Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR

Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we pr...

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Autores principales:	Laurice Beatrice Raphaelle O. dela Peña, Kevin L. Labrador, Mae Ashley G. Nacario, Nicole R. Bolo, Windell L. Rivera
Formato:	article
Lenguaje:	EN
Publicado:	IWA Publishing 2021
Materias:	dna fingerprinting laguna lake microbial source tracking random forest rep-pcr Public aspects of medicine RA1-1270
Acceso en línea:	https://doaj.org/article/552f750e73534f5fa10d2112fb92ea5a
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spelling	oai:doaj.org-article:552f750e73534f5fa10d2112fb92ea5a2021-11-06T06:30:50ZMicrobial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR1477-89201996-782910.2166/wh.2021.119https://doaj.org/article/552f750e73534f5fa10d2112fb92ea5a2021-10-01T00:00:00Zhttp://jwh.iwaponline.com/content/19/5/762https://doaj.org/toc/1477-8920https://doaj.org/toc/1996-7829Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we predicted sources of Escherichia coli in lake stations and tributaries by establishing a fecal source library composed of rep-PCR DNA fingerprints of human, cattle, swine, poultry, and sewage samples (n = 1,408). We also evaluated three statistical methods for predicting fecal contamination sources in surface waters. Random forest (RF) outperformed k-nearest neighbors and discriminant analysis of principal components in terms of average rates of correct classification in two- (84.85%), three- (82.45%), and five-way (74.77%) categorical splits. Overall, RF exhibited the most balanced prediction, which is crucial for disproportionate libraries. Source tracking of environmental isolates (n = 332) revealed the dominance of sewage (47.59%) followed by human sources (29.22%), poultry (12.65%), swine (7.23%), and cattle (3.31%) using RF. This study demonstrates the promising utility of a library-dependent method in augmenting current monitoring systems for source attribution of fecal contamination in Laguna Lake. This is also the first known report of microbial source tracking using rep-PCR conducted in surface waters of the Laguna Lake watershed. HIGHLIGHTS DNA fingerprinting of E. coli, coupled with machine learning algorithms, can be used to discriminate fecal pollution sources in Laguna Lake, Philippines.; The majority of E. coli isolates can be attributed to sewage contamination, followed by human and agricultural sources.; Source-tracking methods can empower local agencies responsible for water quality management to minimize public health and economic risks.;Laurice Beatrice Raphaelle O. dela PeñaKevin L. LabradorMae Ashley G. NacarioNicole R. BoloWindell L. RiveraIWA Publishingarticledna fingerprintinglaguna lakemicrobial source trackingrandom forestrep-pcrPublic aspects of medicineRA1-1270ENJournal of Water and Health, Vol 19, Iss 5, Pp 762-774 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	dna fingerprinting laguna lake microbial source tracking random forest rep-pcr Public aspects of medicine RA1-1270
spellingShingle	dna fingerprinting laguna lake microbial source tracking random forest rep-pcr Public aspects of medicine RA1-1270 Laurice Beatrice Raphaelle O. dela Peña Kevin L. Labrador Mae Ashley G. Nacario Nicole R. Bolo Windell L. Rivera Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR
description	Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we predicted sources of Escherichia coli in lake stations and tributaries by establishing a fecal source library composed of rep-PCR DNA fingerprints of human, cattle, swine, poultry, and sewage samples (n = 1,408). We also evaluated three statistical methods for predicting fecal contamination sources in surface waters. Random forest (RF) outperformed k-nearest neighbors and discriminant analysis of principal components in terms of average rates of correct classification in two- (84.85%), three- (82.45%), and five-way (74.77%) categorical splits. Overall, RF exhibited the most balanced prediction, which is crucial for disproportionate libraries. Source tracking of environmental isolates (n = 332) revealed the dominance of sewage (47.59%) followed by human sources (29.22%), poultry (12.65%), swine (7.23%), and cattle (3.31%) using RF. This study demonstrates the promising utility of a library-dependent method in augmenting current monitoring systems for source attribution of fecal contamination in Laguna Lake. This is also the first known report of microbial source tracking using rep-PCR conducted in surface waters of the Laguna Lake watershed. HIGHLIGHTS DNA fingerprinting of E. coli, coupled with machine learning algorithms, can be used to discriminate fecal pollution sources in Laguna Lake, Philippines.; The majority of E. coli isolates can be attributed to sewage contamination, followed by human and agricultural sources.; Source-tracking methods can empower local agencies responsible for water quality management to minimize public health and economic risks.;
format	article
author	Laurice Beatrice Raphaelle O. dela Peña Kevin L. Labrador Mae Ashley G. Nacario Nicole R. Bolo Windell L. Rivera
author_facet	Laurice Beatrice Raphaelle O. dela Peña Kevin L. Labrador Mae Ashley G. Nacario Nicole R. Bolo Windell L. Rivera
author_sort	Laurice Beatrice Raphaelle O. dela Peña
title	Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR
title_short	Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR
title_full	Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR
title_fullStr	Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR
title_full_unstemmed	Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR
title_sort	microbial source tracking of fecal contamination in laguna lake, philippines using the library-dependent method, rep-pcr
publisher	IWA Publishing
publishDate	2021
url	https://doaj.org/article/552f750e73534f5fa10d2112fb92ea5a
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Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR

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