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Toward Forensic Uses of Microbial Source Tracking

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  • Authors: Christopher M. Teaf1, David Flores2, Michele Garber3, Valerie J. Harwood4
  • Editors: Raúl J. Cano5, Gary A. Toranzos6
    Affiliations: 1: Hazardous Substance & Waste Management Research, Inc., Tallahassee, FL 32309; 2: Center for Progressive Reform, Washington, DC 20001; 3: Hazardous Substance & Waste Management Research, Inc., Tallahassee, FL 32309; 4: Department of Integrative Biology, University of South Florida, Tampa, FL 33620; 5: California Polytechnic State University, San Luis Obispo, CA; 6: University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico
  • Source: microbiolspec January 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.EMF-0014-2017
  • Received 11 May 2017 Accepted 30 November 2017 Published 19 January 2018
  • Valerie J. Harwood, [email protected]
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  • Abstract:

    The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

  • Citation: Teaf C, Flores D, Garber M, Harwood V. 2018. Toward Forensic Uses of Microbial Source Tracking. Microbiol Spectrum 6(1):EMF-0014-2017. doi:10.1128/microbiolspec.EMF-0014-2017.


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The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

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A simplified scheme for library-independent MST studies starts with identifying the animals within the study area that are likely to be major contributors to contamination. In this simplified version, we show two sources, cow and human (sewage). In the cow example, a type of fecal bacterium that is strongly associated with cow gastrointestinal tracts is denoted C. The bacterium is detected by extracting DNA and using PCR or qPCR to test for the DNA sequence (marker) that is specific to C. The sewage example follows the same flow, and the human-associated marker is denoted H. Note that in the case of certain viruses with RNA genomes, e.g., , RNA, rather than DNA, is extracted and tested. Water samples, in which the contamination source is unknown (?), can be tested by the MST methods to determine whether (PCR) and how much (qPCR) of the MST marker is present.

Source: microbiolspec January 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.EMF-0014-2017
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Select examples of MST methods currently in use, including some advantages and disadvantages of specific methods

Source: microbiolspec January 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.EMF-0014-2017

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