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Comparison of seven protocols to identify fecal contamination sources using Escherichia coli

January 1, 2004

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% correct classification 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 hosts, three protocols correctly classified 33-100% of isolates as "unknown origin," whereas four protocols classified all isolates to a source category. A relevance test, summarizing interpretations for a hypothetical water sample containing 30 challenge isolates, indicated that false-positive classifications would hinder interpretations for most protocols. Study results indicate that more representation in known-source libraries and better classification accuracy would be needed before field application. Thorough reliability assessment of classification results is crucial before and during application of MST protocols.

Publication Year 2004
Title Comparison of seven protocols to identify fecal contamination sources using Escherichia coli
DOI 10.1021/es0354519
Authors D. M. Stoeckel, M.V. Mathes, K.E. Hyer, C. Hagedorn, H. Kator, J. Lukasik, T. L. O'Brien, T.W. Fenger, M. Samadpour, K.M. Strickler, B.A. Wiggins
Publication Type Article
Publication Subtype Journal Article
Series Title Environmental Science & Technology
Index ID 70026361
Record Source USGS Publications Warehouse