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

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.

Low Concentrations of Antibiotics Alter Microbial Communities and Induce High Abundances of Antibiotic-Resistant Genes in Ornamental Water

“…In particular, intI1 demonstrated a positive correlation with over 10 generals; however, among those, Flavihumibacter (p < 0.05) and Hydrogenophaga (p < 0.05) were the only genera that showed significant and positive associations. This is also in accordance with earlier observations, which showed that Hydrogenophaga plays an important role in the spread and variation of ARGs and intI1 in freshwater environments [54]. For the tetA, 10 of the 30 genera were positively correlated, but only Acinetobacter was significantly and positively correlated (p < 0.01), which has been earlier identified as a host for ARGs in aquaculture ponds [55].…”

Seasonal and spatial variability of antibiotic resistance genes and Class I integrons in rivers of the Mekong Delta, Vietnam

“…Sequencing of 41 plasmid-transmitted ARGs showed the presence of a wide range of ABs, including aminoglycosides, OXA-type ß-lactams, chloramphenicol, fluoroquinolone, macrolides, rifampicin, tetracycline, trimethoprim and sulfonamide. The association of ARGs with mobile genetic elements that enable their dissemination has been demonstrated worldwide (Gillings et al, 2008; Gao et al, 2012; Fang et al, 2021). Previous studies in the Mekong Delta have shown, for example, that sul 2 genes have been detected in association with integrons and plasmids (Pham et al, 2018).…”