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Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture

by 1, 1, 1,2,3,*, 1 and 1
1
Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
2
State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
3
Nanjing Jiangdao Institute of Environmental Research Co., Ltd., Nanjing 210019, China
*
Author to whom correspondence should be addressed.
Academic Editor: Stefano Amalfitano
Water 2021, 13(11), 1461; https://doi.org/10.3390/w13111461
Received: 20 April 2021 / Revised: 13 May 2021 / Accepted: 19 May 2021 / Published: 23 May 2021
(This article belongs to the Section Biodiversity and Functionality of Aquatic Ecosystems)
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. View Full-Text
Keywords: antibiotic resistance genes; bacterial community; shrimp aquaculture; high-throughput sequencing; metagenomic analysis antibiotic resistance genes; bacterial community; shrimp aquaculture; high-throughput sequencing; metagenomic analysis
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MDPI and ACS Style

Fang, H.; Ye, N.; Huang, K.; Yu, J.; Zhang, S. Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture. Water 2021, 13, 1461. https://doi.org/10.3390/w13111461

AMA Style

Fang H, Ye N, Huang K, Yu J, Zhang S. Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture. Water. 2021; 13(11):1461. https://doi.org/10.3390/w13111461

Chicago/Turabian Style

Fang, Hao, Nan Ye, Kailong Huang, Junnan Yu, and Shuai Zhang. 2021. "Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture" Water 13, no. 11: 1461. https://doi.org/10.3390/w13111461

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