1887

Chapter 3.4.3 : Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources

Authors: Orin C. Shanks1, Hyatt Green2, Asja Korajkic3, Katharine G. Field4
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: U.S. EPA, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA; 2: U.S. EPA, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA; 3: U.S. EPA, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Drive, Cincinnati, OH 45268, USA; 4: Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
Content Type: Reference
Publication Year: 2016

Category: Environmental Microbiology

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

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch3.4.3-1.gif /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch3.4.3-2.gif

Abstract:

Human fecal waste is thought to contain the largest number of human pathogens representing the greatest public health risk in comparison to other fecal sources. Human fecal pollution can be introduced into water resources from damaged sewer lines, faulty septic systems, combined sewer overflows, illicit dumping activities, and even recreational bathers themselves. Ensuring public safety and adequate water quality therefore requires methods that can confirm the presence or absence, as well as, determine the concentration human fecal pollution sources. This chapter provides an overview of human-associated fecal source identification methods commonly used to assess water quality. In addition to describing various methods, this chapter will also discuss factors to consider for method selection.

Citation: Shanks O, Green H, Korajkic A, Field K. 2016. Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources, p 3.4.3-1-3.4.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.3
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555818821.ch3.4.3
1. Hagedorn C, Crozier JB, Metnz MA, Booth AM, Graves AK, Nelson NJ, Reneau RBJ. 2003. Carbon source utlization profiles as a method to identify faecal pollution sources in water. J Appl Microbiol 94 : 792– 799.[PubMed][CrossRef]
2. Konopka A, Oliver L, Turco RFJ. 1998. The use of carbon substrate utilization patterns in environmental and ecological microbiology. Microb Ecol 35 : 103– 115.[PubMed][CrossRef]
3. Hagedorn C, Robinson SL, Filtz JR, Grubbs SM, Angier TA, Reneau RBJ. 1999. Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci. Appl Environ Microbiol 65 : 5522– 5531.[PubMed]
4. Harwood VJ, Whitlock J, Withington V. 2000. Classification of antibiotic resistance patterns of indicator bacteria by discriminant analysis: use in predicting the source of fecal contamination in subtropical waters. Appl Environ Microbiol 66 : 3698– 3704.[PubMed][CrossRef]
5. Parveen S, Portier KM, Robinson K, Edmiston L, Tamplin ML. 1999. Discriminant analysis of ribotype profiles of Escherichia coli for differentiating human and nonhuman sources of fecal pollution. Appl Environ Microbiol 65 : 3142– 3147.[PubMed]
6. Wiggins BA, Andrews RW, Conway RA, Corr CL, Dobratz EJ, Dougherty DP, Eppard JR, Knupp SR, Limjoco MC, Mettenburg JM, Rinehardt JM, Sonsino J, Torrijos RL, Zimmerman ME. 1999. Use of antibiotic resistance analysis to identify nonpoint sources of fecal polltuion. Appl Environ Microbiol 65 : 3483– 3486.[PubMed]
7. Dombek PE, Johnson LK, Zimmerley ST, Sadowksy MJ. 2000. Use of repetitive DNA sequences and PCR to differentiate Escherichia coli isolates from human and animal sources. Appl Environ Microbiol 66 : 2572– 2577.[PubMed][CrossRef]
8. Myoda SP, Carson CA, Fuhrmann JJ, Hahm BK, Hartel PG, Yampara-Iquise 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 : 167– 180.[PubMed]
9. Souza V, Rocha M, Valera A. 1999. Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Appl Environ Microbiol 65 : 3373– 3385.[PubMed]
10. Griffith JF, Weisberg SB, McGee C. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. J Water Health 1 : 141– 151.[PubMed]
11. Samadpour M, Roberts MC, Kitts CL, Mulugeta W, Alfi D. 2005. The use of ribotyping and antibiotic resistance patterns for identification of host sources of Escherichia coli strains. Lett Appl Microbiol 40 : 63– 68.[PubMed][CrossRef]
12. Layton BA, Cao Y, Ebentier DL, Hanley K, Ballesté E, Brandão J, Byappanahalli M, Converse R, Farnleitner AH, Gentry-Shields J, Gidley ML, Gourmelon M, Lee CS, Lee J, Lozach S, Madi T, Meijer WG, Noble R, Peed L, Reischer GH, Rodrigues R, Rose JB, Schriewer A, Sinigalliano C, Srinivasan S, Stewart J, Van De Werfhorst LC, Wang D, Whitman R, Wuertz S, Jay J, Holden PA, Boehm AB, Shanks O, Griffith JF. 2013. Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study. Water Res 47 : 6897– 6908.[PubMed][CrossRef]
13. Rosario K, Symonds EM, Sinagalliano CD, Stewart JR, Breitbart RA. 2009. Pepper mild mottle virus as an indicator of fecal pollution. Appl Environ Microbiol 75 : 7261– 7267.[PubMed][CrossRef]
14. 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 : 6281– 6288.[PubMed][CrossRef]
15. 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, Domingo JS, Schriewer A, Sinigalliano CD, Shanks OC, Van De Werfhorst LC, Wang D, Wuertz S, Jay JA. 2013. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Res 47 : 6839– 6848.[PubMed][CrossRef]
16. Boehm AB, Van De Werfhorst LC, 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 : 6812– 6828.[PubMed][CrossRef]
17. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. 2008. Worlds within worlds: evolution of hte vertebrate gut microbiota. Nat Rev Microbiol 6 : 776– 788.[PubMed][CrossRef]
18. Ley RE, Hamady M, Lozupone CA, Turnbaugh PJ, Ramey RR, Bircher SB, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. 2008. Evolution of mammals and their gut microbes. Science 320 : 1647– 1651.[PubMed][CrossRef]
19. Ahmed W, Goonetilleke A, Powell D, Gardner T. 2009. Evaluation of multiple sewage-associated Bacteroides PCR markers for sewage pollution tracking. Water Res 43 : 4872– 4877.[PubMed][CrossRef]
20. 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 : 311– 318.[CrossRef]
21. Shanks OC, Santo 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 : 2416– 2422.[PubMed][CrossRef]
22. 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 polltion in water. J Appl Microbiol 105 : 1686– 1693.[PubMed][CrossRef]
23. McQuaig SM, Scott TM, Harwood VJ, Farrah SR, Lukasik J. 2006. Detection of human-derived fecal pollution in environmental waters by use of a PCR-based human polyomavirus assay. Appl Environ Microbiol 72 : 7567– 7574.[PubMed][CrossRef]
24. McQuaig S, Scott TM, Harwood VJ, Farrah SR, Lukaskik JO. 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 : 3379– 3388.[PubMed][CrossRef]
25. Noble RT, Weisberg SB, Leecaster MK, McGee CD, Ritter KJ, Walker KO, Vainik PM. 2003. Comparison of beach bacterial water quality indicator measurement methods. Environ Monit Assess 81 : 301– 312.[PubMed][CrossRef]
26. 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 DR, Noble RT, Taylor HD, Wicki M. 2013. Performance of viruses and bacteriophages for fecal source determination in a multiple laboratory, comparative study. Water Res 47 : 6929– 6943.[PubMed][CrossRef]
27. Wang Y, Liu VW, Xue WC, Tsang PC, Cheung AN, Ngan HY. 2005. The increase of mitochondrial DNA content in endometrial adenocarcinoma cells: a quantitative study using laser-captured microdissected tissues. Gynecol Oncol 98 : 104– 110.[PubMed][CrossRef]
28. Kamra A, Kessie G, Chen JH, Kalavapudi S, Shores R, McElroy I, Gireesh T, Sudhakaran PR, Dutta SK, Nair PP. 2005. Exfoliated colonic epithelial cells: surrogate targets for evaluation of bioactive food components in cancer prevention. J Nutr 135 : 2719– 2722.[PubMed]
29. Wilson AC, Cannon RL, Carr SM, George MJ, Gyllensten VB, Helm-Bychowski KM, Higuchi R, Palumbi SR, Prager EM, Sage RD, Stoneking M. 1985. Mitochondrial DNA and two perspectives on evolutionary genetics. Biol J Linnean Soc 26 : 375– 400.[CrossRef]
30. Caldwell JM, Raley ME, Levine JF. 2007. Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents. Environ Sci Technol 41 : 3277– 3283.[PubMed][CrossRef]
31. 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 : 541– 548.[PubMed][CrossRef]
32. Kortbaoui R, Locas A, Imbeau M, Payment P, Villemur R. 2009. Universal mitochondrial PCR combined with species- specific dot-blot assay as a source-tracking methond of human, bovine, chicken, ovine, and porcine in fecal-contaminated surface water. Water Res 43 : 2002– 2010.[PubMed][CrossRef]
33. 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 : 1789– 1795.[PubMed][CrossRef]
34. 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 : 5229– 5234.[PubMed][CrossRef]
35. Baker-Austin C, Rangdale R, Lowther J, Lees DN. 2010. Application of mitochondrial DNA analyiss for microbial source tracking purposes in shellfish harvesting waters. Water Sci Technol 61 : 1– 7.[PubMed][CrossRef]
36. Caldwell JM, Levine JF. 2009. Domestic wastewater influent profiling using mitochondrial real-time PCR for source tracking animal contamination. J Microbiol Meth 77 : 17– 22.[CrossRef]
37. 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 for 16S rRNA. Appl Environ Microbiol 66 : 4571– 4574.[PubMed][CrossRef]
38. Cao Y, Van De Werfhorst LC, Dubinsky EA, Badgley BD, Sadowsky MJ, Andersen GL, Griffith JF, Holden PA. 2013. Evaluation of molecular community analysis methods for discerning fecal sources and human waste. Water Res 47 : 6862– 6872.[PubMed][CrossRef]
39. Dubinsky EA, Esmaili L, Hulls JR, Cao Y, Griffith JF, Andersen GL. 2012. Application of phyogentic microarray analysis to discriminate sources of fecal pollution. Environ Sci Technol 46 : 4340– 4347.[PubMed][CrossRef]
40. Wu CH, Sercu B, Van De Werfhorst L, 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]
41. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelly ST. 2011. Bayesian comunity-wide culture-independent microbial source tracking. Nat Meth 8 : 761– 763.[CrossRef]
42. Unno T, Jang J, Han D, Ha Kim J, Sadowsky MJ, Kim O, Chun J, Hur H. 2010. Use of barcoded pyrosequencing and shared OTUs to determine source of fecal bacteria in watersheds. Environ Sci Technol 44 : 7777– 7782.[PubMed][CrossRef]
43. Newton RJ, Bootsma MJ, Morrison HG, Sogin ML, McLellan SL. 2013. A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan. Microb Ecol 65 : 1011– 1023.[PubMed]
44. Derrien M, Jarde E, Grauau G, Pourcher A, Gourmelon M, Jadas-Hecart A, Wickmann AC. 2012. Development of microbial and chemical microbial source tracking tools to identify the origin of the faecal pollution in bathing and shellfish harvesting waters in France. Water Res 44 : 4812– 4824.
45. Mieszkin S, Yala JF, Joubrel R, Gourmelon M. 2010. Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of rumaint faecal pollution by real-time PCR. J Appl Microbiol 108 : 974– 984.[PubMed][CrossRef]
46. McDonald JL, Hartel PG, Gentit LC, Belcher CN, Gates KW, Rodgers K, Fisher JA, Smith KA, Payne KA. 2006. Identifying sources of fecal contamination inexpensively with targeted sampling and bacterial source tracking. J Environ Qual 35 : 889– 897.[PubMed][CrossRef]
47. Boving TB, Merrit DL, Boothryod JC. 2004. Fingerprinting sources of bacteria input into small residential watersheds: fate of flourescent whitening agents. Environ Geol 46 : 228– 232.[CrossRef]
48. Cao Y, Griffith JF, Weisberg SB. 2009. Evaluation of optical brightener photodecay characteristics for detection of human fecal contamination. Water Res 43 : 2273– 2279.[PubMed][CrossRef]
49. Green HC, Field KG. 2012. Sensitive detection of sample interference in environmental qPCR. Water Res 46 : 3251– 3260.[PubMed][CrossRef]
50. Peed LA, Nietch CT, Kelty CA, Meckes M, Mooney T, Sivaganesan M, Shanks OC. 2011. Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution. Environ Sci Technol 45 : 5662– 5659.[CrossRef]
51. Rajal VB, McSwain BS, Thompson DE, Leutenegger CM, Kildare BJ, Wuertz S. 2007. Validation of hollow fiber ultrafiltration and real-time PCR using bacteriophage PP7 as surrogate for the quantification of viruses from water samples. Water Res 41 : 1411– 1422.[PubMed][CrossRef]
52. Green H, Shanks OC, Sivaganesan M, Haugland R, Field K. 2011. Differential decay of human faecal Bacteroides in marine and freshwater. Environ Microbiol 13 : 3235– 3249.[PubMed][CrossRef]
53. Yamahara KM, Layton AL, Santoro AE, Boehm AB. 2007. Beach sands along the California coast are diffuse sources of fecal bacteria to coastal waters. Environ Sci Technol 41 : 4515– 4521.[PubMed][CrossRef]
54. Dickerson JW, 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 : 3758– 3770.[PubMed][CrossRef]
55. Bonjoch X, Balleste E, Blanch AR. 2004. Multiplex PCR with 16S rRNA gene-targeted primers of Biofidobacterium spp. to identify sources of fecal pollution. Appl Environ Microbiol 70 : 3171– 3175.[PubMed][CrossRef]
56. 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 : 3255– 3262.[PubMed][CrossRef]
57. 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 : 890– 901.[PubMed][CrossRef]
58. Seurinck S, Defoirdt T, Verstraete W, Siciliano S. 2005. Detection and quantification of human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ Microbiol 7 : 249– 259.[PubMed][CrossRef]
59. Okabe S, Shimazu Y. 2007. Persistences of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl Microbiol Biotechnol 76 : 935– 944.[PubMed][CrossRef]
60. 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 : 4850– 4859.[PubMed][CrossRef]
61. Sokolova E, Astrom J, Pettersson TJ, Bargstedt 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 : 892– 900.[PubMed][CrossRef]
62. Walters SP, Field KG. 2009. Survival and persistence of human and ruminant-specific faecal Bacteroidales in freshwater microcosms. Environ Microbiol 11 : 1410– 1421.[PubMed][CrossRef]
63. 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 : 3225– 3244.[PubMed][CrossRef]
64. Wang D, Farnleitner AH, Field KG, Green HC, Shanks OC, Boehm AB. 2013. Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers—is it feasible? Water Res 47 : 6849– 6861.[PubMed][CrossRef]
65. 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 : 4760– 4775.[PubMed][CrossRef]
66. Raith MR, Kelty CA, Griffith JF, Schriewer A, Wuertz S, Mieszkin S, Gourmelon M, Reischer GH, Farnleitner AH, Ervin JS, Holden PA, Ebentier DL, Jay JA, Wang D, Boehm AB, Aw TG, Rose JB, Balleste E, Meijer WG, Sivaganesan M, Shanks OC. 2013. Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources. Water Res 47 : 6921– 6928.[PubMed][CrossRef]
67. Walters SP, Gannon VPG, Field KG. 2007. Detection of Bacteroidales fecal indicators and the zoonotic pathogens E. coli O157:H7, Salmonella, and Campylobacter in river water. Environ Sci Technol 41 : 1856– 1862.[PubMed][CrossRef]
68. Soller JA, Schoen ME, Bartrand T, Ravenscroft JE, Ashbolt NJ. 2010. Estimated human health risks from exposure to recreational waters impacted by human and non-human sources of faecal contamination. Water Res 44 : 4674– 4691.[PubMed][CrossRef]
69. Viau EJ, Lee D, Boehm AB. 2011. Swimmer risk of gastrointestinal illness from exposure to tropical coastal waters impacted by terrestrial dry-weathery runoff. Environ Sci Technol 45 : 7158– 7165.[PubMed][CrossRef]
70. Gentry RW, Layton AC, McKay L, McCarthy JF, Williams DE, Koirala SR, Sayler GS. 2007. Efficacy of Bacteroides measurements for reducting the statistical uncertainty associated with hydrologic flow and fecal loads in a mixed use watershed. J Environ Qual 36 : 1324– 1330.[PubMed][CrossRef]
71. Lee JE, Lee S, Sung J, Ko G. 2010. Analysis of human and animal fecal microbiota for microbial source tracking. ISME J 5 : 362– 365.[PubMed][CrossRef]
72. Shanks OC, Nietch C, Simonich MT, 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 : 5537– 5546.[PubMed][CrossRef]
73. Sercu B, Van De Werfhorst L, Murray J, Holden PA. 2009. Storm drains are sources of human fecal pollution during dry weather in three urban soutner California watersheds. Environ Sci Technol 43 : 293– 298.[PubMed][CrossRef]
74. Haugland RA, Varma M, Kelty CA, Peed L, Sivaganesan M, 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 real-time PCR. Syst Appl Microbiol 33 : 348– 357.[PubMed][CrossRef]
75. 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 : 351– 356.[PubMed][CrossRef]
76. Reischer GH, Haider JM, Sommer R, Stadler H, Keiblinger KM, Hornek R, Zerobin W, Mach RL, Farnleitner AH. 2008. Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics. Environ Microbiol 10 : 2598– 2608.[PubMed][CrossRef]
77. 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 : 3701– 3715.[PubMed][CrossRef]
78. Lee CS, Lee J. 2012. Application of host-specific source-tracking tools for rapid identification of fecal contamination in fresh produce by humans and livestock. Sci Food Agric 93 : 1089– 10965.
79. Srinivasan S, Aslan A, Xagoraraki I, Alocilja E, Rose JB. 2011. Escherichia coli, enterococci, and Bacteroides thetaiotaomicron qPCR signals through wastewater and septage treatment. Water Res 45 : 2561– 2572.[PubMed][CrossRef]
80. Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA. 2009. Quantitative PCR for genetic markers of human fecal pollution. Appl Environ Microbiol 75 : 5507– 5513.[PubMed][CrossRef]
81. Ebdon JE, Sellwood J, Shore J, Taylor HD. 2012. Phages of Bacteroidales (GB-124): a novel tool for viral waterborne disease control? Environ Sci Technol 46 : 1163– 1169.[PubMed][CrossRef]
82. Santiago-Rodriquez TM, Davila C, Gonzalez J, Bonilla N, Marcos P, Urdaneta M, Cadete M, Monteiro S, Santos R, Domingo JS, Toranzos GA. 2010. Characterization of Enterococcus faecalis-infecting phages (enterophages) as markers of human fecal polltuion in recrational waters. Water Res 44 : 4716– 4725.[CrossRef]
83. Kirs M, Smith DC. 2007. Multiplex quantitative real-time reverse transcriptase PCR for F +-specific RNA coliphages: a method for use in microbial source tracking. Appl Environ Microbiol 73 : 808– 814.[PubMed][CrossRef]

Tables

Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch3.4.3-1,webId=/content/author/10.1128/9781555818821.ch3.4.3-1,properties={foaf_givenname=Orin C., foaf_name=Orin C. Shanks, foaf_surname=Shanks, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch3.4.3-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch3.4.3-2,webId=/content/author/10.1128/9781555818821.ch3.4.3-2,properties={foaf_givenname=Hyatt, foaf_name=Hyatt Green, foaf_surname=Green, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch3.4.3-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch3.4.3-3,webId=/content/author/10.1128/9781555818821.ch3.4.3-3,properties={foaf_givenname=Asja, foaf_name=Asja Korajkic, foaf_surname=Korajkic, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch3.4.3-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch3.4.3-4,webId=/content/author/10.1128/9781555818821.ch3.4.3-4,properties={foaf_givenname=Katharine G., foaf_name=Katharine G. Field, foaf_surname=Field, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch3.4.3-aff4]]}]]
Citation: Shanks O, Green H, Korajkic A, Field K. 2016. Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources, p 3.4.3-1-3.4.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.3
/content/10.1128/9781555818821.ch3.4.3.ch3.4.3tab01
TABLE 1

Selected PCR-based human-associated MST methods targeting bacterial genes

Generic image for table
TABLE 1

Selected PCR-based human-associated MST methods targeting bacterial genes

Citation: Shanks O, Green H, Korajkic A, Field K. 2016. Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources, p 3.4.3-1-3.4.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.3
/content/10.1128/9781555818821.ch3.4.3.ch3.4.3tab02
TABLE 2

Selected human-associated MST methods targeting viruses

Generic image for table
TABLE 2

Selected human-associated MST methods targeting viruses

Citation: Shanks O, Green H, Korajkic A, Field K. 2016. Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources, p 3.4.3-1-3.4.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.3
/content/10.1128/9781555818821.ch3.4.3.ch3.4.3tab03
TABLE 3

MST applications

Generic image for table
TABLE 3

MST applications

Citation: Shanks O, Green H, Korajkic A, Field K. 2016. Overview of Microbial Source Tracking Methods Targeting Human Fecal Pollution Sources, p 3.4.3-1-3.4.3-8. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.3

Back to top
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