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A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Lookup NU author(s): Dr Kishor AcharyaORCiD, Professor Russell DavenportORCiD, Professor David WernerORCiD



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


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.

Publication metadata

Author(s): Acharya K, Khanal S, Pantha K, Amatya N, Davenport RJ, Werner D

Publication type: Article

Publication status: Published

Journal: Scientific Reports

Year: 2019

Volume: 9

Online publication date: 31/10/2019

Acceptance date: 10/10/2019

Date deposited: 01/11/2019

ISSN (electronic): 2045-2322

Publisher: Nature Publishing Group


DOI: 10.1038/s41598-019-51997-x


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