Abstract
Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people’s lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.
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All raw data used in this study can be found in online repositories. The names of the repository and accession number(s) can be found as: (https://www.ncbi.nlm.nih.gov/), PRJNA400857.
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This research work has been supported by Natural Science Foundation of China (NSFC) for international young scientist under grant No. 42150410383.
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Conceptualizing, methodology, empirical estimations, writing, and drafting of the original draft by Sohail M. Noman; supervision by Xiaoyang Jiao; data collection by Sohail M. Noman, Muhammad Shafiq, Yumeng Yuan, Mi Zeng, and Xin Li; review and editing by Sohail M. Noman, Shabana Bibi, Bharti Mittal, Oluwaseyi Abraham Olawale, and Muhammad Irshad. All authors have read and approved the final manuscript.
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Noman, S.M., Shafiq, M., Bibi, S. et al. Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis. Environ Sci Pollut Res 30, 2977–2990 (2023). https://doi.org/10.1007/s11356-022-22197-4
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DOI: https://doi.org/10.1007/s11356-022-22197-4