Evaluation of two quantitative PCR assays using Bacteroidales and mitochondrial DNA markers for tracking dog fecal contamination in waterbodies

• Published in: Journal of microbiological methods 2012-12, Vol.91 (3), p.459-467
• Main Authors: Tambalo, Dinah D., Boa, Tyler, Liljebjelke, Karen, Yost, Christopher K.
• Format: Article
• Language: English
• Subjects: Alces alces; Animals; Bacteroidales markers; Bacteroidetes - classification; Bacteroidetes - genetics; Bacteroidetes - isolation & purification; Biological and medical sciences; bison; deer; DNA, Bacterial - genetics; DNA, Mitochondrial - genetics; Dogs; Environmental Monitoring; Fecal pollution; Fecal source tracking; Feces - chemistry; Feces - microbiology; Fresh Water - chemistry; Fresh Water - microbiology; Freshwater; Fundamental and applied biological sciences. Psychology; genetic markers; horses; Humans; Microbiology; Mitochondrial DNA; nontarget organisms; Oreamnos americanus; parks; Persistence; Polymerase Chain Reaction - methods; quantitative polymerase chain reaction; Rangifer tarandus; ribosomal RNA; RNA, Ribosomal, 16S - genetics; sewage; surface water; swine; Water Pollutants - chemistry
• ISSN: 0167-7012; 1872-8359
• DOI: 10.1016/j.mimet.2012.09.029

This study describes a comparative performance evaluation of two qPCR assays targeting a dog-associated Bacteroidales 16S rRNA genetic marker (CanBac-UCD) and a dog mitochondrial DNA (mtDNA) marker. The same fecal and environmental samples were assayed for the two markers thereby allowing direct comparison. A wide range of non-target species including, human, pig, horse, deer, mountain goat, bison, caribou, and moose were tested. Marker persistence was also monitored in freshwater microcosms. Both markers were prevalent in the canine samples collected in Regina, Saskatchewan and Calgary, Alberta, Canada (91% and 98% sensitivity, respectively). The mtDNA marker was detected exclusively in the target species while the CanBac-UCD marker was detected in all the non-target species (31% specificity). The CanBac-UCD marker exhibited faster decay in freshwater microcosms. The markers were rarely detected in the water samples collected from dog parks in Calgary and in Regina as well as from waterbodies and sewage influents in Saskatchewan, indicating possibly low to negligible levels of dog fecal contamination in the sampling areas. Altogether, the results of this study support the utility of the dog mtDNA assay in detecting dog fecal contamination in waterbodies. ► Two qPCR assays for tracking dog fecal contamination in waterbodies were compared. ► The Bacteroidales and the mtDNA markers had equally high (>90%) sensitivity. ► The mtDNA marker was superior for specificity. ► The Bacteroidales marker exhibited a faster decay in freshwater microcosms. ► Rare detection of the markers in urban water samples suggests low contamination levels.