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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.
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
URL: https://doi.org/10.1038/s41598-019-51997-x
DOI: 10.1038/s41598-019-51997-x
Data Access Statement: https://doi.org/10.25405/data.ncl.9693533
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