Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds

© 2018 Elsevier Ltd Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixte...

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Main Authors: Pornjira Somnark, Natcha Chyerochana, Skorn Mongkolsuk, Kwanrawee Sirikanchana
Other Authors: Chulabhorn Research Institute
Format: Article
Published: 2019
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Online Access:https://repository.li.mahidol.ac.th/handle/123456789/45886
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spelling th-mahidol.458862019-08-28T13:51:38Z Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds Pornjira Somnark Natcha Chyerochana Skorn Mongkolsuk Kwanrawee Sirikanchana Chulabhorn Research Institute Thailand Ministry of Education Mahidol University Chulabhorn Royal Academy Environmental Science Pharmacology, Toxicology and Pharmaceutics © 2018 Elsevier Ltd Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixteen endpoint and quantitative PCR (qPCR) assays targeting universal and human-, swine-, and cattle-specific Bacteroidales gene markers were modified for endpoint PCR, evaluated for their performance with sewage and fecal samples from the Tha Chin watershed and subsequently validated with samples from the Chao Phraya watershed, Thailand. Sample sizes of 81 composite samples (from over 1620 individual samples) of farm animals of each type as well as 19 human sewage samples from the Tha Chin watershed were calculated using a stratified random sampling design to achieve a 90% confidence interval and an expected prevalence (i.e., desired assay's sensitivity) of 0.80. The best universal and human-, swine-, and cattle-specific fecal markers were BacUni EP, HF183/BFDrev EP, Pig-2-Bac EP, and Bac3 assays, respectively. The detection limits for these assays ranged from 30 to 3000 plasmid copies per PCR. The positive predictive values were high in universal and swine- and cattle-specific markers (85–100%), while the positive predictive value of the human-specific assay was 52.2%. The negative predictive values in all assays were relatively high (90.8–100%). A suite of PCR assays in Thailand was established for potential MST use in environmental waters, which supports the worldwide applicability of Bacteroidales gene markers. This study also emphasizes the importance of using a proper sample size in assessing the performance of MST markers in a new geographic region. The successful validation of the Bacteroidales fecal markers for MST with fecal samples in Southeast Asia strongly supports their global use, with an emphasis on significant sample size calculation as a vital approach for evaluating MST markers. 2019-08-23T11:12:52Z 2019-08-23T11:12:52Z 2018-05-01 Article Environmental Pollution. Vol.236, (2018), 100-110 10.1016/j.envpol.2018.01.052 18736424 02697491 2-s2.0-85041655185 https://repository.li.mahidol.ac.th/handle/123456789/45886 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85041655185&origin=inward
institution Mahidol University
building Mahidol University Library
continent Asia
country Thailand
Thailand
content_provider Mahidol University Library
collection Mahidol University Institutional Repository
topic Environmental Science
Pharmacology, Toxicology and Pharmaceutics
spellingShingle Environmental Science
Pharmacology, Toxicology and Pharmaceutics
Pornjira Somnark
Natcha Chyerochana
Skorn Mongkolsuk
Kwanrawee Sirikanchana
Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
description © 2018 Elsevier Ltd Microbial source tracking (MST) DNA-based assays have been used to successfully solve fecal pollution problems in many countries, particularly in developed nations. However, their application in developing countries has been limited but continues to increase. In this study, sixteen endpoint and quantitative PCR (qPCR) assays targeting universal and human-, swine-, and cattle-specific Bacteroidales gene markers were modified for endpoint PCR, evaluated for their performance with sewage and fecal samples from the Tha Chin watershed and subsequently validated with samples from the Chao Phraya watershed, Thailand. Sample sizes of 81 composite samples (from over 1620 individual samples) of farm animals of each type as well as 19 human sewage samples from the Tha Chin watershed were calculated using a stratified random sampling design to achieve a 90% confidence interval and an expected prevalence (i.e., desired assay's sensitivity) of 0.80. The best universal and human-, swine-, and cattle-specific fecal markers were BacUni EP, HF183/BFDrev EP, Pig-2-Bac EP, and Bac3 assays, respectively. The detection limits for these assays ranged from 30 to 3000 plasmid copies per PCR. The positive predictive values were high in universal and swine- and cattle-specific markers (85–100%), while the positive predictive value of the human-specific assay was 52.2%. The negative predictive values in all assays were relatively high (90.8–100%). A suite of PCR assays in Thailand was established for potential MST use in environmental waters, which supports the worldwide applicability of Bacteroidales gene markers. This study also emphasizes the importance of using a proper sample size in assessing the performance of MST markers in a new geographic region. The successful validation of the Bacteroidales fecal markers for MST with fecal samples in Southeast Asia strongly supports their global use, with an emphasis on significant sample size calculation as a vital approach for evaluating MST markers.
author2 Chulabhorn Research Institute
author_facet Chulabhorn Research Institute
Pornjira Somnark
Natcha Chyerochana
Skorn Mongkolsuk
Kwanrawee Sirikanchana
format Article
author Pornjira Somnark
Natcha Chyerochana
Skorn Mongkolsuk
Kwanrawee Sirikanchana
author_sort Pornjira Somnark
title Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
title_short Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
title_full Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
title_fullStr Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
title_full_unstemmed Performance evaluation of Bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
title_sort performance evaluation of bacteroidales genetic markers for human and animal microbial source tracking in tropical agricultural watersheds
publishDate 2019
url https://repository.li.mahidol.ac.th/handle/123456789/45886
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