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Journal article
National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches
Water research (Oxford), Vol.265, 121989
2024
Abstract
Wastewater serves as an important reservoir of antimicrobial resistance (AMR), and its surveillance can provide insights into population-level trends in AMR to inform public health policy. This study compared two common high-throughput screening approaches, namely (i) high-throughput quantitative PCR (HT qPCR), targeting 73 antimicrobial resistance genes, and (ii) metagenomic sequencing. Weekly composite samples of wastewater influent were taken from 47 wastewater treatment plants (WWTPs) across Wales, as part of a national AMR surveillance programme, alongside 4 weeks of daily wastewater effluent samples from a large municipal hospital. Metagenomic analysis provided more comprehensive resistome coverage, detecting 545 genes compared to the targeted 73 genes by HT qPCR. It further provided contextual information critical to risk assessment (i.e. potential bacterial hosts). In contrast, HT qPCR exhibited higher sensitivity, quantifying all targeted genes including those of clinical relevance present at low abundance. When limited to the HT qPCR target genes, both methods were able to reflect the spatiotemporal dynamics of the complete metagenomic resistome, distinguishing that of the hospital and the WWTPs. Both approaches revealed correlations between resistome compositional shifts and environmental variables like ammonium wastewater concentration, though differed in their interpretation of some potential influencing factors. Overall, metagenomics provides more comprehensive resistome profiling, while qPCR permits sensitive quantification of genes significant to clinical resistance. We highlight the importance of selecting appropriate methodologies aligned to surveillance aims to guide the development of effective wastewater-based AMR monitoring programmes.
Details
- Title
- National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches
- Authors/Creators
- Margaret E. KnightGordon WebsterWilliam B. PerryAmy BaldwinLaura RushtonDaniel A. PassGareth CrossIsabelle DuranceWindi MuziasariPeter KilleKata FarkasAndrew J. WeightmanDavey L. Jones
- Publication Details
- Water research (Oxford), Vol.265, 121989
- Publisher
- Elsevier Ltd.
- Number of pages
- 10
- Grant note
- Welsh Government under the Welsh Wastewater Programme: C035/2021/2022
This research was supported by Welsh Government under the Welsh Wastewater Programme (C035/2021/2022). We thank Tony Harrington and Ian Trick at Dwr Cymru Welsh Water, UK and Elizabeth Franks at Hafren Dyfrdwy for their assistance in setting up wastewater sample collections. We thank the Welsh Wastewater Monitoring Group, Bangor, UK and the WEWASH sample collection and laboratory team at Cardiff University for their assistance in sample processing, and members of the genomics research hub and Wales gene park, Cardiff University for help with metagenomic sequencing. We thank Steve Cobley at Welsh Gov- ernment for project supervision and management. We thank Dr Mandy Wootten at the Specialist Antimicrobial Chemotherapy Unit, Public Health Wales, University Hospital of Wales and Prof David Graham, Newcastle University for advice on the AMR gene targets.
- Identifiers
- 991005680136907891
- Copyright
- © 2024 The Authors.
- Murdoch Affiliation
- Centre for Sustainable Farming Systems
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.23 Antibiotics & Antimicrobials
- 1.23.146 Antimicrobial Resistance
- Web Of Science research areas
- Engineering, Environmental
- Environmental Sciences
- Water Resources
- ESI research areas
- Environment/Ecology