A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>

ABSTRACT Nontuberculous mycobacteria (NTM) frequently detected in drinking water (DW) include species associated with human infections, as well as species rarely linked to disease. Methods for improved the recovery of NTM DNA and high-throughput identification of NTM are needed for risk assessment o...

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Autores principales:	Sarah-Jane Haig, Nadine Kotlarz, John J. LiPuma, Lutgarde Raskin
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	DNA extraction drinking water Mycobacterium avium NTM PacBio premise plumbing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b985a90742a24843a7ee439ae9f0e935
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spelling	oai:doaj.org-article:b985a90742a24843a7ee439ae9f0e9352021-11-15T15:53:26ZA High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>10.1128/mBio.02354-172150-7511https://doaj.org/article/b985a90742a24843a7ee439ae9f0e9352018-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02354-17https://doaj.org/toc/2150-7511ABSTRACT Nontuberculous mycobacteria (NTM) frequently detected in drinking water (DW) include species associated with human infections, as well as species rarely linked to disease. Methods for improved the recovery of NTM DNA and high-throughput identification of NTM are needed for risk assessment of NTM infection through DW exposure. In this study, different methods of recovering bacterial DNA from DW were compared, revealing that a phenol-chloroform DNA extraction method yielded two to four times as much total DNA and eight times as much NTM DNA as two commercial DNA extraction kits. This method, combined with high-throughput, single-molecule real-time sequencing of NTM rpoB genes, allowed the identification of NTM to the species, subspecies, and (in some cases) strain levels. This approach was applied to DW samples collected from 15 households serviced by a chloraminated distribution system, with homes located in areas representing short (<24 h) and long (>24 h) distribution system residence times. Multivariate statistical analysis revealed that greater water age (i.e., combined distribution system residence time and home plumbing stagnation time) was associated with a greater relative abundance of Mycobacterium avium subsp. avium, one of the most prevalent NTM causing infections in humans. DW from homes closer to the treatment plant (with a shorter water age) contained more diverse NTM species, including Mycobacterium abscessus and Mycobacterium chelonae. Overall, our approach allows NTM identification to the species and subspecies levels and can be used in future studies to assess the risk of waterborne infection by providing insight into the similarity between environmental and infection-associated NTM. IMPORTANCE An extraction method for improved recovery of DNA from nontuberculous mycobacteria (NTM), combined with single-molecule real-time sequencing (PacBio) of NTM rpoB genes, was used for high-throughput characterization of NTM species and in some cases strains in drinking water (DW). The extraction procedure recovered, on average, eight times as much NTM DNA and three times as much total DNA from DW as two widely used commercial DNA extraction kits. The combined DNA extraction and sequencing approach allowed high-throughput screening of DW samples to identify NTM, revealing that the relative abundance of Mycobacterium avium subsp. avium increased with water age. Furthermore, the two-step barcoding approach developed as part of the PacBio sequencing method makes this procedure highly adaptable, allowing it to be used for other target genes and species.Sarah-Jane HaigNadine KotlarzJohn J. LiPumaLutgarde RaskinAmerican Society for MicrobiologyarticleDNA extractiondrinking waterMycobacterium aviumNTMPacBiopremise plumbingMicrobiologyQR1-502ENmBio, Vol 9, Iss 1 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA extraction drinking water Mycobacterium avium NTM PacBio premise plumbing Microbiology QR1-502
spellingShingle	DNA extraction drinking water Mycobacterium avium NTM PacBio premise plumbing Microbiology QR1-502 Sarah-Jane Haig Nadine Kotlarz John J. LiPuma Lutgarde Raskin A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>
description	ABSTRACT Nontuberculous mycobacteria (NTM) frequently detected in drinking water (DW) include species associated with human infections, as well as species rarely linked to disease. Methods for improved the recovery of NTM DNA and high-throughput identification of NTM are needed for risk assessment of NTM infection through DW exposure. In this study, different methods of recovering bacterial DNA from DW were compared, revealing that a phenol-chloroform DNA extraction method yielded two to four times as much total DNA and eight times as much NTM DNA as two commercial DNA extraction kits. This method, combined with high-throughput, single-molecule real-time sequencing of NTM rpoB genes, allowed the identification of NTM to the species, subspecies, and (in some cases) strain levels. This approach was applied to DW samples collected from 15 households serviced by a chloraminated distribution system, with homes located in areas representing short (<24 h) and long (>24 h) distribution system residence times. Multivariate statistical analysis revealed that greater water age (i.e., combined distribution system residence time and home plumbing stagnation time) was associated with a greater relative abundance of Mycobacterium avium subsp. avium, one of the most prevalent NTM causing infections in humans. DW from homes closer to the treatment plant (with a shorter water age) contained more diverse NTM species, including Mycobacterium abscessus and Mycobacterium chelonae. Overall, our approach allows NTM identification to the species and subspecies levels and can be used in future studies to assess the risk of waterborne infection by providing insight into the similarity between environmental and infection-associated NTM. IMPORTANCE An extraction method for improved recovery of DNA from nontuberculous mycobacteria (NTM), combined with single-molecule real-time sequencing (PacBio) of NTM rpoB genes, was used for high-throughput characterization of NTM species and in some cases strains in drinking water (DW). The extraction procedure recovered, on average, eight times as much NTM DNA and three times as much total DNA from DW as two widely used commercial DNA extraction kits. The combined DNA extraction and sequencing approach allowed high-throughput screening of DW samples to identify NTM, revealing that the relative abundance of Mycobacterium avium subsp. avium increased with water age. Furthermore, the two-step barcoding approach developed as part of the PacBio sequencing method makes this procedure highly adaptable, allowing it to be used for other target genes and species.
format	article
author	Sarah-Jane Haig Nadine Kotlarz John J. LiPuma Lutgarde Raskin
author_facet	Sarah-Jane Haig Nadine Kotlarz John J. LiPuma Lutgarde Raskin
author_sort	Sarah-Jane Haig
title	A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>
title_short	A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>
title_full	A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>
title_fullStr	A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>
title_full_unstemmed	A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>
title_sort	high-throughput approach for identification of nontuberculous mycobacteria in drinking water reveals relationship between water age and <italic toggle="yes">mycobacterium avium</italic>
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/b985a90742a24843a7ee439ae9f0e935
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A High-Throughput Approach for Identification of Nontuberculous Mycobacteria in Drinking Water Reveals Relationship between Water Age and <italic toggle="yes">Mycobacterium avium</italic>

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