Rutgers New Jersey Agricultural Experiment Station [Water Resources Program]

Microbial Source Tracking (MST)

The Microbial Source Tracking Working Group at Rutgers, the State University has established this library of microbial source tracking (MST) related documents, which is hosted and maintained by the RCE Water Resources Program.  This library has been created to provide a common source for up-to-date information as it applies to MST. 

This database consists of reports and background material from Source Molecular Corporation (Miami, FL) and articles on various aspects of microbial source tracking compiled by David Scala
(Tuesday, June 20, 2006).

If you would like to add to this database, please contact
Lisa Galloway Evrard at 848-932-6726 or at evrard@rci.rutgers.edu.

Table of Contents

Microbial Source Tracking
     Bacteroidetes
     Enterococcus
          PCR Analyses: Enterococcus
               GenBank Sequences: Enterococcus
     qPCR
Bibliography

Microbial Source Tracking

Bacteroidetes

Enterococcus

PCR Analyses: Enterococcus

GenBank Sequences: Enterococcus

qPCR

Bibliography

  1. Essentials of Real-Time PCR. Foster City, CA: Applied Biosystems.
  2. Human Bacteroidetes "Quantification" ID. Miami, FL: Source Molecular Corporation.
  3. Human Bacteroidetes "Quantification" ID. Miami, FL: Source Molecular Corporation.
  4. Human Bacteroidetes ID. Miami, FL: Source Molecular Corporation.
  5. Human Bacteroidetes ID. Miami, FL: Source Molecular Corporation.
  6. Human Enterococcus "Quantification" ID. Miami, Fl: Source Molecular Corporation.
  7. Human Enterococcus "Quantification" ID: Sample Report.pdf. Miami, Fl: Source Molecular Corporation.
  8. An Overview of DNA Fingerprinting for the Water Industry. Miami, FL: Source Molecular Corporation.
  9. Real-Time Vs. Traditional PCR. Foster City, CA: Applied Biosystems.
  10. 2005. Microbial Source Tracking Guide Document. EPA/600/R-05/064: U.S. Environmental Protection Agency.
  11. 2005. Real Time PCR brochure. Foster City, CA: Applied Biosystems.
  12. 2005. Selection and Application of Microbial Source Tracking Tools For Water-Quality Investigations. Techniques and Methods Book 2, Chapter A3: U.S. Geological Survey.
  13. AF034779. 1999. Enterococcus faecalis surface protein precursor, gene. GenBank (NCBI).
  14. AF443999. 2001. Enterococcus faecium surface protein esp variant esp-1. GenBank (NCBI).
  15. AF444000. 2001. Enterococcus faecium surface protein esp variant esp-2. GenBank (NCBI).
  16. AH013271. 2004. Enterococcus faecium isolate E470 putative enterococcal surface protein (esp). GenBank (NCBI).
  17. AY322499. 2004. Enterococcus faecium isolate E734 putative enterococcal surface protein (esp). GenBank (NCBI).
  18. AY322500. 2004. Enterococcus faecium isolate E470 putative enterococcal surface protein (esp). GenBank (NCBI).
  19. AY322501. 2004. Enterococcus faecium isolate E470 putative enterococcal surface protein (esp). GenBank (NCBI).
  20. AY322502. 2004. Enterococcus faecium isolate E470 putative enterococcal surface protein (esp). GenBank (NCBI).
  21. Baldassarri L, Bertuccini L, Ammendolia MG, Gherardi G, Creti R. 2001. Variant esp gene in vancomycin-sensitive Enterococcus faecium. The Lancet 357(9270):1802.
  22. 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. Applied and Environmental Microbiology 66(4):1587-1594.
  23. 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. Applied and Environmental Microbiology 66(10):4571-4574.
  24. Cheng S, McCleskey FK, Gress MJ, Petroziello JM, Liu R, Namdari H, Beninga K, Salmen A, DelVecchio VG. 1997. A PCR assay for identification of Enterococcus faecium. Journal of Clinical Microbiology 35(5):1248-1250.
  25. Deasy BM, Rea MC, Fitzgerald GF, Cogan TM, Beresford TP. 2000. A Rapid PCR Based Method to Distinguish between Lactococcus and Enterococcus. Systematic and Applied Microbiology 23:510-522.
  26. Dick LK, Bernhard AE, Brodeur TJ, Santo-Domingo JW, Simpson JM, Walters SP, Field KG. 2005. Host Distributions of Uncultivated Fecal Bacteroidales Bacteria Reveal Genetic Markers for Fecal Source Identification. Applied and Environmental Microbiology 71(6):3184-3191.
  27. Dick LK, Field KG. 2005. Rapid Estimation of Numbers of Fecal Bacteroidetes by Use of a Quantitative PCR Assay for 16S rRNA Genes. Applied and Environmental Microbiology 70(9):5695-5697.
  28. Dick LK, Simonich MT, Field KG. 2005. Microplate Subtractive Hybridization To Enrich for Bacteroidales Genetic Markers for Fecal Source Identification. Applied and Environmental Microbiology 71(6):3179-3183.
  29. Field KG, Bernhard AE, Brodeur TJ. 2003. Molecular Approaches To Microbiological Monitoring: Fecal Source Detection. Environmental Monitoring and Assessment 81:313-326.
  30. Hammerum AM, Jensen LB. 2002. Prevalence of esp, Encoding the Enterococcal Surface Protein, in Enterococcus faecalis and Enterococcus faecium Isolates from Hospital Patients, Poultry, and Pigs in Denmark. Journal of Clinical Microbiology 40(11):4396.
  31. 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 Research 39:559-568.
  32. Jackson CR, Fedorka-Cray PJ, Barrett JB. 2004. Use of a Genus- and Species-Specific Multiplex PCR for Identification of Enterococci. Journal of Clinical Microbiology 42(8):3558-3565.
  33. Johnson BC . 2004. The Application of a DNA-based Molecular Approach to Identify Sources of Fecal Contamination: The Search for Pathogens. U.S. EPA, Region 4, Ecological Assessment Branch.
  34. Ke D, Picard FJ, Martineau F, Menard C, Roy PH, Ouellette M, Bergeron MG. 1999. Development of a PCR Assay for Rapid Detection of Enterococci. Journal of Clinical Microbiology 37(11):3497-3503.
  35. Kreader CA. 1995. Design and Evaluation of Bacteroides DNA Probes for the Specific Detection of Human Fecal Pollution. Applied and Environmental Microbiology 61(4):1171-1179.
  36. Kreader CA. 1998. Persistence of PCR-Detectable Bacteroides distasonis from Human Feces in River Water. Applied and Environmental Microbiology 64(10):4103-4105.
  37. 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. Applied and Environmental Microbiology 72(6):4214-4224.
  38. McDaniels AE, Wymer L, Rankin C, Haugland R. 2005. Evaluation of quantitative real time PCR for the measurement of Helicobacter pylori at low concentrations in drinking water. Water Research 39:4808-4816.
  39. 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. Journal of Environmental Quality 35:889-897.
  40. Phelps C. 2006. Update on Microbial Source Tracking from the ASM General Meeting in Orlando. ASM General Meeting. Orlando, FL.
  41. Quednau M, Ahrne S, Molin G. 1999. Genomic Relationships between Enterococcus faecium Strains from Different Sources and with Different Antibiotic Resistance Profiles Evaluated by Restriction Endonuclease Analysis of Total Chromosomal DNA Using EcoRI and PvuII. Applied and Environmental Microbiology 65(4):1777-1780.
  42. 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. Enivronmental Science & Technology 39(1):283-287.
  43. Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J. 2002. Microbial Source Tracking: Current Methodology and Future Directions. Applied and Environmental Microbiology 68(12):5796-5803.
  44. 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. Environmental Microbiology 7(2):249-259.
  45. Shankar V, Baghdayan AS, Huycke MM, Lindahl G, Gilmore MS. 1999. Infection-Derived Enterococcus faecalis Strains Are Enriched in esp, a Gene Encoding a Novel Surface Protein. Infection and Immunity 67(1):193-200.
  46. Shanks OC. 2005. Microbial Source Tracking: Genomics Training Workshop Presentation. Genomics Training Workshop. US EPA Region 5: US EPA Region 5.
  47. 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. Applied and Environmental Microbiology 72(6):4054-4060.
  48. Simpson JM, Santo Domingo JW, Reasoner DJ. 2002. Microbial Source Tracking: State of the Science. Environmental Science & Technology 36(24):5279-5288.
  49. Soule M, Kuhn E, Loge F, Gay J, Call DR. 2006. Using DNA Microarrays To Identify Library-Independent Markers for Bacterial Source Tracking. Applied and Environmental Microbiology 72(3):1843-1851.
  50. U.S.EPA. 2002. EPA Method 1600: Enterococci by Membrane Filtration Using membrane-Enterococcus Indoxyl-B-D-Glucoside Agar (mEI). EPA 821-R-02-022. Washington, DC.
  51. Wade TJ, Calderon RL, Sams E, Beach M, Brenner KP, Williams AH, Dufour AP. 2006. Rapidly Measured Indicators of Recreational Water Quality Are Predictive of Swimming-Associated Gastrointestinal Illness. Environmental Health Perspectives 114(1):24-28.
  52. Wade TJ, Pai N, Eisenberg JNS, John M. Colford J. 2003. Do U.S. Environmental Protection Agency Water Quality Guidelines for Recreational Waters Prevent Gastrointestinal Illness? A Systematic Review and Meta-analysis. Environmental Health Perspectives 111(8):1102-1109.
  53. Wheeler AL, Hartel PG, Godfrey DG, Hill JL, Segars WI. 2002. Potential of Enterococcus faecalis as a Human Fecal Indicator for Microbial Source Tracking. Applied and Environmental Microbiology 31(4):1286-1293.
  54. Willems RJL, Homan W, Top J, Santen-Verheuvel Mv, Tribe D, Manzioros X, Gaillard C, Vandenbroucke-Grauls CMJE, Mascini EM, Kregten Ev and others. 2001. Variant esp gene as a marker of a distinct genetic lineage of vancomycin-resistant Enterococcus faecium spreading in hospitals. The Lancet 357(9259):853-855.
  55. Woodford N, Soltani M, Hardy KJ. 2001. Frequency of esp in Enterococcus faecium isolates. The Lancet 358(9281):584.

    Additions by the Water Resources Program since June 20, 2006:

  56. Hamilton MJ, Yan T, Sadowsky MJ. 2006. Development of Goos-and Duck-Specific DNA Markers to Determine Sources of Escherichia coli in Waterways. Applied and Environmental Microbiology 72(6): 4012-4019.
  57. 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. Applied and Environmental Microbiology 72(6): 4054-4060.
  58. Altherholt T. 2005. Microbial Source Tracking: Library Based Methods. NJDEP Division of Science, Research and Technology, Technology Critique.
  59. Griffith JF, Weisberg, SB. 2006. Evaluation of Rapid Microbial Methods for Measuring Recreational Water Quality. Southern California Coastal Water Research Project Techinical Report 485 May 2006.
  60. Buckley, K, Phelps, K. 2006. Developing Microbial Source Tracking Methodologies Using PCR for Bacteroides and Other Indicators. Monmouth University Coastal Watershed Seminar Series.

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