Microbial Source Tracking Method Comparison


Recommendations for Microbial Source Tracking

Microbiological Source Tracking Workshop Workgroup Findings and Recommendations

Evaluation of Microbial Source Tracking Methods

A Comparative Study of Culture-Independent, Library-Independent Genotypic Methods of Fecal Source Tracking

Assessment of Statistical Methods


There are numerous waterbodies throughout southern California, both marine and freshwater, that suffer contamination of fecal indicator bacteria such as total coliforms, fecal coliforms, and enterococcus.  Several Microbial Source Tracking (MST) techniques are now being developed for determining sources (i.e. humans, dogs, cats, horses, etc.) of fecal indicator bacteria in receiving waters.  However, all of them are in the early stages of development and none have been tested side-by-side for their ability to accurately discriminate or quantify these sources of fecal contamination.

This study was designed to evaluate each of these new methods for accuracy and precision, using bacterial sources from southern California, and then make recommendations to the management community on the most effective and efficient method application(s).

Twenty-one of the most prominent researchers in the field are testing nine different MST techniques all at the same time on the same split samples.  These techniques include techniques such as ribotyping, antibiotic resistance (ARA), pulsed-field gel electrophoresis (PFGE), polymerase chain reaction (PCR), and terminal restriction fragment length polymorphism (TRFLP). Each researcher will be asked three questions regarding blind samples:

  • Are human or non-human sources of indicator bacteria are present?
  • If non-human sources are present, what source are they (i.e., dog, cow, seagull)?
  • What fraction of the sample is attributable to each source?

Results shows no MST method tested predicted the source material in the blind samples perfectly.

  • Host-specific PCR performed best at differentiating between human and non-human sources, but primers are not yet available for differentiating among the non-human sources.
  • Virus and F+ coliphage methods reliably identified sewage, but were not able to identify fecal contamination from individual humans.
  • Library-based isolate methods were able to identify the dominant source in most samples, but had difficulty with false positives, identifying the presence of fecal sources that were not in the samples.
  • Among the library-based methods, genotypic methods generally performed better than phenotypic methods.

A copy of the final report, including reports from each of the individual researchers, was published in the December 2003 volume of the Journal of Water and Health that is dedicated to this study.