Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples

Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

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.

Genre:

USGS Numbered Series

ProdID:

70038985

Citation Author:

Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.

Citation Contributing Office:

Ohio Water Science Center

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Citation Language:

English

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Citation LatN:

0404000

Citation LatS:

0371000

Citation LonE:

-0774000

Citation LonW:

-0824000

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Citation Phsyical Description:

iv, 10 p.

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Prepared in cooperation with the West Virginia Department of Agriculture

Citation Publisher:

U.S. Geological Survey

Citation Series:

Scientific Investigations Report

Citation Series Code:

SIR

Citation Series Number:

2012-5087

Citation Search Results Text:

Interlaboratory comparison of three microbial source tracking quantitative polymerase chain reaction (qPCR) assays from fecal-source and environmental samples; 2012; SIR; 2012-5087; Stelzer, Erin A.; Strickler, Kriston M.; Schill, William B.