National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches

Knight, Margaret E., Webster, Gordon ORCID: https://orcid.org/0000-0002-9530-7835, Perry, William B., Baldwin, Amy ORCID: https://orcid.org/0000-0002-2162-3771, Rushton, Laura, Pass, Daniel A. ORCID: https://orcid.org/0000-0003-2799-8432, Cross, Gareth, Durance, Isabelle ORCID: https://orcid.org/0000-0002-4138-3349, Muziasari, Windi, Kille, Peter ORCID: https://orcid.org/0000-0001-6023-5221, Farkas, Kata, Weightman, Andrew J. ORCID: https://orcid.org/0000-0002-6671-2209 and Jones, Davey L. 2024. National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches. Water Research 262 , 121989. 10.1016/j.watres.2024.121989

PDF - Accepted Post-Print Version Download (1MB)

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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Biosciences
Publisher:	Elsevier
ISSN:	0043-1354
Date of First Compliant Deposit:	5 July 2024
Date of Acceptance:	19 June 2024
Last Modified:	15 Nov 2024 22:30
URI:	https://orca.cardiff.ac.uk/id/eprint/170147

Actions (repository staff only)

Edit Item