Estimating true human and animal host source contribution in quantitative microbial source tracking using the Monte Carlo method

Water Research

Volumn 44, Issue 16, 2010, Pages 4760-4775

  Wang, Dan ^a   Silkie, Sarah S ^b   Nelson, Kara L ^b   Wuertz, Stefan ^a  

^a Davis   (United States)

^b Univ of California   (United States)

Author keywords

Bacteroidales; Microbial source tracking (MST); Monte Carlo method; Quantitative PCR (qPCR)

Indexed keywords

ANIMALS; MEASUREMENT ERRORS; POLYMERASE CHAIN REACTION; PROBABILITY DISTRIBUTIONS; RISK ASSESSMENT;

BACTEROIDALES; DISTRIBUTIONS OF PROBABILITIES; FALSE POSITIVE AND FALSE NEGATIVES; MICROBIAL SOURCE TRACKING; QUANTITATIVE MICROBIAL RISK ASSESSMENT; QUANTITATIVE PCR; STATISTICAL CHARACTERISTICS; TOTAL MAXIMUM DAILY LOAD;

MONTE CARLO METHODS;

BIOASSAY; CONFIDENCE INTERVAL; GENETIC MARKER; GENOME; MICROORGANISM; MODEL TEST; MONTE CARLO ANALYSIS; POLLUTANT SOURCE; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS;

ACCURACY; ARTICLE; BACTEROIDALES; ENVIRONMENTAL MONITORING; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FECES; GENETIC MARKER; HOST; HUMAN; MEASUREMENT ERROR; MICROBIAL IDENTIFICATION; MONTE CARLO METHOD; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RELIABILITY; RISK ASSESSMENT; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; WATERSHED;

ANIMALIA; BACTEROIDALES;

EID: 77957019131     PISSN: 00431354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.watres.2010.07.076     Document Type: Article

References (37)

1. Ahmed W., Goonetilleke A., Powell D., Gardner T. Evaluation of multiple sewage-associated Bacteroidales PCR markers for sewage pollution tracking. Water Res. 2009, 43(19):4872-4877.
2. Anderson K.L., Whitlock J.E., Harwood V.J. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl. Environ. Microbiol. 2005, 71:3041-3048.
3. Bae S., Wuertz S. Rapid decay of host-specific fecal Bacteriodales cells in seawater as measured by quantitative PCR with prodidium monoazide. Water Res. 2009, 43(19):4850-4859.
4. Bambic D., Wuertz S., Ban M. Fecal source tracking using human toolkits based on library-independent chemical and microbial markers. Proc. Water Environ. Feder. 2007, 15:931-945.
5. Bernhard A.E., Field K.G. A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteriodales-Prevotella genes encoding 16S rRNA. Appl. Environ. Microbiol. 2000, 66(10):4571-4574.
6. Cooter W.S. Clean water act assessment processes in relation to changing U.S. Environmental Protection Agency management strategies. Environ. Sci. Technol. 2004, 38(20):5265-5273.
7. Dick L.K., Simonich M.T., Field K.G. Microplate subtractive hybridization to enrich for Bacteroidales genetic markers for fecal source identification. Appl. Environ. Microbiol. 2005, 71:3179-3183.
8. Dick L.K., Bernhard A.E., Brodeur T.J., Santo Domingo J.W., Simpson J.M., Walters S.P., Field K.G. Host distribution of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl. Environ. Microbiol. 2005, 3184-3191.
9. Field K., Bernhard A.E., Brodeur T.J. Molecular approaches to microbiological monitoring: fecal source detection. Environ. Monit. Assess. 2003, 81:313-326.
10. Houck O.A. The Clean Water Act TMDL Program: Law, Policy, and Implementation 2002, Environmental Law Institute, Washington, D.C. second ed.
11. Hong P., Wu J., Liu W. A high-throughput and quantitative hierarchical oligonucleotide primer extension (HOPE)-based approach to identify sources of faecal contamination in water bodies. Environ. Microbiol. 2009, 11(7):1672-1681.
12. Jenkins M.W., Tiwari S., Lorente M., Gichaba C.M., Wuertz S. Identifying human and livestock sources of fecal contamination in Kenya with host-specific Bacteroidales assays. Water Res. 2009, 43(19):4956-4966.
13. Jeter S.N., McDermott C.M., Bower P.A., Kinzelman J.K., Bootsma M.J., Goetz G.W., McLellan S.L. Bacteroidales diversity in ring-billed gulls (Laurus delawarensis) residing at lake Michigan beaches. Appl. Environ. Microbiol. 2009, 75(6):1525-1533.
14. Kildare B.J., Leutenegger C.M., McSwain B.S., Bambic D.G., Rajal V.B., Wuertz S. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. Water Res. 2007, 41:3701-3715.
15. Lamendella R., Santo Domingo J.W., Yannarell A.C., Ghosh S., Di Giovanni G., Mackie R.I., Oerther D.B. Evaluation of swine-specific PCR assays used for fecal source tracking and analysis of molecular diversity of swine-specific " Bacteroidales" populations. Appl. Environ. Microbiol. 2009, 75(18):5787-5796.
16. Layton A., McKay L., Williams D., Garrett V., Gentry R., Sayler G. Development of Bacteroidales 16S rRNA gene Taqman-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl. Environ. Microbiol. 2006, 72(6):4214-4224.
17. Leach M.D., Broschat S.L., Call D.R. A discrete, stochastic model and correction method for bacterial source tracking. Environ. Sci. Technol. 2008, 42:524-529.
18. Marti R., Dabert P., Pourcher A.M. Pig manure contamination marker selection based on the influence of biological treatment on the dominant fecal microbial groups. Appl. Environ. Microbiol. 2009, 75(5):4967-4974.
19. McLain J.E., Ryu H., Kabiri-Badr L., Rock C., Abbaszadegan M. Lack of specificity for PCR assays targeting human Bacteriodales 16S rRNA gene: cross-amplification with fish feces. FEMS Microbial. Lett. 2009, 299(1):38-43.
20. McLellan S.L., Huse S.M., Mueller-Spitz S.R., Andreishcheva E.N., Sogin M.L. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ. Microbiol. 2010, 12(2):378-392.
21. Mieszkin S., Furet J.P., Corthier G., Gourmelon M. Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific Bacteroidales 16S rRNA genetic markers. Appl. Environ. Microbiol. 2009, 75(10):3045-3054.
22. Okabe S., Okayama N., Savichtcheva O., Ito T. Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl. Environ. Microbiol. 2007, 74:890-901.
23. Okabe S., Shimazu Y. Persistence of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl. Microbiol. Biotechnol. 2007, 76:935-944.
24. Rajal V.B., McSwain B.S., Thompson D.E., Leutenegger C.M., Kildare B.J., Wuertz S. Validation of hollow fiber ultrafiltration and real-time PCR using bacteriophage PP7 as surrogate for the quantification of viruses from water samples. Water Res. 2007, 41(7):1411-1422.
25. Reckhow K.H. On the need for uncertainty assessment in TMDL modeling and implementation. J. Water Resour. Plann. Manag. - ASCE 2003, 129(4):245-246.
26. Reischer G.H., Kasper D.C., Steinborn R., Mach R.L., Farnleitner A.D. Quantitative PCR method for sensitive detection of ruminant fecal pollution in freshwater and evaluation of this method in alpine karstic regions. Appl. Environ. Microbiol. 2006, 5610-5614.
27. Santo Domingo J.W., Bambic D.G., Edge T.A., Wuertz S. Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. Water Res. 2007, 41(16):3539-3552.
28. Scott T.M., Rose J.B., Jenkins T.M., Farrah S.R., Lukasik J. Microbial source tracking: current methodology and future directions. Appl. Environ. Microbiol. 2002, 68:5796-5803.
29. Shanks O.C., Santo Domingo J.W., Lamendella R., Kelty C.A., Graham J.E. Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples. Appl. Environ. Microbiol. 2006, 4054-4060.
30. Shanks O.C., Atikovic E., Blackwood A.D., Lu J., Nobel R.T., Santo Domingo J., Seifring S., Sivaganesan M., Haugland R.A. Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Appl. Environ. Microbiol. 2008, 745-752.
31. Shanks O.C., Kelty C.A., Sivaganesan M., Varma M., Haugland R.A. Quantitative PCR for genetic markers of human fecal pollution. Appl. Environ. Microbiol. 2009, 75(17):5507-5513.
32. Silkie S.S., Nelson K.L. Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Res. 2009, 43(19):4860-4871.
33. Stapleton C.M., Kay D., Wyer M.D., Davies C., Watkins J., Kay C., McDonald A.T., Porter J., Gawler A. Evaluating the operational utility of a Bacteroidales quantitative PCR-based MST approach in determining the source of faecal indicator organisms at a UK bathing water. Water Res. 2009, 43:4888-4899.
34. Stoeckel D.M., Harwood V.J. Performance, design, and analysis in microbial source tracking studies. Appl. Environ. Microbiol. 2007, 73(8):2405-2415.
35. Microbial Source Tracking Guide Document 2005, US EPA.
36. Wilson D.J., Gabriel E., Leatherbarrow A.J.H., Cheesbrough J., Gee S., Bolton E., Fox A., Fearnhead P., Hart C.A., Diggle P.J. Tracking the source of campylobacteriosis. Genet 2008, 4(9):e1000203.
37. Witty M., Nickels J., Lisa J., Tiedemann J. Ecology, DNA, and the future of microbial source tracking. Water Air Soil Poll. 2009, 201:219-232.