The impacts of different high-throughput profiling approaches on the understanding of bacterial antibiotic resistance genes in a freshwater reservoir

• Published in: The Science of the total environment 2019-11, Vol.693, p.133585, Article 133585
• Main Authors: Liu, Xuan, Xiao, Peng, Guo, Yunyan, Liu, Lemian, Yang, Jun
• Format: Article
• Language: English
• Subjects: Antibiotic resistance gene; Aquatic environment; Bacterioplankton; Cyanobacterial bloom; High-throughput quantitative PCR; Metagenomics
• ISSN: 0048-9697; 1879-1026
• DOI: 10.1016/j.scitotenv.2019.133585

Bacterial antibiotic resistance genes (ARGs), a kind of emerging environmental pollutants, greatly threat human health through pathogenic bacteria. High-throughput quantitative PCR (HT-qPCR) and metagenomic approaches are two popular tools applied in aquatic environmental ARGs monitoring. However, current poor knowledge of different ARG profiling approaches' impacts on the understanding of the ARGs in aquatic environments greatly limit the further field application of these two approaches. For filling such knowledge gap, this study simultaneously employed these two approaches to examine and compare the ARGs in a freshwater reservoir across space and time. We found metagenomic approach detected more ARG subtypes and much higher bacitracin resistance genes' abundances than HT-qPCR. In general, HT-qPCR and metagenomics analyses both revealed similar ARG dynamic patterns and co-occurrence patterns between ARGs and bacterial taxa as well as the relationships between ARGs and environmental factors. Our results indicated the impacts of different ARG profiling approaches on the understanding of bacterial ARGs might be minor or negligible. HT-qPCR approach has the superiorities of time-saving, absolute quantification, low requirement for bioinformatics skills but also has some drawbacks including higher PCR amplification & primer bias, higher primer dependency and relative lower ARG subtype quantification capability compared to metagenomic approach. We suggest HT-qPCR approach can be employed for routine aquatic environmental monitoring, and metagenomic approach could be applied in comprehensive surveys for getting more ARG subtype information. Our data can be a useful reference for choosing right ARG profiling approaches for bacterial ARGs monitoring and risk assessment in aquatic environments. [Display omitted] •High-throughput qPCR and metagenomic approaches were used to profile bacterial ARGs.•More ARG subtypes were revealed by metagenomics than high-throughput qPCR.•Similar ARGs dynamic patterns were revealed by different ARG profiling approaches.•High-throughput qPCR approach is suitable for routine environmental ARG monitoring.•Metagenomics is an ideal tool for more comprehensive survey of environmental ARGs