Performance Assessment PCR-Based Assays Targeting Bacteroidales Genetic Markers of Bovine Fecal Pollution

• DOI: 10.1128/aem.02033-09
• Publication Date: 2010-01-09T02:50:12Z
• Authors: Orin C. Shanks; Karen White; Catherine A. Kelty; Sam Hayes; Mano Sivaganesan; Michael Jenkins; Manju Varma; Richard A. Haugland
• Keywords: DNA, Bacterial; Genetic Markers; 0301 basic medicine; Bacteroidetes; DNA, Ribosomal; Polymerase Chain Reaction; Sensitivity and Specificity; Feces; 03 medical and health sciences; 13. Climate action; RNA, Ribosomal, 16S; Animals; Cattle; Water Pollutants

There are numerous PCR-based assays available to characterize bovine fecal pollution in ambient waters. The determination of which approaches most suitable for field applications can be difficult because each assay targets a different gene, many cases from microorganisms, leading variation performance. We describe performance evaluation seven end-point PCR and real-time quantitative (qPCR) reported associated with either ruminant or feces. Each was tested against reference collection DNA extracts 247 individual samples representing 11 populations 175 24 animal species. Bovine-associated genetic markers were broadly distributed among ranging 39 93%. Specificity levels the spanned 47.4% 100%. End-point sensitivity also varied between populations. For qPCR assays, abundance host-associated marker measured within population compared results targeting 16S rRNA gene sequences Bacteroidales. Experiments indicate large discrepancies bovine-associated across Variability host suggests that use microbial source-tracking will require priori characterization at watershed interest.