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Scientific Investigations Report 2012–5087

Prepared in cooperation with the West Virginia Department of Agriculture

Interlaboratory Comparison of Results for Three Microbial Source Tracking Quantitative Polymerase Chain Reaction (qPCR) Assays from Fecal-Source and Environmental Samples

By Erin A. Stelzer, Kriston M. Strickler, and William B. Schill

Thumbnail of and link to report PDF (372 KB)Abstract

During summer and early fall 2010, 15 river samples and 6 fecal-source samples were collected in West Virginia. These samples were analyzed by three laboratories for three microbial source tracking (MST) markers: AllBac, a general fecal indicator; BacHum, a human-associated fecal indicator; and BoBac, a ruminant-associated fecal indicator. MST markers were analyzed by means of the quantitative polymerase chain reaction (qPCR) method. The aim was to assess interlaboratory precision when the three laboratories used the same MST marker and shared deoxyribonucleic acid (DNA) extracts of the samples, but different equipment, reagents, and analyst experience levels. The term assay refers to both the markers and the procedure differences listed above. Interlaboratory precision was best for all three MST assays when using the geometric mean absolute relative percent difference (ARPD) and Friedman’s statistical test as a measure of interlaboratory precision. Adjustment factors (one for each MST assay) were calculated using results from fecal-source samples analyzed by all three laboratories and applied retrospectively to sample concentrations to account for differences in qPCR results among labs using different standards and procedures. Following the application of adjustment factors to qPCR results, ARPDs were lower; however, statistically significant differences between labs were still observed for the BacHum and BoBac assays. This was a small study and two of the MST assays had 52 percent of samples with concentrations at or below the limit of accurate quantification; hence, more testing could be done to determine if the adjustment factors would work better if the majority of sample concentrations were above the quantification limit.

First posted July 10, 2012

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Suggested citation:

Stelzer, E.A., Strickler, K.M., and Schill, W.B., 2012, Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples: U.S. Geological Survey Scientific Investigations Report 2012–5087, 10 p.




Methods of Study

Interlaboratory Comparison of Standard Curves

Interlaboratory Comparison of Results from Microbial Source Tracking Assays

Summary and Conclusion

References Cited

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