1887

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

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $30.00

Preview this chapter:
Zoom in
Zoomout

Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch3.4.2-1.gif /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch3.4.2-2.gif

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
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555818821.ch3.4.2
1. Simpson JM, Santo Domingo JW, Reasoner DJ. 2002. Microbial source tracking: state of the science. Environ Sci Technol 36:52795288.[PubMed][CrossRef]
2. Samadpour M, Chechowitz N. 1995. Little Soos Creek microbial source tracking—a survey. University of Washington, Department of Environmental Health.
3. Wiggins BA. 1996. Discriminant analysis of antibiotic resistance patterns in fecal streptococci, a method to differentiate human and animal sources of fecal pollution in natural waters. Appl Environ Microbiol 62:39974002.[PubMed]
4. Field KG, Samadpour M. 2007. Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41:35173538.[PubMed][CrossRef]
5. Santo Domingo J, Edge T, Griffith J, Hansel J, Harwood VJ, Jenkins M, Layton A, Molina M, Nakatsu C, Oshiro R, Sadowsky M, Shanks O, Stelma G, Stewart J, Stoeckel D, Wiggins B, Wilbur J. 2005. Microbial source tracking guide document. EPA/600-R-05-064. U.S. EPA.
6. Harwood VJ, Stoeckel DM,. 2011. Performance criteria, p 730. In Hagedorn C,, Blanch AR,, Harwood VJ (eds), Microbial Source Tracking: Methods, Applications, and Case Studies. Springer, New York.
7. Santo Domingo JW, Sadowsky MJ. 2007. Microbial Source Tracking. ASM Press, Washington, DC.
8. Wade TJ, Sams E, Brenner KP, Haugland R, Chern E, Beach M, Wymer L, Rankin CC, Love D, Li Q, Noble R, Dufour AP. 2010. Rapidly measured indicators of recreational water quality and swimming-associated illness at marine beaches: a prospective cohort study. Environ Health 9:66.[PubMed][CrossRef]
9. Bernhard AE, Field KG. 2000. Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Appl Environ Microbiol 66:15871594.[PubMed][CrossRef]
10. Kreader CA. 1998. Persistence of PCR-detectable Bacteroides distasonis from human feces in river water. Appl Environ Microbiol 64:41034105.[PubMed]
11. Seurinck S, Defoirdt T, Verstraete W, Siciliano SD. 2005. Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ Microbiol 7:249259.[PubMed][CrossRef]
12. Shanks OC, Nietch C, Simonich M, Younger M, Reynolds D, Field KG. 2006. Basin-wide analysis of the dynamics of fecal contamination and fecal source identification in Tillamook Bay, Oregon. Appl Environ Microbiol 72:55375546.[PubMed][CrossRef]
13. Lu J, Santo Domingo J, Shanks OC. 2007. Identification of chicken-specific fecal microbial sequences using a metagenomic approach. Water Res 41:35613574.[PubMed][CrossRef]
14. Carson CA, Christiansen JM, Yampara-Iquise H, Benson VW, Baffaut C, Davis JV, Broz RR, Kurtz WB, Rogers WM, Fales WH. 2005. Specificity of a Bacteroides thetaiotaomicron marker for human feces. Appl Environ Microbiol 71:49454949.[PubMed][CrossRef]
15. Shanks OC, White K, Kelty CA, Hayes S, Sivaganesan M, Jenkins M, Varma M, Haugland RA. 2010. Performance assessment PCR-based assays targeting Bacteroidales genetic markers of bovine fecal pollution. Appl Environ Microbiol 76:13591366.[PubMed][CrossRef]
16. Shanks OC, White K, Kelty CA, Sivaganesan M, Blannon J, Meckes M, Varma M, Haugland RA. 2010. Performance of PCR-based assays targeting Bacteroidales genetic markers of human fecal pollution in sewage and fecal samples. Environ Sci Technol 44:62816288.[PubMed][CrossRef]
17. Kirs M, Harwood VJ, Fidler AE, Gillespie PA, Fyfe WR, Blackwood AD, Cornelisen CD. 2011. Source tracking faecal contamination in an urbanised and a rural waterway in the Nelson-Tasman region, New Zealand. New Zealand J Mar Freshw Res 45:4358.[CrossRef]
18. McQuaig SM, Scott TM, Lukasik JO, Paul JH, Harwood VJ. 2009. Quantification of human polyomaviruses JC Virus and BK Virus by TaqMan quantitative PCR and comparison to other water quality indicators in water and fecal samples. Appl Environ Microbiol 75:33793388.[PubMed][CrossRef]
19. Ahmed W, Yusuf R, Hasan I, Goonetilleke A, Gardner T. 2010. Quantitative PCR assay of sewage-associated Bacteroides markers to assess sewage pollution in an urban lake in Dhaka, Bangladesh. Can J Microbiol 56:838845.[PubMed][CrossRef]
20. McLain JE, Ryu H, Kabiri-Badr L, Rock CM, Abbaszadegan M. 2009. Lack of specificity for PCR assays targeting human Bacteroides 16S rRNA gene: cross-amplification with fish feces. FEMS Microbiol Lett 299:3843.[PubMed][CrossRef]
21. Bernhard AE, Field KG. 2000. A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA. Appl Environ Microbiol 66:45714574.[PubMed][CrossRef]
22. Layton A, McKay L, Williams D, Garrett V, Gentry R, Sayler G. 2006. Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl Environ Microbiol 72:42144224.[PubMed][CrossRef]
23. Silkie SS, Nelson KL. 2009. Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Res 43:48604871.[PubMed][CrossRef]
24. Kildare BJ, Leutenegger CM, McSwain BS, Bambic DG, Rajal VB, Wuertz S. 2007. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. Water Res 41:37013715.[PubMed][CrossRef]
25. Reischer GH, Kasper DC, Steinborn R, Farnleitner AH, Mach RL. 2007. A quantitative real-time PCR assay for the highly sensitive and specific detection of human faecal influence in spring water from a large alpine catchment area. Lett Appl Microbiol 44:351356.[PubMed][CrossRef]
26. Lee CS, Lee J. 2010. Evaluation of new gyrB-based real-time PCR system for the detection of B. fragilis as an indicator of human-specific fecal contamination. J Microbiol Meth 82:311318.[CrossRef]
27. Okabe S, Okayama N, Savichtcheva O, Ito T. 2007. Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl Microbiol Biotechnol 74:890901.[PubMed][CrossRef]
28. Haugland RA, Varma M, Sivaganesan M, Kelty C, Peed L, Shanks OC. 2010. Evaluation of genetic markers from the 16S rRNA gene V2 region for use in quantitative detection of selected Bacteroidales species and human fecal waste by qPCR. Syst Appl Microbiol 33:348357.[PubMed][CrossRef]
29. Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA. 2009. Quantitative PCR for genetic markers of human fecal pollution. Appl Environ Microbiol 75:55075513.[PubMed][CrossRef]
30. Shanks OC, Domingo JW, Lu J, Kelty CA, Graham JE. 2007. Identification of bacterial DNA markers for the detection of human fecal pollution in water. Appl Environ Microbiol 73:24162422.[PubMed][CrossRef]
31. Yampara-Iquise H, Zheng G, Jones JE, Carson CA. 2008. Use of a Bacteroides thetaiotaomicron-specific alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water. J Appl Microbiol 105:16861693.[PubMed][CrossRef]
32. Layton BA, Walters SP, Boehm AB. 2009. Distribution and diversity of the enterococcal surface protein (esp) gene in animal hosts and the Pacific coast environment. J Appl Microbiol 106:15211531.[PubMed][CrossRef]
33. Whitman RL, Przybyla-Kelly K, Shively DA, Byappanahalli MN. 2007. Incidence of the enterococcal surface protein (esp) gene in human and animal fecal sources. Environ Sci Technol 41:60906095.[PubMed][CrossRef]
34. Scott TM, Jenkins TM, Lukasik J, Rose JB. 2005. Potential use of a host associated molecular marker in Enterococcus faecium as an index of human fecal pollution. Environ Sci Technol 39:283287.[PubMed][CrossRef]
35. Ahmed W, Stewart J, Gardner T, Powell D. 2008. A real-time polymerase chain reaction assay for quantitative detection of the human-specific enterococci surface protein marker in sewage and environmental waters. Environ Microbiol 10:32553264.[PubMed][CrossRef]
36. Johnston C, Ufnar JA, Griffith JF, Gooch JA, Stewart JR. 2010. A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution. J Appl Microbiol 109:19461956.[PubMed][CrossRef]
37. Harwood VJ, Brownell M, Wang S, Lepo J, Ellender RD, Ajidahun A, Hellein KN, Kennedy E, Ye XY, Flood C. 2009. Validation and field testing of library-independent microbial source tracking methods in the Gulf of Mexico. Water Res 43:48124819.[PubMed][CrossRef]
38. Ufnar JA, Wang SY, Christiansen JM, Yampara-Iquise H, Carson CA, Ellender RD. 2006. Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters. J Appl Microbiol 101:4452.[PubMed][CrossRef]
39. McQuaig SM, Scott TM, Harwood VJ, Farrah SR, Lukasik JO. 2006. Detection of human-derived fecal pollution in environmental waters by use of a PCR-based human polyomavirus assay. Appl Environ Microbiol 72:75677574.[PubMed][CrossRef]
40. Martellini A, Payment P, Villemur R. 2005. Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Res 39:541548.[PubMed][CrossRef]
41. Caldwell JM, Levine JF. 2009. Domestic wastewater influent profiling using mitochondrial real-time PCR for source tracking animal contamination. J Microbiol Meth 77:1722.[CrossRef]
42. Schill WB, Mathes MV. 2008. Real-time PCR detection and quantification of nine potential sources of fecal contamination by analysis of mitochondrial cytochrome b targets. Environ Sci Technol 42:52295234.[PubMed][CrossRef]
43. Mieszkin S, Furet JP, Corthier G, Gourmelon M. 2009. 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 75:30453054.[PubMed][CrossRef]
44. Hundesa A, de Motes CM, Albinana-Gimenez N, Rodriguez-Manzano J, Bofill-Mas S, Sunen E, Girones RR. 2009. Development of a qPCR assay for the quantification of porcine adenoviruses as an MST tool for swine fecal contamination in the environment. J Virol Meth 158:130135.[CrossRef]
45. Shanks OC, Santo Domingo JW, Lamendella R, Kelty CA, Graham JE. 2006. Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples. Appl Environ Microbiol 72:40544060.[PubMed][CrossRef]
46. Shanks OC, Atikovic E, Blackwood AD, Lu J, Noble RT, Domingo JS, Seifring S, Sivaganesan M, Haugland RA. 2008. Quantitative PCR for detection and enumeration of genetic markers of bovine fecal pollution. Appl Environ Microbiol 74:745752.[PubMed][CrossRef]
47. Lee DY, Weir SC, Lee H, Trevors JT. 2010. Quantitative identification of fecal water pollution sources by TaqMan real-time PCR assays using Bacteroidales 16S rRNA genetic markers. Appl Microbiol Biotechnol 88:13731383.[PubMed][CrossRef]
48. Lu JR, Santo Domingo JW, Lamendella R, Edge T, Hill S. 2008. Phylogenetic diversity and molecular detection of bacteria in gull feces. Appl Environ Microbiol 74:39693976.[PubMed][CrossRef]
49. Green HC, Dick LK, Gilpin B, Samadpour M, Field KG. 2011. Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water. Appl Environ Microbiol 78:503510.[PubMed][CrossRef]
50. Fremaux B, Boa T, Yost CK. 2010. Quantitative real-time PCR assays for sensitive detection of Canada goose-specific fecal pollution in water sources. Appl Environ Microbiol 76:48864889.[PubMed][CrossRef]
51. Weidhaas JL, Macbeth TW, Olsen RL, Sadowsky MJ, Norat D, Harwood VJ. 2010. Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assay. J Appl Microbiol 109:334347.[PubMed]
52. Ryu H, Lu JR, Vogel J, Elk M, Chavez-Ramirez F, Ashbolt N, Domingo JS. 2012. Development and evaluation of a quantitative PCR assay targeting sandhill crane (Grus canadensis) fecal pollution. Appl Environ Microbiol 78:43384345.[PubMed][CrossRef]
53. Marti R, Zhang Y, Lapen DR, Topp E. 2011. Development and validation of a microbial source tracking marker for the detection of fecal pollution by muskrats. J Microbiol Methods 87:8288.[PubMed][CrossRef]
54. Dick LK, Field KG. 2004. Rapid estimation of numbers of fecal Bacteroidetes by use of a quantitative PCR assay for 16S rRNA genes. Appl Environ Microbiol 70:56955697.[PubMed][CrossRef]
55. Buhnik-Rosenblau K, Matsko-Efimov V, Jung M, Shin H, Danin-Poleg Y, Kashi Y. 2012. Indication for Co-evolution of Lactobacillus johnsonii with its hosts. BMC Microbiol 12:149.[PubMed][CrossRef]
56. Pace NR, Sapp J, Goldenfeld N. 2012. Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad SciUSA 109:10111018.[CrossRef]
57. Mara DD, Oragui JI. 1983. Sorbitol-fermenting bifidobacteria as specific indicators of human faecal pollution. J Appl Bacteriol 55:349357.[PubMed][CrossRef]
58. Rhodes MW, Kator H. 1999. Sorbitol-fermenting bifidobacteria as indicators of diffuse human faecal pollution in estuarine watersheds. J Appl Microbiol 87:528535.[PubMed][CrossRef]
59. Savill MG, Murray SR, Scholes P, Maas EW, McCormick RE, Moore EB, Gilpin BJ. 2001. Application of polymerase chain reaction (PCR) and TaqMan PCR techniques to the detection and identification of Rhodococcus coprophilus in faecal samples. J Microbiol Meth 47:355368.[CrossRef]
60. Bonjoch X, Balleste E, Blanch AR. 2005. Enumeration of bifidobacterial populations with selective media to determine the source of waterborne fecal pollution. Water Res 39:16211627.[PubMed][CrossRef]
61. Moussa SH, Massengale RD. 2008. Identification of the sources of Escherichia coli in a watershed using carbon-utilization patterns and composite data sets. J Water Health 6:197207.[PubMed][CrossRef]
62. Hagedorn C, Robinson SL, Filtz JR, Grubbs SM, Angier TA, Reneau RBJr. 1999. Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci. Appl Environ Microbiol 65:55225531.[PubMed]
63. Griffith JF, Weisberg SB, McGee CD. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. J Water Health 1:141151.[PubMed]
64. Leeming R, Ball A, Ashbolt N, Nichols PD. 1996. Using faecal sterols from humans and animals to distinguish faecal pollution in receiving waters. Water Res 30:28932900.[CrossRef]
65. Gourmelon M, Caprais MP, Mieszkin S, Marti R, Wery N, Jarde E, Derrien M, Jadas-Hecart A, Communal PY, Jaffrezic A, Pourcher AM. 2010. Development of microbial and chemical MST tools to identify the origin of the faecal pollution in bathing and shellfish harvesting waters in France. Water Res 44:48124824.[PubMed][CrossRef]
66. Hartel PG, Rodgers K, Moody GL, Hemmings SN, Fisher JA, McDonald JL. 2008. Combining targeted sampling and fluorometry to identify human fecal contamination in a freshwater creek. J Water Health 6:105116.[PubMed][CrossRef]
67. Dickerson JWJr, Hagedorn C, Hassall A. 2007. Detection and remediation of human-origin pollution at two public beaches in Virginia using multiple source tracking methods. Water Res 41:37583770.[PubMed][CrossRef]
68. Cao Y, Van De Werfhorst LC, Sercu B, Murray JL, Holden PA. 2012. Application of an integrated community analysis approach for microbial source tracking in a coastal creek. Environ Sci Technol 45:71957201.[CrossRef]
69. Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, Hazen TC, Holden PA, Andersen GL. 2010. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One 5:e11285.[PubMed][CrossRef]
70. Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG. 2010. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44:77777782.[PubMed][CrossRef]
71. Gentry-Shields J, Wang A, Cory RM, Stewart JR. 2013. Determination of specific types and relative levels of QPCR inhibitors in environmental water samples using excitation-emission matrix spectroscopy and PARAFAC. Water Res 47:34673476.[PubMed][CrossRef]
72. Green HC, Field KG. 2012. Sensitive detection of sample interference in environmental qPCR. Water Res 46:32513260.[PubMed][CrossRef]
73. Noble RT, Blackwood AD, Griffith JF, McGee CD, Weisberg SB. 2010. Comparison of rapid quantitative PCR-based and conventional culture-based methods for enumeration of Enterococcus spp. and Escherichia coli in recreational waters. Appl Environ Microbiol 76:74377443.[PubMed][CrossRef]
74. Haugland RA, Siefring S, Lavender J, Varma M. 2012. Influences of sample interference and interference controls on quantification of enterococci fecal indicator bacteria in surface water samples by the qPCR method. Water Res 46:59896001.[PubMed][CrossRef]
75. U.S. Environmental Protection Agency. 2010. Method B: Bacteroidales in Water by TaqMan Quantitative Polymerase Chain Reaction (qPCR) Assay. EPA-822-R-10-003.
76. U.S. Environmental Protection Agency. 2010. Method A: Enterococci in Water by TaqMan Quantitative Polymerase Chain Reaction (qPCR) Assay. EPA-821-R-10-004.
77. Halliday E, Griffith JF, Gast RJ. 2010. Use of an exogenous plasmid standard and quantitative PCR to monitor spatial and temporal distribution of Enterococcus spp. in beach sands. Limnol Oceanog Meth/ASLO 8:146154.[CrossRef]
78. Haugland RA, Siefring SC, Wymer LJ, Brenner KP, Dufour AP. 2005. Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res 39:559568.[PubMed][CrossRef]
79. Geldreich EE. 1969. Water pollution. Microbiol JWater Poll Cont Fed 41:10531069.
80. Geldreich EE. 1976. Microbiology of water. J Water Poll Cont Fed 48:13381356.
81. Pourcher AM, Devriese LA, Hernandez JF, Delattre JM. 1991. Enumeration by a miniaturized method of Escherichia coli, Streptococcus bovis and enterococci as indicators of the origin of faecal pollution of waters. J Appl Bacteriol 70:525530.[PubMed][CrossRef]
82. Mara DD, Oragui JI. 1981. Occurrence of Rhodococcus coprophilus and associated actinomycetes in feces, sewage, and freshwater. Appl Environ Microbiol 42:10371042.[PubMed]
83. McFeters GA, Bissonnette GK, Jezeski JJ, Thomson CA, Stuart DG. 1974. Comparative survival of indicator bacteria and enteric pathogens in well water. Appl Microbiol 27:823829.[PubMed]
84. Stoeckel DM, Stelzer EA, Stogner RW, Mau DP. 2011. Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence. Water Res 45:32253244.[PubMed][CrossRef]
85. Wang D, Silkie SS, Nelson KL, Wuertz S. 2010. Estimating true human and animal host source contribution in quantitative microbial source tracking using the Monte Carlo method. Water Res 44:47604675.[PubMed][CrossRef]
86. Myoda SP, Carson CA, Fuhrmann JJ, Hahm BK, Hartel PG, Yampara-Lquise H, Johnson L, Kuntz RL, Nakatsu CH, Sadowsky MJ, Samadpour M. 2003. Comparison of genotypic-based microbial source tracking methods requiring a host origin database. J Water Health 1:167180.[PubMed]
87. Stoeckel DM, Mathes MV, Hyer KE, Hagedorn C, Kator H, Lukasik J, O'Brien TL, Fenger TW, Samadpour M, Strickler KM, Wiggins BA. 2004. Comparison of seven protocols to identify fecal contamination sources using Escherichia coli. Environ Sci Technol 38:61096117.[PubMed][CrossRef]
88. Harwood VJ, Wiggins B, Hagedorn C, Ellender RD, Gooch J, Kern J, Samadpour M, Chapman AC, Robinson BJ, Thompson BC. 2003. Phenotypic library-based microbial source tracking methods: efficacy in the California collaborative study. J Water Health 1:153166.[PubMed]
89. Rigsbee L, Agans R, Foy BD, Paliy O. 2011. Optimizing the analysis of human intestinal microbiota with phylogenetic microarray. FEMS Microbiol Ecol 75:332342.[PubMed][CrossRef]
90. Boehm AB, Werfhorst LCVD, Griffith JF, Holden PA, Jay JA, Shanks OC, Wang D, Weisberg SB. 2013. Performance of forty-one microbial source tracking methods: a twenty-seven lab evaluation study. Water Res 47:68126828.[PubMed][CrossRef]
91. Stoeckel DM, Harwood VJ. 2007. Performance, design, and analysis in microbial source tracking studies. Appl Environ Microbiol 73:24052415.[PubMed][CrossRef]
92. Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A. 2014. Microbial source tracking markers for detection of fecal contamination in environmental waters: relationship to pathogens and human health outcomes. FEMS Microbiol Rev 38:140.[PubMed][CrossRef]
93. Johnson WO, Su CL, Gardner IA, Christensen R. 2004. Sample size calculations for surveys to substantiate freedom of populations from infectious agents. Biometrics 60:165171.[PubMed][CrossRef]
94. Ebentier DL, Hanley KT, Cao Y, Badgley BD, Boehm AB, Ervin JS, Goodwin KD, Gourmelon M, Griffith JF, Holden PA, Kelty CA, Lozach S, McGee C, Peed LA, Raith M, Ryu H, Sadowsky MJ, Scott EA, Santo Domingo J, Sinigalliano CD, Shanks OC, Werfhorst LCVD, Wang D, Wuertz S, Jay JA. 2012. Evaluation of the repeatability and reproducibility of a suite of qOCR-based microbial source tracking methods. Water Res 47:68396848.[CrossRef]
95. Harwood VJ, Gordon KV, Staley C. 2011. Validation of rapid methods for enumeration of markers for human sewage contamination in recreational water. Water Environment Research Foundation, Alexandria, VA, PATH3C09.
96. Staley C, Gordon KV, Schoen ME, Harwood VJ. 2012. Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters. Appl Environ Microbiol 78:73177326.[PubMed][CrossRef]
97. Cao YP, Sivaganesan M, Kinzelman J, Blackwood AD, Noble RT, Haugland RA, Griffith JF, Weisberg SB. 2013. Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods. Water Res 47:233241.[PubMed][CrossRef]
98. Stewart JR, Gast RJ, Fujioka RS, Solo-Gabriele HM, Meschke JS, Amaral-Zettler LA, Del Castillo E, Polz MF, Collier TK, Strom MS, Sinigalliano CD, Moeller PD, Holland AF. 2008. The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs. Environ Health 7(Suppl 2):S3.[PubMed][CrossRef]
99. Stoeckel DM, Stelzer EA, Dick LK. 2009. Evaluation of two spike-and-recovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Res 43:48204827.[PubMed][CrossRef]
100. Siefring S, Varma M, Atikovic E, Wymer L, Haugland RA. 2008. Improved real-time PCR assays for the detection of fecal indicator bacteria in surface waters with different instrument and reagent systems. J Water Health 6:225237.[PubMed][CrossRef]
101. Shanks OC, Sivaganesan M, Peed L, Kelty CA, Blackwood AD, Greene MR, Noble RT, Bushon RN, Stelzer EA, Kinzelman J, Anan'eva T, Sinigalliano C, Wanless D, Griffith J, Cao Y, Weisberg S, Harwood VJ, Staley C, Oshima KH, Varma M, Haugland RA. 2012. Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria. Environ Sci Technol 46:945953.[PubMed][CrossRef]
102. Kelty CA, Varma M, Sivaganesan M, Haugland RA, Shanks OC. 2012. Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces. Appl Environ Microbiol 78:42254232.[PubMed][CrossRef]
104. Teo IA, Choi JW, Morlese J, Taylor G, Shaunak S. 2002. LightCycler qPCR optimisation for low copy number target DNA. J Immunol Meth 270:119133.[CrossRef]
105. Lee SB, Crouse CA, Kline MC. 2010. Optimizing storage and handling of DNA extracts. Forensic Sci Rev 22:131144.[PubMed]
106. Sivaganesan M, Seifring S, Varma M, Haugland RA, Shanks OC. 2008. A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinformatics 9:120.[PubMed][CrossRef]
107. Dick LK, Stelzer EA, Bertke EE, Fong DL, Stoeckel DM. 2010. Relative decay of Bacteroidales microbial source tracking markers and cultivated Escherichia coli in freshwater microcosms. Appl Environ Microbiol 76:32553262.[PubMed][CrossRef]
108. Noble RT, Allen SM, Blackwood AD, Chu W, Jiang SC, Lovelace GL, Sobsey MD, Stewart JR, Wait DA. 2003. Use of viral pathogens and indicators to differentiate between human and non-human fecal contamination in a microbial source tracking comparison study. J Water Health 1:195207.[PubMed]
109. Harwood VJ, Boehm AB, Sassoubre LM, Vijayavel K, Stewart JR, Fong TT, Caprais MP, Converse RR, Diston D, Ebdon JE, Fuhrman JA, Gourmelon M, Gentry-Shields J, Griffith JF, Kashian D, Noble RT, Taylor H, Wicki M. 2013. Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study. Water Res 47:69296943.[PubMed][CrossRef]
110. Balleste E, Bonjoch X, Belanche LA, Blanch AR. 2010. Molecular indicators used in the development of predictive models for microbial source tracking. Appl Environ Microbiol 76:17891795.[PubMed][CrossRef]
111. Korajkic A, McMinn BR, Shanks OC, Sivaganesan M, Fout GS, Ashbolt NJ. 2014. Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the upper Mississippi river. Appl Environ Microbiol 80:39523961.[PubMed][CrossRef]
112. Green HC, Shanks OC, Sivaganesan M, Haugland RA, Field KG. 2011. Differential decay of human fecal Bacteroides in marine and freshwater. Environ Microbiol 13:32353249.[PubMed][CrossRef]
113. Bae S, Wuertz S. 2009. Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide. Water Res 43:48504859.[PubMed][CrossRef]
114. Bae S, Wuertz S. 2012. Survival of host-associated bacteroidales cells and their relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica serovar Typhimurium, and adenovirus in freshwater microcosms as measured by propidium monoazide-quantitative PCR. Appl Environ Microbiol 78:922932.[PubMed][CrossRef]
115. Sokolova E, Astrom J, Pettersson TJ, Bergstedt O, Hermansson M. 2012. Decay of Bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources. Environ Sci Technol 46:892900.[PubMed][CrossRef]
116. Walters SP, Yamahara KM, Boehm AB. 2009. Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: implications for their use in assessing risk in recreational waters. Water Res 43:49294939.[PubMed][CrossRef]
117. Korajkic A, Wanjugi P, Harwood VJ. 2013. Indigenous microbiota and habitat influence Escherichia coli survival more than sunlight in simulated aquatic environments. Appl Environ Microbiol 79:53295337.[PubMed][CrossRef]
118. Korajkic A, McMinn BR, Harwood VJ, Shanks OC, Fout GS, Ashbolt NJ. 2013. Differential decay of enterococci and Escherichia coli originating from two fecal pollution sources. Appl Environ Microbiol 79:24882492.[PubMed][CrossRef]

Tables

Generic image for table
TABLE 1

Host range and known cross-reactivity of MST markers

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

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error