中文版 | English
Title

Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body

Author
Corresponding AuthorXia, Yu
Publication Years
2022-11-01
DOI
Source Title
ISSN
0043-1354
EISSN
1879-2448
Volume226
Abstract
Wastewater treatment plant (WWTP) effluent discharge could induce the resistome enrichment in the receiving water environments. However, because of the general lack of a robust antibiotic-resistant bacteria (ARB) identification method, the driving mechanism for resistome accumulation in receiving environment is unclear. Here, we took advantage of the enhanced ARBs recognition by nanopore long reads to distinguish the indigenous ARBs and the accumulation of WWTP-borne ARBs in the receiving water body of a domestic WWTP. A bioinformatic framework (named ARGpore2: https://github.com/sustc-xylab/ARGpore2) was constructed and evaluate to facilitate antibiotic resistance genes (ARGs) and ARBs identification in nanopore reads. ARGs identification by ARGpore2 showed comparable precision and recall to that of the commonly adopt BLASTP-based method, whereas the spectrum of ARBs doubled that of the assembled Illumina dataset. Totally, we identified 33 ARBs genera carrying 65 ARG subtypes in the receiving seawater, whose concentration was in general 10 times higher than clean seawater's. Notably we report a primary resistome intrusion caused by the revival of residual microbes survived from disinfection treatment. These WWTP-borne ARBs, including several animal/human enteric pathogens, contributed up to 85% of the receiving water resistome. Plasmids and class 1 integrons were reckoned as major vehicles facilitating the persistence and dissemination of ARGs. Moreover, our work demonstrated the importance of extensive carrier identification in determining the driving force of multifactor coupled resistome booming in complicated environmental conditions, thereby paving the way for establishing priority for effective ARGs mitigation strategies.

© 2022

Keywords
URL[Source Record]
Indexed By
SCI ; EI
Language
English
Important Publications
NI Journal Papers
SUSTech Authorship
First ; Corresponding
Funding Project
Our research was funded by National Key R&D Program of China (Grant No.2022YFE0103200), National Natural Science Foundation of China (Grand No. 42007216, 42277103 and 42177357) and Natural Science Foundation of Guangdong Province (Grant No. 2021A1515012191). Also, we would like to thank centre for Computational Science and Engineering at Southern University of Science and Technology (SUSTech) and core research facilities at SUSTech to provide quality resources and services. Finally, we express our sincere acknowledgement to Dr. Yu Ke from Peking University Shenzhen Graduate School for the kind supply of whole genome datasets of isolated strains.Our research was funded by National Key R&D Program of China (Grant No. 2022YFE0103200 ), National Natural Science Foundation of China (Grand No. 42007216 , 42277103 and 42177357 ) and Natural Science Foundation of Guangdong Province (Grant No. 2021A1515012191 ) . Also, we would like to thank centre for Computational Science and Engineering at Southern University of Science and Technology (SUSTech) and core research facilities at SUSTech to provide quality resources and services. Finally, we express our sincere acknowledgement to Dr. Yu Ke from Peking University Shenzhen Graduate School for the kind supply of whole genome datasets of isolated strains.
WOS Research Area
Engineering ; Environmental Sciences & Ecology ; Water Resources
WOS Subject
Engineering, Environmental ; Environmental Sciences ; Water Resources
WOS Accession No
WOS:000884794600005
Publisher
EI Accession Number
20224413051255
EI Keywords
Bacteria ; Effluent Treatment ; Effluents ; Genes ; Nanopores ; Seawater ; Wastewater Treatment
ESI Classification Code
Industrial Wastes:452.3 ; Industrial Wastes Treatment And Disposal:452.4 ; Biological Materials And Tissue Engineering:461.2 ; Medicine And Pharmacology:461.6 ; Seawater, Tides And Waves:471.4 ; Nanotechnology:761 ; Solid State Physics:933
ESI Research Field
ENVIRONMENT/ECOLOGY
Data Source
EV Compendex
Citation statistics
Cited Times [WOS]:5
Document TypeJournal Article
Identifierhttp://kc.sustech.edu.cn/handle/2SGJ60CL/411683
DepartmentSchool of Environmental Science and Engineering
Affiliation
1.School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen; 518055, China
2.Section of Microbiology, University of Copenhagen, Universitetsparken 15, Copenhagen; 2100, Denmark
3.Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong
4.State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen; 518055, China
5.Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen; 518055, China
First Author AffilicationSchool of Environmental Science and Engineering
Corresponding Author AffilicationSchool of Environmental Science and Engineering
First Author's First AffilicationSchool of Environmental Science and Engineering
Recommended Citation
GB/T 7714
Wu, Ziqi,Che, You,Dang, Chenyuan,et al. Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body[J]. WATER RESEARCH,2022,226.
APA
Wu, Ziqi.,Che, You.,Dang, Chenyuan.,Zhang, Miao.,Zhang, Xuyang.,...&Xia, Yu.(2022).Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body.WATER RESEARCH,226.
MLA
Wu, Ziqi,et al."Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body".WATER RESEARCH 226(2022).
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