Comparison of 7 microbial source identification techniques

["Richard L Whitman" <rwhitman@usgs.gov>]

Below  is  a  very  important abstract of an article that has been recently
published  by  Stoeckel  et  al.  in the Journal, Environmental Science and
Technology.   It  is a national survey comparing seven different techniques
for Microbial Source Tracking.  They looked at: "Reproducibility, accuracy,
and  robustness  of 7 phenotypic and genotypic MST protocols were evaluated
by  use of Escherichia coli from an 8-host library of known-source isolates
and a separate, blinded challenge library".  Anyone interested in investing
or  evaluating  source  identification  using these techniques will benefit
from  this  long  awaited article.  Don will be review the work at the GLBA
meeting this year as well.


































Comparison of Seven Protocols to Identify Fecal Contamination Sources using
                             Escherichia coli



    Donald M. Stoeckel1*, Melvin V. Mathes2, Kenneth E. Hyer3, Charles
   Hagedorn4, Howard Kator5, Jerzy Lukasik6, Tara L. O'Brien7, Terry W.
Fenger7, Mansour Samadpour8, Kriston M. Strickler9, and Bruce A. Wiggins10


  1U.S. Geological Survey, 6480 Doubletree Avenue, Columbus, Ohio 43229.


         2USGS, 11 Dunbar Street, Charleston, West Virginia 25301.


          3USGS, 1730 East Parham Road, Richmond, Virginia 23228.


4Virginia Polytechnic Institute and State University, Blacksburg, Virginia
                                  24061.


 5College of William and Mary, Virginia Institute of Marine Science, 1208
              Greate Road, Gloucester Point, Virginia 23062.


   6Biological Consulting Services of North Florida, 4641 NW 6th Street,
                        Gainesville, Florida 32609.


    7Marshall University School of Medicine, 1542 Spring Valley Drive,
                     Huntington, West Virginia, 25704.


   8Institute for Environmental Health, 8279 Lake City Way NE, Seattle,
                             Washington 98115.


 9West Virginia Department of Agriculture, 60B Moorefield Industrial Park
                   Rd, Moorefield, West Virginia 26836.


         10James Madison University, Harrisonburg, Virginia 22807


RECEIVED DATE


running header:  Comparison of seven MST protocols


* Corresponding author phone:  (614) 430-7780; fax: (614) 430-7777; e-mail:
stoeckel@usgs.gov





ABSTRACT:  Microbial  source  tracking  (MST)  uses  various  approaches to
classify  fecal-indicator microorganisms to source hosts.  Reproducibility,
accuracy,  and  robustness of 7 phenotypic and genotypic MST protocols were
evaluated by use of Escherichia coli from an 8-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  EcoR1  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
non-library 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.



KEYWORDS:   microbial source tracking, Escherichia coli, library dependent,
fecal contamination


 Richard Whitman
Chief, Lake Michigan Ecological Research Station
219-926-8336 Ext. 424

1100 North Mineral Springs Road
Porter, IN 46304




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