TY - JOUR
T1 - Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study
AU - Layton, Blythe A.
AU - Cao, Yiping
AU - Ebentier, Darcy L.
AU - Hanley, Kaitlyn
AU - Ballesté, Elisenda
AU - Brandão, João
AU - Byappanahalli, Muruleedhara
AU - Converse, Reagan
AU - Farnleitner, Andreas H.
AU - Gentry-Shields, Jennifer
AU - Gidley, Maribeth L.
AU - Gourmelon, Michèle
AU - Lee, Chang Soo
AU - Lee, Jiyoung
AU - Lozach, Solen
AU - Madi, Tania
AU - Meijer, Wim G.
AU - Noble, Rachel
AU - Peed, Lindsay
AU - Reischer, Georg H.
AU - Rodrigues, Raquel
AU - Rose, Joan B.
AU - Schriewer, Alexander
AU - Sinigalliano, Chris
AU - Srinivasan, Sangeetha
AU - Stewart, Jill
AU - Van De Werfhorst, Laurie C.
AU - Wang, Dan
AU - Whitman, Richard
AU - Wuertz, Stefan
AU - Jay, Jenny
AU - Holden, Patricia A.
AU - Boehm, Alexandria B.
AU - Shanks, Orin
AU - Griffith, John F.
N1 - Funding Information:
The authors are deeply grateful to Meredith Raith for her vital contribution to sample creation, data generation and data analysis. Steve Weisberg and Chuck Hagedorn helped develop the manuscript. We also greatly appreciate the students and staff of all labs that participated in the SIPP method evaluation study. Work in the Farnleitner Lab was funded by the Austrian Science Fund (FWF) projects # P22309-B20 and DK-plus #W1219-N22 . Work in the Rose Lab was funded by the National Oceanic and Atmospheric Administration ( NA04OAR4600199 ). Funding for the method evaluation study was through a Clean Beach Initiative Grant from the California State Water Resources Control Board. This article is Contribution 1758 of the U.S. Geological Survey Great Lakes Science Center. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
PY - 2013/11/15
Y1 - 2013/11/15
N2 - A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman®, HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman® was found to be the most effective marker of human fecal contamination in this California-based study.
AB - A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman®, HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman® was found to be the most effective marker of human fecal contamination in this California-based study.
KW - Bacteroidales
KW - Bacteroides
KW - Microbial source tracking
KW - QPCR
KW - Water quality
UR - http://www.scopus.com/inward/record.url?scp=84887163231&partnerID=8YFLogxK
U2 - 10.1016/j.watres.2013.05.060
DO - 10.1016/j.watres.2013.05.060
M3 - Journal article
C2 - 23992621
AN - SCOPUS:84887163231
SN - 0043-1354
VL - 47
SP - 6897
EP - 6908
JO - Water Research
JF - Water Research
IS - 18
ER -