Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study
| Autor: | Patricia A. Holden, Darcy L. Ebentier, Jakob Bartkowiak, Jared S. Ervin, Jorge Santo-Domingo, Louise Deering, Annie M. Cox, Kelly D. Goodwin, David Wanless, Orin C. Shanks, Lindsay Peed, Wim G. Meijer, Christopher D. Sinigalliano, Kaitlyn T. Hanley, John F. Griffith, Alexander Schriewer, Stefan Wuertz, Jennifer A. Jay |
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| Rok vydání: | 2012 |
| Předmět: |
Normalization (statistics)
DNA Bacterial Environmental Engineering Computational biology Bioinformatics Real-Time Polymerase Chain Reaction Data treatment Sensitivity and Specificity California law.invention Feces Dogs law RNA Ribosomal 16S Animals Single-Blind Method Waste Management and Disposal Polymerase chain reaction Water Science and Technology Civil and Structural Engineering Microbial source tracking Cycle threshold biology Bacteroidetes Ecological Modeling Water Pollution Data interpretation biology.organism_classification Pollution Bacteroidales Comparison study Water Microbiology Environmental Monitoring |
| Zdroj: | Water research. 47(18) |
| ISSN: | 1879-2448 |
| Popis: | The contribution of fecal pollution from dogs in urbanized areas can be significant and is an often underestimated problem. Microbial source tracking methods (MST) utilizing quantitative PCR of dog-associated gene sequences encoding 16S rRNA of Bacteroidales are a useful tool to estimate these contributions. However, data about the performance of available assays are scarce. The results of a multi-laboratory study testing two assays for the determination of dog-associated Bacteroidales (DogBact and BacCan-UCD) on 64 single and mixed fecal source samples created from pooled fecal samples collected in California are presented here. Standardization of qPCR data treatment lowered inter-laboratory variability of sensitivity and specificity results. Both assays exhibited 100% sensitivity. Normalization methods are presented that eliminated random and confirmed non-target responses. The combination of standardized qPCR data treatment, use of normalization via a non-target specific Bacteroidales assay (GenBac3), and application of threshold criteria improved the calculated specificity significantly for both assays. Such measures would reasonably improve MST data interpretation not only for canine-associated assays, but for all qPCR assays used in identifying and monitoring fecal pollution in the environment. |
| Databáze: | OpenAIRE |
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