Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India

Mitsunori Odagiri, Alexander Schriewer, Kaitlyn Hanley, Stefan Wuertz, Pravas R. Misra, Pinaki Panigrahi, Marion W. Jenkins

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

We compared host-associated Bacteroidales qPCR assays developed in the continental United States and Europe for the purpose of measuring the effect of improved sanitation on human fecal exposure in rural Indian communities where both human and animal fecal loading are high. Ten candidate Bacteroidales qPCR assays were tested against fecal samples (human, sewage, cow, buffalo, goat, sheep, dog and chicken) from a test set of 30 individual human, 5 sewage, and 60 pooled animal samples collected in coastal Odisha, India. The two universal/general Bacteroidales assays tested (BacUni, GenBac3) performed equally well, achieving 100% sensitivity on the test set. Across the five human-associated assays tested (HF183 Taqman, BacHum, HumM2, BacH, HF183 SYBR), we found low sensitivity (17 to 49%) except for HF183 SYBR (89%), and moderate to high cross-reactivity with dog (20 to 80%) and chicken fecal samples (60 to 100%). BacHum had the highest accuracy (67%), amplified all sewage samples within the range of quantification (ROQ), and did not cross-react with any fecal samples from cows, the most populous livestock animal in India. Of the ruminant- and cattle-associated assays tested (BacCow, CowM2), BacCow was more sensitive in detecting the full range of common Indian livestock animal fecal sources, while CowM2 only detected cow sources with 50% sensitivity. Neither assay cross-reacted with human sources. BacCan, the dog-associated assay tested, showed no cross-reactivity with human sources, and high sensitivity (90%) for dog fecal samples. Overall, our results indicate BacUni, BacHum, HumM2, BacCan and BacCow would be the most suitable MST assays to distinguish and quantify relative amounts of human-associated and livestock/domestic animal-associated contributions to fecal contamination in Odisha, India.

Original languageEnglish (US)
Pages (from-to)462-470
Number of pages9
JournalScience of the Total Environment
Volume502
DOIs
StatePublished - Jan 1 2015

Fingerprint

Public Sector
targeting
India
Assays
Animals
Contamination
assay
Polymerase Chain Reaction
animal
Livestock
Sewage
Dogs
Agriculture
livestock
sewage
Chickens
Sanitation
contamination
public
ruminant

Keywords

  • Bacteroidales
  • Fecal pollution
  • India
  • Microbial source tracking
  • Quantitative PCR

ASJC Scopus subject areas

  • Environmental Engineering
  • Environmental Chemistry
  • Waste Management and Disposal
  • Pollution

Cite this

Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India. / Odagiri, Mitsunori; Schriewer, Alexander; Hanley, Kaitlyn; Wuertz, Stefan; Misra, Pravas R.; Panigrahi, Pinaki; Jenkins, Marion W.

In: Science of the Total Environment, Vol. 502, 01.01.2015, p. 462-470.

Research output: Contribution to journalArticle

Odagiri, Mitsunori ; Schriewer, Alexander ; Hanley, Kaitlyn ; Wuertz, Stefan ; Misra, Pravas R. ; Panigrahi, Pinaki ; Jenkins, Marion W. / Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India. In: Science of the Total Environment. 2015 ; Vol. 502. pp. 462-470.
@article{5f57d23354534ec9b3b9167d4ab1c04c,
title = "Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India",
abstract = "We compared host-associated Bacteroidales qPCR assays developed in the continental United States and Europe for the purpose of measuring the effect of improved sanitation on human fecal exposure in rural Indian communities where both human and animal fecal loading are high. Ten candidate Bacteroidales qPCR assays were tested against fecal samples (human, sewage, cow, buffalo, goat, sheep, dog and chicken) from a test set of 30 individual human, 5 sewage, and 60 pooled animal samples collected in coastal Odisha, India. The two universal/general Bacteroidales assays tested (BacUni, GenBac3) performed equally well, achieving 100{\%} sensitivity on the test set. Across the five human-associated assays tested (HF183 Taqman, BacHum, HumM2, BacH, HF183 SYBR), we found low sensitivity (17 to 49{\%}) except for HF183 SYBR (89{\%}), and moderate to high cross-reactivity with dog (20 to 80{\%}) and chicken fecal samples (60 to 100{\%}). BacHum had the highest accuracy (67{\%}), amplified all sewage samples within the range of quantification (ROQ), and did not cross-react with any fecal samples from cows, the most populous livestock animal in India. Of the ruminant- and cattle-associated assays tested (BacCow, CowM2), BacCow was more sensitive in detecting the full range of common Indian livestock animal fecal sources, while CowM2 only detected cow sources with 50{\%} sensitivity. Neither assay cross-reacted with human sources. BacCan, the dog-associated assay tested, showed no cross-reactivity with human sources, and high sensitivity (90{\%}) for dog fecal samples. Overall, our results indicate BacUni, BacHum, HumM2, BacCan and BacCow would be the most suitable MST assays to distinguish and quantify relative amounts of human-associated and livestock/domestic animal-associated contributions to fecal contamination in Odisha, India.",
keywords = "Bacteroidales, Fecal pollution, India, Microbial source tracking, Quantitative PCR",
author = "Mitsunori Odagiri and Alexander Schriewer and Kaitlyn Hanley and Stefan Wuertz and Misra, {Pravas R.} and Pinaki Panigrahi and Jenkins, {Marion W.}",
year = "2015",
month = "1",
day = "1",
doi = "10.1016/j.scitotenv.2014.09.040",
language = "English (US)",
volume = "502",
pages = "462--470",
journal = "Science of the Total Environment",
issn = "0048-9697",
publisher = "Elsevier",

}

TY - JOUR

T1 - Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India

AU - Odagiri, Mitsunori

AU - Schriewer, Alexander

AU - Hanley, Kaitlyn

AU - Wuertz, Stefan

AU - Misra, Pravas R.

AU - Panigrahi, Pinaki

AU - Jenkins, Marion W.

PY - 2015/1/1

Y1 - 2015/1/1

N2 - We compared host-associated Bacteroidales qPCR assays developed in the continental United States and Europe for the purpose of measuring the effect of improved sanitation on human fecal exposure in rural Indian communities where both human and animal fecal loading are high. Ten candidate Bacteroidales qPCR assays were tested against fecal samples (human, sewage, cow, buffalo, goat, sheep, dog and chicken) from a test set of 30 individual human, 5 sewage, and 60 pooled animal samples collected in coastal Odisha, India. The two universal/general Bacteroidales assays tested (BacUni, GenBac3) performed equally well, achieving 100% sensitivity on the test set. Across the five human-associated assays tested (HF183 Taqman, BacHum, HumM2, BacH, HF183 SYBR), we found low sensitivity (17 to 49%) except for HF183 SYBR (89%), and moderate to high cross-reactivity with dog (20 to 80%) and chicken fecal samples (60 to 100%). BacHum had the highest accuracy (67%), amplified all sewage samples within the range of quantification (ROQ), and did not cross-react with any fecal samples from cows, the most populous livestock animal in India. Of the ruminant- and cattle-associated assays tested (BacCow, CowM2), BacCow was more sensitive in detecting the full range of common Indian livestock animal fecal sources, while CowM2 only detected cow sources with 50% sensitivity. Neither assay cross-reacted with human sources. BacCan, the dog-associated assay tested, showed no cross-reactivity with human sources, and high sensitivity (90%) for dog fecal samples. Overall, our results indicate BacUni, BacHum, HumM2, BacCan and BacCow would be the most suitable MST assays to distinguish and quantify relative amounts of human-associated and livestock/domestic animal-associated contributions to fecal contamination in Odisha, India.

AB - We compared host-associated Bacteroidales qPCR assays developed in the continental United States and Europe for the purpose of measuring the effect of improved sanitation on human fecal exposure in rural Indian communities where both human and animal fecal loading are high. Ten candidate Bacteroidales qPCR assays were tested against fecal samples (human, sewage, cow, buffalo, goat, sheep, dog and chicken) from a test set of 30 individual human, 5 sewage, and 60 pooled animal samples collected in coastal Odisha, India. The two universal/general Bacteroidales assays tested (BacUni, GenBac3) performed equally well, achieving 100% sensitivity on the test set. Across the five human-associated assays tested (HF183 Taqman, BacHum, HumM2, BacH, HF183 SYBR), we found low sensitivity (17 to 49%) except for HF183 SYBR (89%), and moderate to high cross-reactivity with dog (20 to 80%) and chicken fecal samples (60 to 100%). BacHum had the highest accuracy (67%), amplified all sewage samples within the range of quantification (ROQ), and did not cross-react with any fecal samples from cows, the most populous livestock animal in India. Of the ruminant- and cattle-associated assays tested (BacCow, CowM2), BacCow was more sensitive in detecting the full range of common Indian livestock animal fecal sources, while CowM2 only detected cow sources with 50% sensitivity. Neither assay cross-reacted with human sources. BacCan, the dog-associated assay tested, showed no cross-reactivity with human sources, and high sensitivity (90%) for dog fecal samples. Overall, our results indicate BacUni, BacHum, HumM2, BacCan and BacCow would be the most suitable MST assays to distinguish and quantify relative amounts of human-associated and livestock/domestic animal-associated contributions to fecal contamination in Odisha, India.

KW - Bacteroidales

KW - Fecal pollution

KW - India

KW - Microbial source tracking

KW - Quantitative PCR

UR - http://www.scopus.com/inward/record.url?scp=84908354746&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84908354746&partnerID=8YFLogxK

U2 - 10.1016/j.scitotenv.2014.09.040

DO - 10.1016/j.scitotenv.2014.09.040

M3 - Article

C2 - 25285421

AN - SCOPUS:84908354746

VL - 502

SP - 462

EP - 470

JO - Science of the Total Environment

JF - Science of the Total Environment

SN - 0048-9697

ER -