QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

3 Scopus Citations
View graph of relations

Author(s)

  • Wanwan Zhao
  • Shuxian Li
  • Chao Yang
  • Tong Zhang

Detail(s)

Original languageEnglish
Article number119858
Journal / PublicationWater Research
Volume235
Online published11 Mar 2023
Publication statusPublished - 15 May 2023
Externally publishedYes

Abstract

The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment. © 2023 Elsevier Ltd.

Research Area(s)

  • Absolute quantification, Antibiotic resistance, Faecal indicator bacteria, PMA treatment, Quantitative microbial risk assessment, Viability

Citation Format(s)

QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification. / Yang, Yu; Deng, Yu; Shi, Xianghui et al.
In: Water Research, Vol. 235, 119858, 15.05.2023.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review