Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation

Asja Korajkic; Don Stoeckel; John F. Griffith

doi:10.1128/9781555818821.ch3.4.2

Chapter 3.4.2 : Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation

Authors: Asja Korajkic¹, Don Stoeckel², John F. Griffith³

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Affiliations: 1: U.S. Environmental Protection Agency; 2: Battelle Memorial Institute; 3: Southern California Coastal Water Research Program

Content Type: Reference

Publication Year: 2016

Category: Environmental Microbiology

Book DOI: 10.1128/9781555818821

Chapter DOI: 10.1128/9781555818821.ch3.4.2

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Abstract:

The goal of this chapter is to provide an overview of MST marker characteristics, to describe performance criteria of detection protocols used and to offer guidelines for the effective interpretation of the results. Since the trend in the research community has shifted towards (q)PCR detection of MST markers targeting either a variable region of the 16S rDNA or functional genes involved in host-microbe interactions, the focus of this chapter is on validation of these specific targets and protocols used to detect them. The most basic performance criteria applied to MST markers are based on the sensitivity and specificity characteristics, which are assessed by testing the marker against fecal material from a broad range of target and non-target hosts. While some information may be gathered through in silico, theoretical testing (e.g. hypergeometric tables, NCBI/BLAST searches), empirical data is needed in order to accurately assess performance of a given marker.

Citation: Korajkic A, Stoeckel D, Griffith J. 2016. Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation, p 3.4.2-1-3.4.2-13. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.2

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Tables

Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation

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TABLE 1

Host range and known cross-reactivity of MST markers

TABLE 1

Host range and known cross-reactivity of MST markers