Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources

Raith, Meredith R.; Kelty, Catherine A.; Griffith, John F.; Schriewer, Alexander; Wuertz, Stefan; Mieszkin, Sophie; Gourmelon, Michèle; Reischer, Georg H.; Farnleitner, Andreas H.; Ervin, Jared; Holden, Patricia A.; Ebentier, Darcy L.; Jay, Jennifer A.; Wang, Dan; Boehm, Alexandria B.; Aw, Tiong Gim; Rose, Joan B.; Ballesté, Elisenda; Meijer, Wim G.; Sivaganesan, Mano; Shanks, Orin C.

doi:10.1016/j.watres.2013.03.061

Cited by 48 publications

(42 citation statements)

References 23 publications

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“…The review of 32 studies focusing on the HF183 marker by Ahmed and co-workers in 2016 (Ahmed et al, 2016) show an overall host sensitivity and specificity of 83.1% (n=1242 targeted fecal samples analysed) and 94.6% (n=2966 non targeted fecal samples tested). In addition, Pig2Bac marker was also found highly specific in USA and Israel and Rum2Bac in USA (Raith et al, 2013;Heaney et al, 2015;Ohad et al, 2015).…”

Section: Introductionmentioning

confidence: 88%

Application of a microbial source tracking based on bacterial and chemical markers in headwater and coastal catchments

Jardé

Jeanneau

Harrault

et al. 2018

Science of The Total Environment

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This study identified sources of fecal contamination in three different French headwater and coastal catchments (the Justiçou, Pen an Traon, and La Fresnaye) using a combination of microbial source tracking tools. The tools included bacterial markers (three host-associated Bacteroidales) and chemical markers (six fecal stanols), which were monitored monthly over one or two years in addition to fecal indicator bacteria. 168 of the 240 freshwater and marine water samples had Escherichia coli (E. coli) or enterococci concentrations higher than "excellent" European water quality threshold. In the three catchments, the results suggested that the fecal contamination appeared to be primarily from an animal origin and particularly from a bovine origin in 52% (Rum2Bac) and 46% (Bstanol) of the samples and to a lesser extent from a porcine origin in 19% (Pig2Bac) and 21% (Pstanol) of the samples. Our results suggested a human fecal contamination in 56% (HF183) and 32% (Hstanol) of the samples. Rainfall also impacted the source identification of microbial contamination. In general, these findings could inform effective implementation of microbial source tracking strategies, specifically that the location of sampling points must include variability at the landscape scale.

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Section: Introductionmentioning

confidence: 88%

Application of a microbial source tracking based on bacterial and chemical markers in headwater and coastal catchments

Jardé

Jeanneau

Harrault

et al. 2018

Science of The Total Environment

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show abstract

“…Data from all labs were used in this analysis, even though there were differing sizes of datasets and clear lab-to-lab variation (see Section 4.6), and our results should be interpreted with those factors in mind. To our knowledge, the present work and other manuscripts from this study Raith et al, 2013; are the first to examine the effects of changing fecal units of measure on the performance outcomes of molecular MST methods. We focused on total DNA mass as the primary challenge filter sample unit of measure.…”

Section: 2mentioning

confidence: 97%

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

Layton

Cao

Ebentier³

et al. 2013

Water Research

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121

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“…The false positive reaction maybe an significant issue when the target is present at low concentration in a background of high numbers of nontarget in DNA samples (Morisset et al 2013). The performance characteristics may vary due to uncharacterized factors such as LOD suggests that these methods must be tested before implementation in a particular region as confirmed by others (Raith et al 2013). In general, testing results out of clinical DNA samples show strong agreement between ddPCR and qPCR methods.…”

Section: Resultsmentioning

confidence: 54%

“…The performance characteristics may vary due to uncharacterized factors such as LOD suggests that these methods must be tested before implementation in a particular region as confirmed by others (Raith et al . ). In general, testing results out of clinical DNA samples show strong agreement between ddPCR and qPCR methods.…”

Section: Resultsmentioning

confidence: 97%

Comparison of next-generation droplet digital PCR with quantitative PCR for enumeration of Naegleria fowleri in environmental water and clinical samples

Xue

Caton

Sherchan

2018

Letters in Applied Microbiology

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This study explored the application of ddPCR and qPCR methods in identifying Naegleria fowleri from both clinical and environmental water samples. Strong agreement between ddPCR and qPCR methods over clinical DNA samples was observed. Naegleria fowleri was present in surface water samples from Lake Pontchartrain during our study period. The ability of N. fowleri to survive in brackish water is therefore a potential risk factor for people who engage in water-related recreational activities. The ddPCR performance demonstrated in this study on clinical and environmental samples lead to greater confidence of ddPCR technology on field application.

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Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources

Cited by 48 publications

References 23 publications

Application of a microbial source tracking based on bacterial and chemical markers in headwater and coastal catchments

Application of a microbial source tracking based on bacterial and chemical markers in headwater and coastal catchments

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

Comparison of next-generation droplet digital PCR with quantitative PCR for enumeration of Naegleria fowleri in environmental water and clinical samples

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