ArticleScientific reports2019
A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 62 citations in OpenAlex.
- Microbial bioindicators for multidimensional assessment of environmental alterations and ecosystem functioning.World journal of microbiology & biotechnology · 2026Review
- Microbial and Chemical Water Quality Assessments Across the Rural and Urban Areas of Nepal: A Scoping Review.International journal of environmental research and public health · 2025Article
- Multi-platform metagenomic characterization of the microbial community during spontaneous cacao fermentation.Frontiers in bioengineering and biotechnology · 2025Article
- Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.International journal of microbiology · 2025Article
- Influence of sewage effluent discharge on putative pathogen community in drinking water sources: insights from full-length 16S rRNA gene amplicon sequencing.Journal of water and health · 2025Article
- Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons.Journal of water and health · 2024Article
- A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.Archives of microbiology · 2024Article
- Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana.Current issues in molecular biology · 2024Article
- Nanopore Sequencing Assessment of Bacterial Pathogens and Associated Antibiotic Resistance Genes in Environmental Samples.Microorganisms · 2023Article
- The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.Applied and environmental microbiology · 2023Article
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- It's a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality.International journal of environmental research and public health · 2022Review
- Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique.Environmental science & technology · 2021Article
- Next generation sequencing for pathogen detection in periprosthetic joint infections.EFORT open reviews · 2021Review
- Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?FEMS microbiology ecology · 2021Article
- Freshwater monitoring by nanopore sequencing.eLife · 2021Article
- Metagenomic water quality monitoring with a portable laboratory.Water research · 2020Article
- Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality.Current environmental health reports · 2020Review
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Authors and funding
6 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed the need to ascertain MinION sequencing results for putative pathogens at species level with complementary qPCR assays. Vibrio cholerae hazards were poorly associated with plate count faecal coliforms, but flagged up by the MinION screening method, and confirmed by a qPCR assay. Plate counting methods remain important to assess viability of faecal coliforms in disinfected water sources. We outline a systematic approach for data collection and interpretation of such complementary results. In the Kathmandu Valley, there is high variability of water quality from different sources, including for treated water samples, illustrating the importance of disinfection at the point of use.
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Registered trials
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