include Aeromonas [ 98 ], the causative agent of motile Aeromonas septicaemia disease, and the highly contagious tilapia lake virus (TiLV) [ 99 ].…”

Comparison of planktonic bacterial communities indoor and outdoor of aquaculture greenhouses

“…Bacteria are crucial for the functioning of agricultural soil ecosystems (Song et al, 2020; Sun et al, 2018). In aquatic ecosystems, bacteria are also widely recognized for their role in water purification, pollutant reduction and their importance for fish health (Fan et al, 2020; Patil et al, 2020). There are significant differences in bacterial diversity and community composition between environments.…”