Abstract
Shrimp aquaculture environments are a natural reservoir of multiple antibiotic resistance genes (ARGs) due to the overuse of antibiotics. Nowadays, the prevalence of these kinds of emerging contaminants in shrimp aquaculture environments is still unclear. In this study, high-throughput sequencing techniques were used to analyze the distribution of ARGs and mobile genetic elements (MGEs), bacterial communities, and their correlations in water and sediment samples in two types of typical shrimp (Procambarus clarkii and Macrobrachium rosenbergii) freshwater aquaculture environments. A total of 318 ARG subtypes within 19 ARG types were detected in all the samples. The biodiversity and relative abundance of ARGs in sediment samples showed much higher levels compared to water samples from all ponds in the study area. Bacitracin (17.44–82.82%) and multidrug (8.57–49.70%) were dominant ARG types in P. clarkii ponds, while sulfonamide (26.33–39.59%) and bacitracin (12.75–37.11%) were dominant ARG types in M. rosenbergii ponds. Network analysis underlined the complex co-occurrence patterns between bacterial communities and ARGs. Proteobacteria, Cyanobacteria, and Actinobacteria exhibited a high abundance in all samples, in which C39 (OTU25355) and Hydrogenophaga (OTU162961) played important roles in the dissemination of and variation in ARGs based on their strong connections between ARGs and bacterial communities. Furthermore, pathogens (e.g., Aeromonadaceae (OTU195200) and Microbacteriaceae (OTU16033)), which were potential hosts for various ARGs, may accelerate the propagation of ARGs and be harmful to human health via horizontal gene transfer mediated by MGEs. Variation partitioning analysis further confirmed that MGEs were the most crucial contributor (74.76%) driving the resistome alteration. This study may help us to understand the non-ignorable correlations among ARGs, bacterial diversity, and MGEs in the shrimp freshwater aquaculture environments.
Highlights
The increasing prevalence of antibiotic resistance genes (ARGs) caused by the use of antibiotics has been recognized as serious emerging contaminants [1]
Bacitracin and sulfonamides were predominant in all water samples, while multidrug and vancomycin were predominant in all sediment samples (Figure 1b)
In P. clarkii aquaculture ponds, multidrug was predominant in sediment samples, with percentages ranging from 19.34% to 49.70%, followed by vancomycin (10.39–33.37%), bacitracin (17.44–19.49%), and macrolide-lincosamidestreptogramin (M-L-S) (6.20–10.61%)
Summary
The increasing prevalence of antibiotic resistance genes (ARGs) caused by the use of antibiotics has been recognized as serious emerging contaminants [1]. The uncontrolled use of antimicrobial agents drives the development and dissemination of ARGs among different microorganisms, in which the increasing levels of human and animal pathogens obviously pose serious risks to the environment [8,9]. In addition to natural aquaculture environments, great amounts of Vibrio parahaemolyticus strains isolated from commonly consumed fresh shrimps (Litopenaeus vannamei, Macrobrachium rosenbergii, Penaeus monodon, and Exopalaemon carinicauda) in fish markets were observed to display multidrug resistance [20]. This combined method cannot indicate the ARGs level of the whole bacterial community, which is restricted by the cultivability of different bacteria. The use of such a traditional method limited these studies only to investigating target ARGs with known primers for amplification; they could not perform a comprehensive analysis of all ARGs in aquaculture environments [16]
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