Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study

• Published in: Water research (Oxford) 2013-11, Vol.47 (18), p.6909-6920
• Main Authors: Schriewer, Alexander, Goodwin, Kelly D., Sinigalliano, Christopher D., Cox, Annie M., Wanless, David, Bartkowiak, Jakob, Ebentier, Darcy L., Hanley, Kaitlyn T., Ervin, Jared, Deering, Louise A., Shanks, Orin C., Peed, Lindsay A., Meijer, Wim G., Griffith, John F., SantoDomingo, Jorge, Jay, Jennifer A., Holden, Patricia A., Wuertz, Stefan
• Format: Article
• Language: English
• Subjects: Animals; Bacteroidales; Bacteroidetes - classification; Bacteroidetes - genetics; Bacteroidetes - isolation & purification; Bacteroidetes - metabolism; California; Canine fecal pollution; DNA, Bacterial - classification; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; dogs; Dogs - microbiology; Environmental Monitoring - methods; Feces; Microbial source tracking; monitoring; nucleotide sequences; pollution; Quantitative PCR; quantitative polymerase chain reaction; Real-Time Polymerase Chain Reaction - methods; ribosomal RNA; RNA, Ribosomal, 16S - classification; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - metabolism; Sensitivity and Specificity; Single-Blind Method; urbanization; Water Microbiology; Water Pollution - analysis
• ISSN: 0043-1354; 1879-2448
• DOI: 10.1016/j.watres.2013.03.062

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. [Display omitted] •Evaluation of two dog-associated MST assays on created single & mixed fecal source samples.•Classification and treatment method of qPCR data influenced performance assessment.•Normalization methods significantly influenced the evaluation of assay performance.•Methods presented to eliminate random and confirmed non-target assay responses.