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Chapter 3.4.1 : The Evolving Science of Microbial Source Tracking

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Abstract:

Section X of the Manual of Environmental Microbiology addresses the burgeoning area of microbial source tracking (MST), a collection of methodologies and approaches whose aim is to determine the dominant source(s) of fecal contamination of water bodies. Many health- and management-related areas can benefit from MST analyses, including total maximum daily load (TMDL) determinations, beach and water resource management, quantitative microbial risk assessment (QMRA), and epidemiology. This chapter provides a brief overview of the rationale for and theory of MST, followed by chapters that detail MST methodologies and practice. This chapter also suggests future directions for a field that has changed considerably over the last two decades - as it has evolved from an emphasis on building large databases of bacterial phenotypes or genotypes toward the use of culture-independent methods that focus on single genetic targets or microbial community structure. The field is in the process of adopting high-throughput DNA sequencing methods that allow consideration of genomic and metagenomic data to identify host-associated microorganisms and/or patterns in communities that may contribute to accurate identification of fecal pollution sources in the environment.

Citation: Harwood V, Hagedorn C, Sadowsky M. 2016. The Evolving Science of Microbial Source Tracking, p 3.4.1-1-3.4.1-7. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.1
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The essential objective of microbial source tracking doi: 10.1128/9781555818821.ch3.4.1

Citation: Harwood V, Hagedorn C, Sadowsky M. 2016. The Evolving Science of Microbial Source Tracking, p 3.4.1-1-3.4.1-7. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch3.4.1
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1. Dorfman M, Rosselot KS. 2010. Testing the Waters: A Guide to Water Quality at Vacation Beaches. Natural Resources Defense Council, Washington, DC.
2. Dorfman M, Haren A. 2013. Testing the Waters 2013: Executive Overview. Natural Resources Defense Council, Washington, DC.
3. USEPA. 2012. Recreational Water Quality Criteria. EPA:820-F-12-058, U.S. Environmental Protection Agency—Office of Water, Washington, DC.
4. NOAA. 2005. Welfare Estimates for Five Scenarios of Water Quality Change in Southern California: A Report from the Southern California Beach Valuation Project. National Oceanic and Atmospheric Administration, Washington, DC.
5. Allender-Hagedorn A,. 2011. Public perception of and public participation in microbial source tracking, p 283 300. In Hagedorn C, Blanch A, Harwood VJ (eds.), Microbial Source Tracking: Methods, Applications, and Case Studies. Springer-Verlag, New York, NY.
6. Given S, Pendleton LH, Boehm AB. 2006. Regional public health cost estimates of contaminated coastal waters: a case study of gastroenteritis at southern California beaches. Environ Sci Technol 40: 4851 4858.[PubMed][CrossRef]
7. U.S. EPA. 2007. Report of the experts scientific workshop on critical research needs for the development of new or revised recreational water quality criteria. EPA:823-R-07-006. U.S. Environmental Protection Agency, Office of Water, Washington, DC.
8. Staley C, Gordon KV, Schoen ME, Harwood VJ. 2012. Performance of two human-associated microbial source tracking qPCR methods in various Florida water types and implications for microbial risk assessments. Appl Environ Microbiol, 78 : 7317 7326.[PubMed]
9. Schoen ME, Soller JA, Ashbolt NJ. 2011. Evaluating the importance of fecal sources in human-impacted waters. Water Res 45 : 2670 2680.[PubMed][CrossRef]
10. Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A. 2014. Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships to pathogens and human health outcomes. FEMS Microbiol Rev 38 : 1 40.[PubMed][CrossRef]
11. U.S. EPA. 2005. Microbial source tracking guide document. EPA:600-R-05-064. U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH.
12. Boehm AB, Fuhrman JA, MRSE RD, Grant SB. 2003. Tiered approach for identification of a human fecal pollution source at a recreational beach: case study at Avalon Cay, Catalina Island, California. Environ Sci Technol 37 : 673 680.[PubMed][CrossRef]
13. Whitlock JE, Jones DT, Harwood VJ. 2002. Identification of the sources of fecal coliforms in an urban watershed using antibiotic resistance analysis. Water Res 36 : 4273 4282.[PubMed][CrossRef]
14. Grant SB, Sanders BF, Boehm AB, Redman JA, Kim JH, Mrše R.D, Chu AK, Gouldin M, McGee CD, Gardiner NA, Jones BH, Svejkovsky J, Leipzig GV, Brown A. 2001. Generation of Enterococci bacteria in a coastal saltwater marsh and its impact on surf zone water quality. Environ Sci Technol 35 : 2407 2416.[PubMed][CrossRef]
15. Ahmed W, Sritharan T, Palmer A, Sidhu JP, Toze S. 2013. Evaluation of bovine feces-associated microbial source tracking markers and their correlations with fecal indicators and zoonotic pathogens in a Brisbane, Australia reservoir. Appl Environ Microbiol 79 : 2682 2691.[PubMed][CrossRef]
16. Hagedorn C, Robinson SL, Filtz JR, Grubbs SM, Angier TA, Beneau RB. 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]
17. Harwood VJ, Whitlock J, Withington VH. 2000. Classification of the antibiotic resistance patterns of indicator bacteria by discriminant analysis: use in predicting the source of fecal contamination in subtropical Florida waters. Appl Environ Microbiol 66 : 3698 3704.[PubMed][CrossRef]
18. Weidhass JL, Macbeth TW, Olsen RL, Harwood VJ. 2011. Correlation of quantitative PCR for a poultry-specific Brevibacterium marker gene with bacterial and chemical indicators of water pollution in a watershed impacted by land application of poultry litter. Appl Environ Microbiol 77 : 2094 2102.[PubMed][CrossRef]
19. Burnes BS. 2003. Antibiotic resistance analysis of fecal coliforms to determine fecal pollution sources in a mixed-use watershed. Environ Monit Assess 85 : 87 98.[PubMed][CrossRef]
20. Badgley BD, Nayak BN, Harwood VJ. 2011. The importance of sediment and submerged aquatic vegetation as potential habitats for persistent strains of enterococci in a subtropical watershed. Water Res 44 : 5857 5866.[CrossRef]
21. Byappanahali M, Nevers MN, Korajkic A, Staley ZS, Harwood VJ. 2012. Enterococci in the environment. Microbiol Mol Rev 76 : 685 706.[CrossRef]
22. Whitman RL, Harwood VJ, Edge TA, Nevers MB, Byappanahali M, Vijayavel K, Brandão J, Sadowsky MJ, Alm EW, Crowe A, Ferguson D, Ge Z, Halliday E, Kinzelman J, Kleinheinz G, Przybyla-Kelly K, Staley C, Staley Z, Solo-Gabriele HM. 2014. Microbes in beach sands: integrating environment, ecology, and public health. Rev Environ Sci Bio/Tech 13 : 329 368.[CrossRef]
23. Weiskel PK, Howes BL, Heufelder GR. 1996. Coliform contamination of a coastal embayment: sources and transport pathways. Environ Sci Technol 30 : 1872 1881.[CrossRef]
24. Whitman RL, Shively DA, Pawlik H, Nevers MB, Byappanahali MN. 2003. Occurrence of Escherichia coli and Enterococci in Cladophora (Chlorphyta) in nearshore water and beach sand of Lake Michigan. Appl Environ Microbiol 69 : 4714 4719.[PubMed][CrossRef]
25. Sauer EP, VandeWalle JL, Bootsma MJ, McLellan SL. 2011. Detection of the human specific Bacteroides genetic marker provides evidence of widespread sewage contamination of stormwater in the urban environment. Water Res 45 : 4081 4091.[PubMed][CrossRef]
26. Mallin MA, Johnson VL, Ensign SH. 2009. Comparative impacts of stormwater runoff on water quality of an urban, a suburban, and a rural stream. Environ Monit Assess 159 : 475 491.[PubMed][CrossRef]
27. Jiang S, Noble R, Chui WP. 2001. Human adenovirus and coliphages in urban runoff-impacted coastal waters of Southern California. Appl Environ Microbiol 67 : 179 184.[PubMed][CrossRef]
28. Petersen TM, Rifai H, Suarez M, Stein A. 2005. Bacteria loads from point and nonpoint sources in an urban watershed. J Environ Engin 131 : 1414 1425.[CrossRef]
29. Dorsey JH. 2010. Improving water quality through California's Clean Beach Initiative: an assessment of 17 projects. Environ Monit Assess 166 : 95 111.[PubMed][CrossRef]
30. 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 PDR, Holland AF. 2008. The coastal environment and human health: microbial indicators, pathogens, sentinels, and reservoirs. Environ Health 7(Suppl2) : S3.[PubMed][CrossRef]
31. 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]
32. U.S. EPA. 2009. Review of published studies to characterize relative risks from different sources of fecal contamination in recreational water. EPA:822-R-09-001, U.S. Environmental Protection Agency, Office of Water, Washington, DC.
33. Propst CW, Harwood VJ, Morrison G,. 2011. Case studies of urban and suburban watersheds. In Hagedorn C, Blanch AR, Harwood VJ (eds.), Microbial Source Tracking: Methods, Applications, and Case Studies. Springer Scientific, New York, NY.
34. Converse RR, Kinzelman JL, Sams EA, Hudgens E, Dufour AP, Ryu H, Santo-Domingo JW, Kelty CA, Shanks OC, Siefring SD, Haugland RA, Wade TJ. 2012. Dramatic improvements in beach water quality following gull removal. Environ Sci Technol 46 : 206 213.[CrossRef]
35. Wiggins BA, Cash PW, Creamer WS, Dart SE, Garcia PP, Gerecke TM, Han J, Henry BL, Hoover KB, Johnson EL, Jones KC, McCarthy JG, McDonough JA, Mercer SA, Noto MJ, Park H, Phillips MS, Purner SM, Smith BM, Stevens EN, Varner AK. 2003. Use of antibiotic resistance analysis for representativeness testing of multiwatershed libraries. Appl Environ Microbiol 69 : 3399 3405.[PubMed][CrossRef]
36. Dombek PE, Johnson LK, Zimmerley ST, Sadowsky MJ. 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl Environ Microbiol 66 : 2572 2577.[PubMed][CrossRef]
37. Stoeckel DM, Harwood VJ. 2007. Performance, design, and analysis in microbial source tracking studies. Appl Environ Microbiol 73 : 2405 2415.[PubMed][CrossRef]
38. 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 : 6109 6117.[PubMed][CrossRef]
39. Griffith JF, Weisberg SB, McGee CD. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. J Wat Health 1 : 141 151.
40. Johnson LK, Brown MB, Carruthers EA, Ferguson JA, Dombek PE, Sadowsky MJ. 2004. Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl Environ Microbiol 70 : 4478 4485.[PubMed][CrossRef]
41. Heim S, Lleo MM, Bonato B, Guzman CA, Canepari P. 2002. The viable but nonculturable state and starvation are different stress responses of Enterococcus faecalis, as determined by proteome analysis. J Clin Microbiol 184 : 6739 6745.[CrossRef]
42. Kell DB, Kaprelyants AS, Weichart DH, Harwood CR, Barer MR. 1998. Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Antonie Van Leeuwenhoek 73 : 169 187.
43. Oliver JD. 2010. Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev 34 : 415 425.[PubMed][CrossRef]
44. Ebentier DL, Hanley KT, Cao Y, Badgley BD, Boehm AB, Ervin J, Goodwin KD, Gourmelon M, Griffith JF, Holden PA, Kelty CA, Lozach S, McGee C, Peed L, Raith M, Ryu H, Sadowsky MJ, Scott E, Santo-domingo JW, Schriewer A, Sinagalliano CD, Shanks OC, Van De Werfhorst L, Wang D, Wuertz S, Jay J. 2013. Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Res 47 : 6839 6848.[PubMed][CrossRef]
45. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. 2009. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55 : 611 622.[PubMed][CrossRef]
46. Shanks OC, Peed L, Sivaganesan M, Haugland RA, Chern EC. 2014. Human fecal source identification with real-time quantitative PCR. Meth Mol Biol 1096 : 85 99.[CrossRef]
47. Boehm AB, Van De Werfhorst L, Griffith JF, Holden P, Jay J, 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]
48. Wang D, Farnleitner A, 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]
49. McLellan SL, Eren AM. 2014. Discovering new indicators of fecal pollution. Trends Microbiol 22 : 697 706.[PubMed][CrossRef]
50. McLellan SL, Huse SM, Mueller-Spitz S, Andreishcheva E, Sogin ML. 2010. Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12 : 378 392.[PubMed][CrossRef]
51. Unno T, Di DY, Jang J, Suh YS, Sadowsky MJ, Hur HG. 2012. Integrated online system for a pyrosequencing-based microbial source tracking method that targets Bacteroidetes 16S rDNA. Environ Sci Technol 46 : 93 98.[PubMed][CrossRef]
52. Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim O, Chun J, Hur H. 2010. Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44 : 7777 7782.[PubMed][CrossRef]
53. Weidhass 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. Appl Environ Microbiol 109 : 334 347.
54. Cao Y, Wu CH, Andersen GL, Holden PA,. 2011. Community analysis-based methods. p 251 281. In Hagedorn C, Blanch AR, Harwood VJ (eds.), Microbial Source Tracking: Methods, Applications, and Case Studies. Springer Scientific, New York, NY.
55. Li X, Harwood VJ, Nayak BN, Staley C, Sadowsky MJ, Weidhass J. 2015. A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems. Environ Sci Technol 49 : 7319 7329.[CrossRef]
56. Staley C, Gould TJ, Wang P, Phillips J, Cotner JB, Sadowsky MJ. 2014. Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River. Front Microbiol 5 : 524.[CrossRef]
57. 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]
58. Kent AD, Smith DJ, Benson BJ, Triplett EW. 2003. Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69 : 6768 6776.[PubMed][CrossRef]
59. Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ. 2007. MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol 53 : 562 570.[PubMed][CrossRef]
60. Field KG, Chern EC, Dick LK, Fuhrman JA, Griffith JF, Holden PA, LaMontagne MG, Le J, Olson B, Simonich MT. 2003. A comparative study of culture-independent library-independent genotypic methods of fecal source tracking. Journal of Water Health 1 : 181 194.[PubMed]
61. Ishii S, Segawa T, Okabe S. 2013. Simultaneous quantification of multiple food and waterborne pathogens by use of microfluidic quantitative PCR. Appl Environ Microbiol 79 : 2891 2898.[CrossRef]
62. Lee JH, Yi H, Chun J. 2011. rRNASelector: a computer program for selecting Ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries. J Microbiol 49 : 689 691.[PubMed][CrossRef]
63. Baker GC, Smith JJ, Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. J Microbiol Meth 55 : 541 555.[CrossRef]
64. Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML. 2011. Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol 77 : 2992 3001.[PubMed][CrossRef]
65. Staley ZR, Chase E, Mitraki C, Crisman TL, Harwood VJ. 2013. Microbial water quality in freshwater lakes with different land uses. J Appl Microbiol 115 : 1240 1250.[PubMed][CrossRef]
66. Harwood VJ, Boehm AB, Sassoubre LM, Vijayavel K, Stewart JR, Fong TT, Caprais MP, Converse RR, Diston D, Ebdon J, Fuhrman JA, Gourmelon M, Gentry-Shields J, Griffith JF, Kashian DR, 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 : 6929 6943.[PubMed][CrossRef]
67. Layton BA, Cao Y, Ebentier DL, Hanley K, Ballesté E, Brandão J, Byappanahali M, Converse RR, 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, Srinivivasan 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-associated PCR-based assays: an international source identification method evaluation. Water Res 47 : 6897 6908.[PubMed][CrossRef]
68. Schriewer A, Goodwin KD, Sinagalliano CD, Cox AM, Wanless D, Bartkowiak J, Ebentier DL, Hanley KT, Ervin J, Deering LA, Shanks OC, Peed LA, Meijer WG, Griffith JF, Santo-Domingo JW, Jay JA, Holden PA, Wuertz S. 2013. Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study. Water Res 47 : 6909 6920.[PubMed][CrossRef]
69. Sinigalliano CD, Ervin JS, Van De Werfhorst LC, Badgley BD, Ballesté E, Bartkowiak J, Boehm AB, Byappanahali M, Goodwin KD, Gourmelon M, Griffith JF, Holden PA, Jay J, Layton BA, Lee CS, Lee J, Meijer WG, Noble R, Raith M, Ryu H, Sadowsky MJ, Schriewer A, Wang D, Wanless D, Whitman R, Wuertz S, Santo-Domingo JW. 2013. Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources. Water Res 47 : 6883 6896.[PubMed][CrossRef]
70. Stewart JR, Boehm AB, Dubinsky EA, Fong T, Goodwin KD, Griffith JF, Noble RT, Shanks OC, Vijayavel K, Weisberg SB. 2013. Recommendations following a multi-laboratory comparison of microbial source tracking methods. Water Res 47 : 6829 6838.[PubMed][CrossRef]
71. Dubinsky EA, Esmaili L, Hulls JR, Cao Y, Griffith JF, Andersen GL. 2012. Application of phylogenetic microarrary analysis to discriminate sources of fecal pollution. Environ Sci Technol 46 : 4340 4347.[PubMed][CrossRef]
72. Schoen ME, Ashbolt NJ. 2010. Assessing pathogen risk to swimmers at non-sewage impacted recreational beaches. Environ Sci Technol 44 : 2286 2291.[PubMed][CrossRef]
73. USEPA. 2010. Quantitative microbial risk assessment to estimate illness in freshwater impacted by agricultural animal sources of fecal contamination. U.S. Environmental Protection Agency, Office of Water, Washington, DC.
74. Ashbolt NJ, Schoen ME, Soller JA, Roser DJ. 2010. Predicting pathogen risks to aid beach management: the Real value of quantitative microbial risk assessment (QMRA). Water Res 44 : 4692 4703.[PubMed][CrossRef]
75. Girones R, Ferrús MA, Alonso JL, Rodriguez-Manzano J, Calgua B, de Abreu Corrêa A, Hundesa A, Carratala A, Bofill-Mas S. 2010. Molecular detection of pathogens in water—the Pros and cons of molecular techniques. Water Res 44 : 4325 4339.[PubMed][CrossRef]

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