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Comparison of genotypic-based microbial source tracking methods requiring a host origin database.

Samuel P Myoda1, C Andrew Carson, Jeffry J Fuhrmann

  • 1University of Missouri, Department of Veterinary Pathobiology, Columbia, MO 65211, USA. samuel.myoda@state.de.us

Journal of Water and Health
|September 24, 2004
PubMed
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Comparing microbial source tracking (MST) methods like PFGE, rep-PCR, and ribotyping revealed high accuracy in identifying fecal sources in water. However, significant false positive rates necessitate method optimization for reliable environmental monitoring.

Area of Science:

  • Environmental microbiology
  • Molecular biology techniques
  • Water quality assessment

Background:

  • Microbial source tracking (MST) is crucial for identifying fecal pollution in water bodies.
  • Common MST methods include pulsed field gel electrophoresis (PFGE), repetitive element PCR (rep-PCR), and ribotyping.
  • Standardization and validation of these methods are essential for accurate results.

Purpose of the Study:

  • To compare the performance of PFGE, rep-PCR, and ribotyping for MST.
  • To evaluate the accuracy and reliability of these methods across different fecal sources.
  • To identify sources of error and areas for improvement in MST techniques.

Main Methods:

  • Six investigators analyzed blind, duplicate water samples spiked with known fecal sources (sewage, human, dog, cow, seagull).

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  • PFGE, rep-PCR, and ribotyping techniques were applied to identify the dominant microbial source.
  • Fecal material samples were used to construct host origin databases for comparison.

    • Main Results:

    • All MST methods correctly identified the dominant fecal source in most samples.
    • Modified methods achieved over 90% accuracy in identifying dominant sources.
    • False positive rates reached as high as 57%, inversely correlated with pattern analysis stringency.

    Conclusions:

    • While MST methods provide valuable data for identifying fecal pollution, their accuracy is limited by false positives.
    • Optimization and modification of PFGE, rep-PCR, and ribotyping are necessary to minimize errors.
    • Standardized, stringent analysis is key to improving the reliability of microbial source tracking.