1887
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

Toward Forensic Uses of Microbial Source Tracking

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Buy this Microbiology Spectrum Article
Price Non-Member $15.00
  • Authors: Christopher M. Teaf1, David Flores2, Michele Garber3, Valerie J. Harwood4
  • Editors: Raúl J. Cano5, Gary A. Toranzos6
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Hazardous Substance & Waste Management Research, Inc., Tallahassee, FL 32309; 2: Center for Progressive Reform, Washington, DC 20001; 3: Hazardous Substance & Waste Management Research, Inc., Tallahassee, FL 32309; 4: Department of Integrative Biology, University of South Florida, Tampa, FL 33620; 5: California Polytechnic State University, San Luis Obispo, CA; 6: University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico
  • Source: microbiolspec January 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.EMF-0014-2017
  • Received 11 May 2017 Accepted 30 November 2017 Published 19 January 2018
  • Valerie J. Harwood, [email protected]
image of Toward Forensic Uses of Microbial Source Tracking
    Preview this microbiology spectrum article:
    Zoom in
    Zoomout

    Toward Forensic Uses of Microbial Source Tracking, Page 1 of 2

    | /docserver/preview/fulltext/microbiolspec/6/1/EMF-0014-2017-1.gif /docserver/preview/fulltext/microbiolspec/6/1/EMF-0014-2017-2.gif
  • Abstract:

    The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

  • Citation: Teaf C, Flores D, Garber M, Harwood V. 2018. Toward Forensic Uses of Microbial Source Tracking. Microbiol Spectrum 6(1):EMF-0014-2017. doi:10.1128/microbiolspec.EMF-0014-2017.

References

1. Snow J. 1855. On the Mode of Communication of Cholera. John Churchill, London, England.
2. Escherich T. 1885. Die darmbakterien des neugeborenen und säuglings. Fortschr Med 3:515–522.
3. Hacker J, Blum-Oehler G. 2007. In appreciation of Theodor Escherich. Nat Rev Microbiol 5:902.
4. Wolf HW. 1972. The coliform count as a measure of water quality. In Mitchell R (ed), Water Pollution Microbiology. Wiley Interscience, New York, NY.
5. American Water Works Association. 1990. Water Quality and Treatment: A Handbook of Community Water Supplies, 4th ed. McGraw-Hill, New York, NY.
6. U.S. Environmental Protection Agency. 2005. Microbial Source Tracking Guide. U.S. Environmental Protection Agency, Washington, DC.
7. Harwood VJ, Staley C, Badgley BD, Borges K, Korajkic A. 2014. Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes. FEMS Microbiol Rev 38:1–40. [PubMed]
8. Whitman R, Harwood VJ, Edge TA, Nevers M, Byappanahalli 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. Ecol Public Health 13:329–368.
9. Byappanahalli MN, Nevers MB, Korajkic A, Staley ZR, Harwood VJ. 2012. Enterococci in the environment. Microbiol Mol Biol Rev 76:685–706. [PubMed]
10. Oliver DM, van Niekerk M, Kay D, Heathwaite AL, Porter J, Fleming LE, Kinzelman JL, Connolly E, Cummins A, McPhail C, Rahman A, Thairs T, de Roda Husman AM, Hanley ND, Dunhill I, Globevnik L, Harwood VJ, Hodgson CJ, Lees DN, Nichols GL, Nocker A, Schets C, Quilliam RS. 2014. Opportunities and limitations of molecular methods for quantifying microbial compliance parameters in EU bathing waters. Environ Int 64:124–128. [PubMed]
11. Ishii S, Sadowsky MJ. 2008. Escherichia coli in the environment: implications for water quality and human health. Microbes Environ 23:101–108. [PubMed]
12. Rochelle-Newall E, Nguyen TM, Le TP, Sengtaheuanghoung O, Ribolzi O. 2015. A short review of fecal indicator bacteria in tropical aquatic ecosystems: knowledge gaps and future directions. Front Microbiol 6:308. [PubMed]
13. Harwood J, Hagedord C, Sadowsky M. 2016. The evolving science of microbial source tracking, p 3.4.5-1–3.4.5-11. In Yates MV, Nakatsu CH, Miller RV, Pillai SD (ed), Manual of Environmental Microbiology, 4th ed. http://dx.doi.org/10.1128/9781555818821.ch3.4.1. ASM Press, Washington, DC.
14. Harwood V, Shanks O, Koraijkic A, Verbyla M, Ahmed W, Iriate M. 2017. General and host-associated bacterial indicators of fecal pollution. In Rose JB, Jiménez-Cisneros B, (ed), Global Water Pathogens Project. Part 2. Indicators and Microbial Source Tracking Markers, Farnleitner A, Blanch A (ed). www.waterpathogens.org/book/bacterial-indicators. Michigan State University, UNESCO, E. Lansing, MI.
15. Kinzelman J, Ahmed W. 2016. Microbial source tracking: field study planning and implementation, p 3.4.5-1–3.4.5-11. In Yates MV, Nakatsu CH, Miller RV, Pillai SD (ed), Manual of Environmental Microbiology, 4th ed. http://dx.doi.org/10.1128/9781555818821.ch3.4.5. American Society of Microbiology, Washington, DC.
16. Schoen ME, Ashbolt NJ. 2010. Assessing pathogen risk to swimmers at non-sewage impacted recreational beaches. Environ Sci Technol 44:2286–2291. [PubMed]
17. Schoen ME, Soller JA, Ashbolt NJ. 2011. Evaluating the importance of faecal sources in human-impacted waters. Water Res 45:2670–2680. [PubMed]
18. U.S. Environmental Protection Agency. 2009. Review of Published Studies To Characterize Relative Risks from Different Sources of Fecal Contamination in Recreational Water. U.S. Environmental Protection Agency, Office of Water, Washington, DC.
19. Patterson S, Ashbolt N. 2016. Exposure assessment, p 3.5.2-1–3.5.2-18. In Yates MV, Nakatsu CH, Miller RV, Pillai SD (ed), Manual of Environmental Microbiology, 4th ed. http://dx.doi.org/10.1128/9781555818821.ch3.4.1. ASM Press, Washington, DC.
20. Yates M. 2016. Risk assessment framework, p 3.5.1-1–3.5.1-10. In Yates MV, Nakatsu CH, Miller RV, Pillai SD (ed), Manual of Environmental Microbiology, 4th ed. http://dx.doi.org/10.1128/9781555818821.ch3.4.1. ASM Press, Washington, DC.
21. Hagedorn C, Benham B, Zeckoski S. 2009. Microbial source tracking and the TMDL (total maximum daily loads) process. Virginia Cooperative Extension pub 442-554.
22. 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 75:3379–3388. [PubMed]
23. Blanch AR, Belanche-Muñoz L, Bonjoch X, Ebdon J, Gantzer C, Lucena F, Ottoson J, Kourtis C, Iversen A, Kühn I, Mocé L, Muniesa M, Schwartzbrod J, Skraber S, Papageorgiou GT, Taylor H, Wallis J, Jofre J. 2006. Integrated analysis of established and novel microbial and chemical methods for microbial source tracking. Appl Environ Microbiol 72:5915–5926. [PubMed]
24. Griffith JF, Weisberg SB, McGee CD. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. J Water Health 1:141–151. [PubMed]
25. Jellison KL, Lynch AE, Ziemann JM. 2009. Source tracking identifies deer and geese as vectors of human-infectious Cryptosporidium genotypes in an urban/suburban watershed. Environ Sci Technol 43:4267–4272. [PubMed]
26. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI. 2008. Evolution of mammals and their gut microbes. Science 320:1647–1651. [PubMed]
27. 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]
28. Geldreich EE, Kenner BA. 1969. Concepts of fecal streptococci in stream pollution. J Water Pollut Control Fed 41(Suppl):R336. [PubMed]
29. Clescerl LS, Greenberg AE, Eaton AD. 1998. Standard Methods for the Examination of Water and Wastewater, 20th ed. American Public Health Association, American Water Works Association, and Water Environment Federation, Washington, DC.
30. Hagedorn C, Blance AR, Harwood VJ (ed). 2011. Microbial Source Tracking: Methods, Applications, and Case Studies. Springer-U.S., New York, NY.
31. Harwood VJ, Hodon R, Santo Domingo J. 2011. Microbial source tracking, p 189–216. In Sadowsky MJ, Whitman RL (ed), The Fecal Bacteria. ASM Press, Washington, DC. http://dx.doi.org/10.1128/9781555816865.ch9.
32. Stoeckel DM, Harwood VJ. 2007. Performance, design, and analysis in microbial source tracking studies. Appl Environ Microbiol 73:2405–2415. [PubMed]
33. Li X, Harwood VJ, Nayak B, Staley C, Sadowsky MJ, Weidhaas J. 2015. A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems. Environ Sci Technol 49:7319–7329. [PubMed]
34. Li X, Harwood VJ, Nayak B, Weidhaas JL. 2016. Ultrafiltration and microarray for detection of microbial source tracking marker and pathogen genes in riverine and marine systems. Appl Environ Microbiol 82:1625–1635. [PubMed]
35. Dubinsky EA, Butkus SR, Andersen GL. 2016. Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification. Water Res 105:56–64. [PubMed]
36. Ahmed W, Staley C, Sadowsky MJ, Gyawali P, Sidhu JP, Palmer A, Beale DJ, Toze S. 2015. Toolbox approaches using molecular markers and 16S rRNA gene amplicon data sets for identification of fecal pollution in surface water. Appl Environ Microbiol 81:7067–7077. [PubMed]
37. 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]
38. Fisher JC, Eren AM, Green HC, Shanks OC, Morrison HG, Vineis JH, Sogin ML, McLellan SL. 2015. Comparison of sewage and animal fecal microbiomes by using oligotyping reveals potential human fecal indicators in multiple taxonomic groups. Appl Environ Microbiol 81:7023–7033. [PubMed]
39. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. 2011. Bayesian community-wide culture-independent microbial source tracking. Nat Methods 8:761–763. [PubMed]
40. McEwen SA, Wilson TM, Ashford DA, Heegaard ED, Kournikakis B. 2006. Microbial forensics for natural and intentional incidents of infectious disease involving animals. Rev Sci Tech 25:329–339. [PubMed]
41. Teaf C, Garber MM, Harwood VJ. 2011. Use of microbial source tracking in the legal arena: benefits and challenges, p 301–312. In Hagedorn C, Blanch AR, Harwood VJ (ed), Microbial Source Tracking: Methods, Applications, and Case Studies. Springer-U.S., New York, NY.
42. Unger S. 2008. Microbial Source Tracking: New Forensic Approaches to Identify Sources of Fecal Pollution. Environment Canada Science and Technology Research Impact Study Series: S&T into Action to Benefit Canadians.
43. Badgley B, Hagedorn C. 2015. Microbial source tracking: advances in research and a guide to application, p 267–288. In Younos T, Parece TE (ed). Advances in Watershed Science and Assessment. The Handbook of Environmental Chemistry, vol 33. Springer International, Cham, Switzerland.
44. Budowle B, Schutzer SE, Ascher MS, Atlas RM, Burans JP, Chakraborty R, Dunn JJ, Fraser CM, Franz DR, Leighton TJ, Morse SA, Murch RS, Ravel J, Rock DL, Slezak TR, Velsko SP, Walsh AC, Walters RA. 2005. Toward a system of microbial forensics: from sample collection to interpretation of evidence. Appl Environ Microbiol 71:2209–2213. [PubMed]
45. Simpson JM, Santo Domingo JW, Reasoner DJ. 2002. Microbial source tracking: state of the science. Environ Sci Technol 36:5279–5288. [PubMed]
46. Stoeckel DM. 2005. Selection and Application of Microbial Source Tracking Tools for Water-Quality Investigations. U.S. Department of the Interior, U.S. Geological Survey, Reston, VA.
47. Duran M, Yurtsever D, Dunaev T. 2009. Choice of indicator organism and library size considerations for phenotypic microbial source tracking by FAME profiling. Water Sci Technol 60:2659–2668. [PubMed]
48. Harwood VJ, Wiggins B, Hagedorn C, Ellender RD, Gooch J, Kern J, Samadpour M, Chapman ACH, Robinson BJ, Thompson BC. 2003. Phenotypic library-based microbial source tracking methods: efficacy in the California collaborative study. J Water Health 1:153–166. [PubMed]
49. Indest KJ, Betts K, Furey JS. 2005. Application of oligonucleotide microarrays for bacterial source tracking of environmental Enterococcus sp. isolates. Int J Environ Res Public Health 2:175–185. [PubMed]
50. Ritter KJ, Carruthers E, Carson CA, Ellender RD, Harwood VJ, Kingsley K, Nakatsu C, Sadowsky M, Shear B, West B, Whitlock JE, Wiggins BA, Wilbur JD. 2003. Assessment of statistical methods used in library-based approaches to microbial source tracking. J Water Health 1:209–223. [PubMed]
51. Seurinck S, Verstraete W, Siciliano SD. 2005. Microbial source tracking for identification of fecal pollution. Rev Environ Sci Biotechnol 4:19–37.
52. Hsu FC, Shieh YS, van Duin J, Beekwilder MJ, Sobsey MD. 1995. Genotyping male-specific RNA coliphages by hybridization with oligonucleotide probes. Appl Environ Microbiol 61:3960–3966. [PubMed]
53. Osawa S, Furuse K, Watanabe I. 1981. Distribution of ribonucleic acid coliphages in animals. Appl Environ Microbiol 41:164–168. [PubMed]
54. Puig A, Queralt N, Jofre J, Araujo R. 1999. Diversity of Bacteroides fragilis strains in their capacity to recover phages from human and animal wastes and from fecally polluted wastewater. Appl Environ Microbiol 65:1772–1776. [PubMed]
55. Tartera C, Lucena F, Jofre J. 1989. Human origin of Bacteroides fragilis bacteriophages present in the environment. Appl Environ Microbiol 55:2696–2701. [PubMed]
56. 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]
57. Kirs M, Caffaro-Filho RA, Wong M, Harwood VJ, Moravcik P, Fujioka RS. 2016. Human-associated Bacteroides spp. and human polyomaviruses as microbial source tracking markers in Hawaii. Appl Environ Microbiol 82:6757–6767. [PubMed]
58. Symonds EM, Young S, Verbyla ME, McQuaig-Ulrich SM, Ross E, Jiménez JA, Harwood VJ, Breitbart M. 2017. Microbial source tracking in shellfish harvesting waters in the Gulf of Nicoya, Costa Rica. Water Res 111:177–184. [PubMed]
59. Fujioka RS, Solo-Gabriele HM, Byappanahalli MN, Kirs M. 2015. U.S. Recreational Water Quality Criteria: A Vision for the Future. Int J Environ Res Public Health 12:7752–7776. [PubMed]
60. Sirikanchana K, Bombardelli F, Wuertz S. Quantitative pathogen detection & microbial source tracking combined with modeling the fate and transport of Bacteroidales in San Pablo Bay. The NOAA/UNH Cooperative Institute for Coastal and Estuarine Environmental Technology (CICEET), Durham, NH.
61. 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]
62. Lee DY, Lee H, Trevors JT, Weir SC, Thomas JL, Habash M. 2014. Characterization of sources and loadings of fecal pollutants using microbial source tracking assays in urban and rural areas of the Grand River Watershed, Southwestern Ontario. Water Res 53:123–131. [PubMed]
63. Araújo S, Henriques IS, Leandro SM, Alves A, Pereira A, Correia A. 2014. Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study. Sci Total Environ 470–471:84–91. [PubMed]
64. Parveen S, Hodge NC, Stall RE, Farrah SR, Tamplin ML. 2001. Phenotypic and genotypic characterization of human and nonhuman Escherichia coli. Water Res 35:379–386.
65. 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]
66. Boehm AB, Soller JA, Shanks OC. 2015. Human-associated fecal quantitative polymerase chain reaction measurements and simulated risk of gastrointestinal illness in recreational waters contaminated with raw sewage. Environ Sci Technol Lett 2:270–275.
67. 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 78:7317–7326. [PubMed]
68. McQuaig S, Griffith J, Harwood VJ. 2012. Association of fecal indicator bacteria with human viruses and microbial source tracking markers at coastal beaches impacted by nonpoint source pollution. Appl Environ Microbiol 78:6423–6432. [PubMed]
69. Oliver DM, Hanley ND, van Niekerk M, Kay D, Heathwaite AL, Rabinovici SJ, Kinzelman JL, Fleming LE, Porter J, Shaikh S, Fish R, Chilton S, Hewitt J, Connolly E, Cummins A, Glenk K, McPhail C, McRory E, McVittie A, Giles A, Roberts S, Simpson K, Tinch D, Thairs T, Avery LM, Vinten AJ, Watts BD, Quilliam RS. 2016. Molecular tools for bathing water assessment in Europe: balancing social science research with a rapidly developing environmental science evidence-base. Ambio 45:52–62. [PubMed]
70. U.S. Environmental Protection Agency. 2012. Recreational Water Quality Criteria. Office of Water, 820-F-12-058. U.S. EPA, Washington, DC.
71. Di Giovanni G, Casarez E, Gentry T, Martin E, Gregory L, Wagner K. 2013. Support analytical infrastructure and further development of a statewide bacterial source tracking library. Texas Water Resources Institute. http://hdl.handle.net/1969.1/152418.
72. Abdelzaher AM, Solo-Gabriele HM, Phillips MC, Elmir SM, Fleming LE. 2013. An alternative approach to water regulations for public health protection at bathing beaches. J Environ Public Health 2013:138521. http://dx.doi.org/10.1155/2013/138521. [PubMed]
73. Griffith JF, Layton BA, Boehm AB, Holden PA, Jay JA, Hagedom C, McGee CD, Weisberg SB. 2013. The California Microbial Source Identification Manual: A Tiered Approach to Identifying Fecal Pollution Sources to Beaches. Southern California Coastal Water Research Project, Costa Mesa, CA.
74. Lasalde C, Rodríguez R, Toranzos GA. 2005. Statistical analyses: possible reasons for unreliability of source tracking efforts. Appl Environ Microbiol 71:4690–4695. [PubMed]
75. Ervin JS, Van De Werfhorst LC, Murray JL, Holden PA. 2014. Microbial source tracking in a coastal California watershed reveals canines as controllable sources of fecal contamination. Environ Sci Technol 48:9043–9052. [PubMed]
76. Ahmed W, Harwood VJ, Nguyen K, Young S, Hamilton K, Toze S. 2016. Utility of Helicobacter spp. associated GFD markers for detecting avian fecal pollution in natural waters of two continents. Water Res 88:613–622. [PubMed]
77. Green HC, Dick LK, Gilpin B, Samadpour M, Field KG. 2012. Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water. Appl Environ Microbiol 78:503–510. [PubMed]
78. 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]
79. Ervin JS, Russell TL, Layton BA, Yamahara KM, Wang D, Sassoubre LM, Cao Y, Kelty CA, Sivaganesan M, Boehm AB, Holden PA, Weisberg SB, Shanks OC. 2013. Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods. Water Res 47:6873–6882. [PubMed]
80. Gordon KV, Brownell M, Wang SY, Lepo JE, Mott J, Nathaniel R, Kilgen M, Hellein KN, Kennedy E, Harwood VJ. 2013. Relationship of human-associated microbial source tracking markers with enterococci in Gulf of Mexico waters. Water Res 47:996–1004. [PubMed]
81. Green HC, Shanks OC, Sivaganesan M, Haugland RA, Field KG. 2011. Differential decay of human faecal Bacteroides in marine and freshwater. Environ Microbiol 13:3235–3249. [PubMed]
82. Jeanneau L, Solecki O, Wéry N, Jardé E, Gourmelon M, Communal PY, Jadas-Hécart A, Caprais MP, Gruau G, Pourcher AM. 2012. Relative decay of fecal indicator bacteria and human-associated markers: a microcosm study simulating wastewater input into seawater and freshwater. Environ Sci Technol 46:2375–2382. [PubMed]
83. Nayak B, Weidhaas J, Harwood VJ. 2015. LA35 poultry fecal marker persistence is correlated with that of indicators and pathogens in environmental waters. Appl Environ Microbiol 81:4616–4625. [PubMed]
84. Walters SP, Field KG. 2009. Survival and persistence of human and ruminant-specific faecal Bacteroidales in freshwater microcosms. Environ Microbiol 11:1410–1421. [PubMed]
85. 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 43:4929–4939. [PubMed]
86. Wanjugi P, Harwood VJ. 2014. Protozoan predation is differentially affected by motility of enteric pathogens in water vs. sediments. Microb Ecol 68:751–760. [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 38:6109–6117. [PubMed]
88. Hagedorn C, Robinson SL, Filtz JR, Grubbs SM, Angier TA, Reneau RB Jr. 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]
89. Moore DF, Harwood VJ, Ferguson DM, Lukasik J, Hannah P, Getrich M, Brownell M. 2005. Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed. J Appl Microbiol 99:618–628. [PubMed]
90. 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]
91. 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]
92. Kon T, Weir SC, Howell ET, Lee H, Trevors JT. 2009. Repetitive element (REP)-polymerase chain reaction (PCR) analysis of Escherichia coli isolates from recreational waters of southeastern Lake Huron. Can J Microbiol 55:269–276. [PubMed]
93. U.S. Environmental Protection Agency. 2011. Using Microbial Source Tracking to Support TMDL Development and Implementation. Prepared by Tetra Tech and Herrera Environmental Consultants. U.S. EPA, Washington, DC.
94. Bitton G. 2005. Wastewater Microbiology, 3rd ed, chapter 5, p 121–136. Wiley-Liss, New York, NY.
95. Brownell MJ, Harwood VJ, Kurz RC, McQuaig SM, Lukasik J, Scott TM. 2007. Confirmation of putative stormwater impact on water quality at a Florida beach by microbial source tracking methods and structure of indicator organism populations. Water Res 41:3747–3757. [PubMed]
96. Knudsen GR. 2010. Microbial Source Tracking: Pointing the Finger of Blame for Waterborne Pathogens. American Bar Association, ABA Water Quality and Wetlands Committee Newsletter.
97. Korajkic A, Badgley BD, Brownell MJ, Harwood VJ. 2009. Application of microbial source tracking methods in a Gulf of Mexico field setting. J Appl Microbiol 107:1518–1527. [PubMed]
98. Rusiñol M, Fernandez-Cassi X, Hundesa A, Vieira C, Kern A, Eriksson I, Ziros P, Kay D, Miagostovich M, Vargha M, Allard A, Vantarakis A, Wyn-Jones P, Bofill-Mas S, Girones R. 2014. Application of human and animal viral microbial source tracking tools in fresh and marine waters from five different geographical areas. Water Res 59:119–129. [PubMed]
99. Edge T, Schaefer K. 2006. Microbial Source Tracking in Aquatic Ecosystems: The State of the Science and an Assessment of Needs. National Water Research Institute, Burlington, Ontario, Canada.
100. Stapleton CM, Wyer MD, Kay D, Crowther J, McDonald AT, Walters M, Gawler A, Hindle T. 2007. Microbial source tracking: a forensic technique for microbial source identification? J Environ Monit 9:427–439. [PubMed]
101. Hundesa A, Bofill-Mas S, Maluquer de Motes C, Rodriguez-Manzano J, Bach A, Casas M, Girones R. 2010. Development of a quantitative PCR assay for the quantitation of bovine polyomavirus as a microbial source-tracking tool. J Virol Methods 163:385–389. [PubMed]
102. Buchan A, Alber M, Hodson RE. 2001. Strain-specific differentiation of environmental Escherichia coli isolates via denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S intergenic spacer region. FEMS Microbiol Ecol 35:313–321. [PubMed]
103. Scott TM, Parveen S, Portier KM, Rose JB, Tamplin ML, Farrah SR, Koo A, Lukasik J. 2003. Geographical variation in ribotype profiles of Escherichia coli isolates from humans, swine, poultry, beef, and dairy cattle in Florida. Appl Environ Microbiol 69:1089–1092. [PubMed]
104. Weidhaas J, Garner E, Basden T, Harwood VJ. 2014. Run-off studies demonstrate parallel transport behaviour for a marker of poultry fecal contamination and Staphylococcus aureus. J Appl Microbiol 117:417–429. [PubMed]
105. Weidhaas 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]
106. 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 109:334–347. [PubMed]
107. Hartel PG, Summer JD, Hill JL, Collins JV, Entry JA, Segars WI. 2002. Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia. J Environ Qual 31:1273–1278. [PubMed]
108. Jiang SC, Chu W, Olson BH, He JW, Choi S, Zhang J, Le JY, Gedalanga PB. 2007. Microbial source tracking in a small southern California urban watershed indicates wild animals and growth as the source of fecal bacteria. Appl Microbiol Biotechnol 76:927–934. [PubMed]
109. Scott TM, Caren J, Nelson GR, Jenkins TA, Lukasik J. 2004. Tracking sources of fecal pollution in a South Carolina watershed by ribotyping Escherichia coli: a case study. Environ Forensics 5:15–19.
110. PBS&J. 2008. Fecal BMAP Implementation: Source Identification, Hillsborough River Watershed, Final Summary Report. Prepared for the Florida Department of Environmental Protection, Tallahassee, FL.
111. Stoeckel DM, Kephart CM, Harwood VJ, Anderson MA, Dontchev M. Diversity of fecal indicator bacteria subtypes: implications for construction of microbial source tracking libraries. American Society for Microbiology General Meeting, May 23–27, New Orleans, LA.
112. Heaney CD, Myers K, Wing S, Hall D, Baron D, Stewart JR. 2015. Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations. Sci Total Environ 511:676–683. [PubMed]
113. Long S, Plummer J. 2008. Using microbial source tracking in watershed management: is high quality source water sustainable? AWWA Sustainable Water Sources Conference, Reno, NV, February 10–13.
114. 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]
115. Harmon R. 2005. Microbial Forensics. Elsevier Academic Press, Amsterdam, The Netherlands.
116. Pattnaik P, Jana AM. 2005. Microbial forensics: applications in bioterrorism. Environ Forensics 6:197–204.
117. Salyers A. 2004. Microbes in court: The emerging field of microbial forensics. http://www.actionbioscience.org/genomics/salyersarticle.html. Accessed March 21, 2010.
118. Koblentz GD, Tucker JB. 2010. Tracing an attack: the promise and pitfalls of microbial forensics. Survival (Lond) 52:159–186.
119. Daubert v. Merrell Dow Pharmaceuticals, Inc. 509 US at 589. United States Supreme Court, 1993.
120. Shanks OC, Kelty CA, Oshiro R, Haugland RA, Madi T, Brooks L, Field KG, Sivaganesan M. 2016. Data acceptance criteria for standardized human-associated fecal source identification quantitative real-time PCR methods. Appl Environ Microbiol 82:2773–2782. [PubMed]
121. Attorney General of Oklahoma v. Tyson Foods. 565 F.3d 769, 773–774, 777, 778–779, 789, 780, 10th Cir., 2009.
122. Waterkeeper Alliance, Inc. v. Hudson. WL 6651930, 1, Dist. Court (D. Maryland), 2012.
123. Lee YJ, Molina M, Santo Domingo JW, Willis JD, Cyterski M, Endale DM, Shanks OC. 2008. Temporal assessment of the impact of exposure to cow feces in two watersheds by multiple host-specific PCR assays. Appl Environ Microbiol 74:6839–6847. [PubMed]
124. 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 74:745–752. [PubMed]
125. 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 76:1359–1366. [PubMed]
126. Heinzen T, Russ A. 2014. Using emerging pollution tracking methods to address the downstream impacts of factory farm animal welfare abuse. Pace Environ Law Rev 31:475–499.
127. Ishii S, Kitamura G, Segawa T, Kobayashi A, Miura T, Sano D, Okabe S. 2014. Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples. Appl Environ Microbiol 80:7505–7511. [PubMed]
128. Vale FF. 2016. Microarrays/DNA chips for the detection of waterborne pathogens. Methods Mol Biol 1452:143–153. [PubMed]
129. Ahmed W, Staley C, Hamilton KA, Beale DJ, Sadowsky MJ, Toze S, Haas CN. 2017. Amplicon-based taxonomic characterization of bacteria in urban and peri-urban roof-harvested rainwater stored in tanks. Sci Total Environ 576:326–334. [PubMed]
130. McCarthy DT, Jovanovic D, Lintern A, Teakle I, Barnes M, Deletic A, Coleman R, Rooney G, Prosser T, Coutts S, Hipsey MR, Bruce LC, Henry R. 2017. Source tracking using microbial community fingerprints: method comparison with hydrodynamic modelling. Water Res 109:253–265. [PubMed]
131. Marti R, Ribun S, Aubin JB, Colinon C, Petit S, Marjolet L, Gourmelon M, Schmitt L, Breil P, Cottet M, Cournoyer B. 2017. Human-driven microbiological contamination of benthic and hyporheic sediments of an intermittent peri-urban river assessed from MST and 16S rRNA genetic structure analyses. Front Microbiol 8:19. http://dx.doi.org/10.3389/fmicb.2017.00019. [PubMed]
132. Staley C, Unno T, Gould TJ, Jarvis B, Phillips J, Cotner JB, Sadowsky MJ. 2013. Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River. J Appl Microbiol 115:1147–1158. [PubMed]
133. Green HC, Haugland RA, Varma M, Millen HT, Borchardt MA, Field KG, Walters WA, Knight R, Sivaganesan M, Kelty CA, Shanks OC. 2014. Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples. Appl Environ Microbiol 80:3086–3094. [PubMed]
134. 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 66:4571–4574.
Loading

Article metrics loading...

/content/journal/microbiolspec/10.1128/microbiolspec.EMF-0014-2017
2018-01-19
2018-09-18

Abstract:

The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

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

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

A simplified scheme for library-independent MST studies starts with identifying the animals within the study area that are likely to be major contributors to contamination. In this simplified version, we show two sources, cow and human (sewage). In the cow example, a type of fecal bacterium that is strongly associated with cow gastrointestinal tracts is denoted C. The bacterium is detected by extracting DNA and using PCR or qPCR to test for the DNA sequence (marker) that is specific to C. The sewage example follows the same flow, and the human-associated marker is denoted H. Note that in the case of certain viruses with RNA genomes, e.g., , RNA, rather than DNA, is extracted and tested. Water samples, in which the contamination source is unknown (?), can be tested by the MST methods to determine whether (PCR) and how much (qPCR) of the MST marker is present.

Source: microbiolspec January 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.EMF-0014-2017
Permissions and Reprints Request Permissions
Download as Powerpoint

Tables

Generic image for table
TABLE 1

Select examples of MST methods currently in use, including some advantages and disadvantages of specific methods

Source: microbiolspec January 2018 vol. 6 no. 1 doi:10.1128/microbiolspec.EMF-0014-2017

Supplemental Material

No supplementary material available for this content.

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