4.6 Article

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

Journal

WATER
Volume 13, Issue 11, Pages -

Publisher

MDPI
DOI: 10.3390/w13111461

Keywords

antibiotic resistance genes; bacterial community; shrimp aquaculture; high-throughput sequencing; metagenomic analysis

Funding

  1. Open Fund of State Key Laboratory of Pollution Control and Resource Reuse [PCRRF20018]
  2. Natural Science Foundation of Jiangsu Province [BK20200816]
  3. Key University Science Research Project of Jiangsu Province [20KJB610009]
  4. Science and technology innovation project for overseas students in Nanjing
  5. Postgraduate Research & Practice Innovation Program of Jiangsu Province [SJCX19_0307]

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Shrimp aquaculture environments harbor multiple antibiotic resistance genes (ARGs) due to antibiotic overuse, with sediment samples showing higher levels of ARG biodiversity and abundance compared to water samples. Network analysis revealed complex co-occurrence patterns between bacterial communities and ARGs, with mobile genetic elements (MGEs) identified as the most crucial contributor (74.76%) to resistome alteration. This study sheds light on the intricate correlations among ARGs, bacterial diversity, and MGEs in freshwater shrimp aquaculture environments.
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.

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