Addressing gaps in community-level antimicrobial resistance monitoring through wastewater surveillance
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Date
2024-10-02
Authors
Daigle, Jade
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Abstract
Antimicrobial resistance (AMR) is an escalating global health crisis, yet existing monitoring
systems inadequately track AMR at the community level. Wastewater surveillance (WS) offers a
practical solution by providing a scalable, non-invasive approach to monitor community-level
AMR. This thesis contributes to the development of a national WS program in Canada,
enhancing our capacity to detect and manage AMR. Central to this work was the advancement
and validation of a wastewater-specific quantitative metagenomic (wqMeta) workflow, designed
to enrich and quantify thousands of AMR gene families in diverse wastewater samples.
A DNA extraction method was optimized, comparing two extraction kits—PowerMicrobiome
(PMB) and MagNA Pure 96 (MP96). Processing 100 mL of wastewater with the PMB kit
consistently yielded higher DNA concentrations and quality, enabling more effective
downstream analyses. The wqMeta workflow, which normalized data by both total bacterial load
and wastewater flow rates, outperformed the published qMeta method, which relied solely on
bacterial load. The wqMeta approach closely mirrored quantitative PCR (qPCR) in its ability to
quantify absolute AMR gene abundances, demonstrating superior accuracy and scalability.
A nine-week pilot study across six wastewater treatment plants (WWTPs) in urban, rural, and
remote communities in central Canada validated the workflow. Results revealed stable AMR
concentrations over time, with significant spatial differences: urban sites exhibited higher AMR
levels and gene diversity compared to remote sites, highlighting the influence of population
density on AMR dissemination. This study underscores the potential of WS to bridge critical
gaps in AMR monitoring and offers actionable insights for public health interventions.
The findings demonstrate that WS, supported by advanced methodologies such as wqMeta, can
provide real-time, population-wide AMR data. Implementing a national WS program would
strengthen Canada’s ability to detect and respond to AMR trends, guiding evidence-based policy
decisions to mitigate the growing threat of AMR.
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Keywords
AMR, Wastewater surveillance, Bioinformatics, Public Health