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

Environ Sci Technol. 2004 Nov 15;38(22):6109-17. doi: 10.1021/es0354519.


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

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Escherichia coli / classification*
  • Escherichia coli / isolation & purification
  • False Positive Reactions
  • Feces / microbiology*
  • Gene Library
  • Genotype
  • Humans
  • Phenotype
  • Reproducibility of Results
  • Ribotyping
  • Sensitivity and Specificity
  • Water Microbiology*