Comparison of Seven Protocols To Identify Fecal Contamination Sources Using Escherichia coli

Abstract

Microbial source tracking (MST) uses various approaches to classify fecal-indicator microorganisms to source hosts. Reproducibility, accuracy, and robustness of seven phenotypic and genotypic MST protocols were evaluated by use of Escherichia coli from an eight-host library of known-source isolates and a separate, blinded challenge library. In reproducibility tests, measuring each protocol's ability to reclassify blinded replicates, only one (pulsed-field gel electrophoresis; PFGE) correctly classified all test replicates to host species; three protocols classified 48-62% correctly, and the remaining three classified fewer than 25% correctly. In accuracy tests, measuring each protocol's ability to correctly classify new isolates, ribotyping with EcoRI and PvuII approached 100% correctclassification but only 6% of isolates were classified; four of the other six protocols (antibiotic resistance analysis, PFGE, and two repetitive-element PCR protocols) achieved better than random accuracy rates when 30-100% of challenge isolates were classified. In robustness tests, measuring each protocol's ability to recognize isolates from nonlibrary

Novel Bacteroides host strains for detection of human- and animal-specific bacteriophages in water

“…Leser et al (2000) showed that the bacterial species composition in the large intestine of pigs changed with different experimental diets; some profiles obtained by genetic fingerprinting techniques were stable while others varied in distribution and were related to specific diets. Geographical differences might also be due to spatial and temporal differences as previously reported for the composition of E. coli isolates within and between host species (human versus individual animals) (Gordon 2001;Stoeckel et al 2004). In this study, bacteriophages active against human host strains were abundant in human wastewater obtained from plants distributed all over…”

Effects of Stock Use and Backpackers on Water Quality in Wilderness in Sequoia and Kings Canyon National Parks, USA

“…One limitation associated with the use of E. coli in microbial water quality assessments is its limited value in the identification of fecal pollution sources (Stoeckel et al 2004;Stoeckel and Harwood 2007). Library-independent molecular methods based on quantitative polymerase chain reaction (qPCR), collectively known as quantitative microbial source tracking (qMST), have recently been developed (Stoeckel et al 2004;Stoeckel and Harwood 2007;Domingo et al 2007;Simpson et al 2004).…”

“…Library-independent molecular methods based on quantitative polymerase chain reaction (qPCR), collectively known as quantitative microbial source tracking (qMST), have recently been developed (Stoeckel et al 2004;Stoeckel and Harwood 2007;Domingo et al 2007;Simpson et al 2004). The qMST methods have been primarily used in urban and agricultural settings to distinguish human and non-human sources of pollution.…”

Microbial Source Tracking in a Watershed Dominated by Swine

“…Any isolates which failed to grow on the control plates were excluded from the analysis. The details of the ARA procedure have been described and are the same as that used in the method comparison studies [23,32,36]. …”

“…Two source tracking methods comparison studies reported issues with accuracy for numerous source tracking methods, including ARA. However, both studies also described approaches that could compensate for potential problems [35,36]. Such approaches include the application of cross-validation analysis of known-source isolates as well as the removal of clonal isolates to ensure a reliable library.…”