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Marine and Freshwater Fecal Indicators and Source Identification

  • Sandra L. McLellanEmail author
  • Alexandria B. Boehm
  • Orin C. Shanks
Chapter

Abstract

Fecal indicators are organisms or chemical constituents found in fecal material or wastewater from humans and other animals can contaminant surface waters and pose a serious threat to the environment and human health. Fecal pollution serves as a vehicle for disease transmission including pathogenic bacteria, viruses, or protozoa. Fecal waste also carries with it harmless commensal organisms that live in the gastrointestinal (GI) tract and are often used as fecal indicators since they are present in high numbers. The type and amount of pathogens found in fecal pollution is dependent on the host source (human, agricultural animal, wildlife) and the prevalence of illness in the host population. Therefore, employing fecal indicators that provide information about human and other animal contributions is critical for estimating the likelihood that pathogens are present and for directing remediation efforts.

Keywords

Fecal Coliform United States Environmental Protection Agency Much Probable Number Water Quality Criterion Fecal Indicator Bacterium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Glossary

Alternative fecal indicators

Fecal indicators that have not been fully validated for standard water quality methods, but show potential for increased sensitivity or specificity over current indicators.

Commensal

The general meaning of this word is sharing of food and originates from the Latin word cum mensa, meaning “sharing a table.” In the context of bacteria and host interactions, the bacteria benefit from the host without causing harm.

Enterococci

The term “enterococci” is a general reference to members of the genus Enterococcus: however, in the context of water quality standards, enterococci often refers to E. faecalis and E. faecium, which can be enumerated using selective and differential media.

Escherichia coli (E. coli)

Gram-negative bacteria found in the gastrointestinal tract of almost all warm-blooded animals. These bacteria are easily cultured and can be enumerated using selective and differential media.

Fecal indicator

A chemical or biological constituent that is found in fecal matter that can be used to demonstrate the presence of contamination.

Pathogen

A microbe or microorganism such as a bacteria, virus, fungi, prion, or protozoan that causes disease in its animal or plant host.

Polymerase chain reaction (PCR)

A scientific technique in molecular biology to amplify a single or few gene copies of a nucleic acid fragment across several orders of magnitude. Amplification results in the generation of thousands to millions of copies of a particular nucleic acid sequence.

Quantitative PCR

A technique based on PCR which simultaneously amplifies and quantifies a targeted nucleic acid molecule.

Notes

Acknowledgments

We would like to thank Dr. Alford Dufour for insightful discussion and for providing historical information on the use of traditional indicators and evolution of water quality criteria. The US Environmental Protection Agency, through its Office of Research and Development, funded and managed, or partially funded and collaborated in, the research described herein. It has been subjected to the Agency’s peer and administrative review and has been approved for external publication. Any opinions expressed in this entry are those of the author(s) and do not necessarily reflect the views of the Agency; therefore, no official endorsement should be inferred. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Bibliography

  1. 1.
    Ahmed W, Powell D, Goonetilleke A, Gardner T (2008) Detection and source identification of faecal pollution in non-sewered catchment by means of host-specific molecular markers. Water Sci Technol 58:579–586PubMedCrossRefGoogle Scholar
  2. 2.
    Ahmed W, Stewart J, Gardner T, Powell D (2008) A real-time polymerase chain reaction assay for quantitative detection of the human-specific enterococci surface protein marker in sewage and environmental waters. Environ Microbiol 10:3255–3264PubMedCrossRefGoogle Scholar
  3. 3.
    Ahmed W, Stewart J, Powell D, Gardner T (2008) Evaluation of Bacteroides markers for the detection of human faecal pollution. Lett Appl Microbiol 46:237–242PubMedCrossRefGoogle Scholar
  4. 4.
    Ahmed W, Goonetilleke A, Powell D, Chauhan K, Gardner T (2009) Comparison of molecular markers to detect fresh sewage in environmental waters. Water Res 43:4908–4917PubMedCrossRefGoogle Scholar
  5. 5.
    Ahmed W, Sawant S, Huygens F, Goonetilleke A, Gardner T (2009) Prevalence and occurrence of zoonotic bacterial pathogens in surface waters determined by quantitative PCR. Water Res 43:4918–4928PubMedCrossRefGoogle Scholar
  6. 6.
    Ahmed W, Wan C, Goonetilleke A, Gardner T (2010) Evaluating sewage-associated JCV and BKV polyomaviruses for sourcing human fecal pollution in a coastal river in Southeast Queensland, Australia. J Environ Qual 39:1743–1750PubMedCrossRefGoogle Scholar
  7. 7.
    Alm EW, Burke J, Spain A (2003) Fecal indicator bacteria are abundant in wet sand at freshwater beaches. Water Res 37:3978–3982CrossRefGoogle Scholar
  8. 8.
    Alonso JL, Alonso MA (1993) Presence of Campylobacter in marine waters of Valencia. Spain Water Res 27:1559–1562Google Scholar
  9. 9.
    Anderson KL, Whitlock JE, Harwood VJ (2005) Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl Environ Microbiol 71:3041–3048PubMedCrossRefGoogle Scholar
  10. 10.
    Anderson MA, Whitlock JE, Harwood VJ (2006) Diversity and distribution of Escherichia coli genotypes and antibiotic resistance phenotypes in feces of humans, cattle, and horses. Appl Environ Microbiol 72:6914–6922PubMedCrossRefGoogle Scholar
  11. 11.
    Arai T, Ikejima N, Itoh T, Sakai S, Shimada T, Sakazaki R (1980) A survey of Plesiomonas shigelloides from aquatic environments, domestic animals, pets and humans. J Hyg (Lond) 84:203–211CrossRefGoogle Scholar
  12. 12.
    Araujo RM, Puig A, Lasobras J, Lucena F, Jofre J (1997) Phages of enteric bacteria in fresh water with different levels of faecal pollution. J Appl Microbiol 82:281–286PubMedCrossRefGoogle Scholar
  13. 13.
    Arnone RD, Walling JP (2007) Waterborne pathogens in urban watersheds. J Water Health 5:149–162PubMedCrossRefGoogle Scholar
  14. 14.
    Ashbolt NJ, Grabow OK, Snozzi M (2001) Indicators of microbial water quality. In: Fewtrell L, Bartram J (eds) Water quality: guidelines, standards, and health. IWA Publishing, LondonGoogle Scholar
  15. 15.
    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 44:4692–4703PubMedCrossRefGoogle Scholar
  16. 16.
    Association, A. P. H. (1999) Standard methods for the examination of water and wastewater, 18th edn. American Public Health Association, Washington, DCGoogle Scholar
  17. 17.
    Aw TG, Gin KY, Ean Oon LL, Chen EX, Woo CH (2009) Prevalence and genotypes of human noroviruses in tropical urban surface waters and clinical samples in Singapore. Appl Environ Microbiol 75:4984–4992PubMedCrossRefGoogle Scholar
  18. 18.
    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 43:4850–4859PubMedCrossRefGoogle Scholar
  19. 19.
    Bai S, Lung WS (2005) Modeling sediment impact on the transport of fecal bacteria. Water Res 39:5232–5240PubMedCrossRefGoogle Scholar
  20. 20.
    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 76:1789–1795PubMedCrossRefGoogle Scholar
  21. 21.
    Baudart J, Lemarchand K, Brisabois A, Lebaron P (2000) Diversity of Salmonella strains isolated from the aquatic environment as determined by serotyping and amplification of the ribosomal DNA spacer regions. Appl Environ Microbiol 66:1544–1552PubMedCrossRefGoogle Scholar
  22. 22.
    Baums IB, Goodwin KD, Kiesling T, Wanless D, Diaz MR, Fell JW (2007) Luminex detection of fecal indicators in river samples, marine recreational water, and beach sand. Mar Pollut Bull 54:521–536PubMedCrossRefGoogle Scholar
  23. 23.
    Bell A, Layton AC, McKay L, Williams D, Gentry R, Sayler GS (2009) Factors influencing the persistence of fecal Bacteroides in stream water. J Environ Qual 38:1224–1232PubMedCrossRefGoogle Scholar
  24. 24.
    Bernhard AE, Field KG (2000) Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16 S ribosomal DNA genetic markers from fecal anaerobes. Appl Environ Microbiol 66:1587–1594PubMedCrossRefGoogle Scholar
  25. 25.
    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 16 S rRNA. Appl Environ Microbiol 66:4571–4574PubMedCrossRefGoogle Scholar
  26. 26.
    Beversdorf LJ, Bornstein-Forst SM, McLellan SL (2007) The potential for beach sand to serve as a reservoir for Escherichia coli and the physical influences on cell die-off. J Appl Microbiol 102:1372–1381PubMedCrossRefGoogle Scholar
  27. 27.
    Bienfang PK, Defelice SV, Laws EA, Brand LE, Bidigare RR, Christensen S, Trapido-Rosenthal H, Hemscheidt TK, McGillicuddy DJ, Anderson DM, Solo-Gabriele HM, Boehm AB, Backer LC (2011) Prominent human health impacts from several marine microbes: history, ecology, and public health implications. Int J Microbiol 2011:152815PubMedGoogle Scholar
  28. 28.
    Blanch AR, Belanche-Munoz L, Bonjoch X, Ebdon J, Gantzer C, Lucena F, Ottoson J, Kourtis C, Iversen A, Kuhn I, Moce 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 72:5915–5926PubMedCrossRefGoogle Scholar
  29. 29.
    Boehm AB (2007) Enterococci concentrations in diverse coastal environments exhibit extreme variability. Environ Sci Technol 41:8227–8232PubMedCrossRefGoogle Scholar
  30. 30.
    Boehm AB, Keymer DP, Shellenbarger GG (2005) An analytical model of enterococci inactivation, grazing, and transport in the surf zone of a marine beach. Water Res 39:3565–3578PubMedCrossRefGoogle Scholar
  31. 31.
    Boehm AB, Ashbolt NJ, Colford JM Jr, Dunbar LE, Fleming LE, Gold MA, Hansel JA, Hunter PR, Ichida AM, McGee CD, Soller JA, Weisberg SB (2009) A sea change ahead for recreational water quality criteria. J Water Health 7:9–20PubMedCrossRefGoogle Scholar
  32. 32.
    Boehm AB, Yamahara KM, Love DC, Peterson BM, McNeill K, Nelson KL (2009) Covariation and photoinactivation of traditional and novel indicator organisms and human viruses at a sewage-impacted marine beach. Environ Sci Technol 43:8046–8052PubMedCrossRefGoogle Scholar
  33. 33.
    Bolton F, Surman SB, Martin K, Wareing DR, Humphrey TJ (1999) Presence of Campylobacter and Salmonella in sand from bathing beaches. Epidemiol Infect 122:7–13PubMedCrossRefGoogle Scholar
  34. 34.
    Bonde GJ (1963) Bacterial indicators of water pollution. A study of quantitative estimation. Teknisk Forlag, CopenhagenGoogle Scholar
  35. 35.
    Bonjoch X, Balleste E, Blanch AR (2004) Multiplex PCR with 16 S rRNA gene-targeted primers of bifidobacterium spp. to identify sources of fecal pollution. Appl Environ Microbiol 70:3171–3175PubMedCrossRefGoogle Scholar
  36. 36.
    Bothner MH, Takada H, Knight IT, Hill RT, Butman B, Farrington JW, Colwell RR, Grassle JF (1994) Sewage contamination in sediments beneath a deep-ocean dump site off New-York. Mar Environ Res 38:43–59CrossRefGoogle Scholar
  37. 37.
    Bower PA, Scopel CO, Jensen ET, Depas MM, McLellan SL (2005) Detection of genetic markers of fecal indicator bacteria in Lake Michigan and determination of their relationship to Escherichia coli densities using standard microbiological methods. Appl Environ Microbiol 71:8305–8313PubMedCrossRefGoogle Scholar
  38. 38.
    Brion GM, Meschke JS, Sobsey MD (2002) F-specific RNA coliphages: occurrence, types, and survival in natural waters. Water Res 36:2419–2425PubMedCrossRefGoogle Scholar
  39. 39.
    Cabelli VJ, Dufour AP, McCabe LJ, Levin MA (1982) Swimming-associated gastroenteritis and water quality. Am J Epidemiol 115:606–616PubMedGoogle Scholar
  40. 40.
    Caldwell JM, Raley ME, Levine JF (2007) Mitochondrial multiplex real-time PCR as a source tracking method in fecal-contaminated effluents. Environ Sci Technol 41:3277–3283PubMedCrossRefGoogle Scholar
  41. 41.
    Cao Y, Griffith JF, Weisberg SB (2009) Evaluation of optical brightener photodecay characteristics for detection of human fecal contamination. Water Res 43:2273–2279PubMedCrossRefGoogle Scholar
  42. 42.
    Caplenas NR, Kanarek MS (1984) Thermotolerant non-fecal source Klebsiella pneumoniae: validity of the fecal coliform test in recreational waters. Am J Public Health 74:1273–1275PubMedCrossRefGoogle Scholar
  43. 43.
    Carson CA, Shear BL, Ellersieck MR, Asfaw A (2001) Identification of fecal Escherichia coli from humans and animals by ribotyping. Appl Environ Microbiol 67:1503–1507PubMedCrossRefGoogle Scholar
  44. 44.
    Carson CA, Shear BL, Ellersieck MR, Schnell JD (2003) Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Appl Environ Microbiol 69:1836–1839PubMedCrossRefGoogle Scholar
  45. 45.
    Carson CA, Christiansen JM, Yampara-Iquise H, Benson VW, Baffaut C, Davis JV, Broz RR, Kurtz WB, Rogers WM, Fales WH (2005) Specificity of a Bacteroides thetaiotaomicron marker for human feces. Appl Environ Microbiol 71:4945–4949PubMedCrossRefGoogle Scholar
  46. 46.
    Center for Disease Control (2011) posting date. Escherichia coli O157:H7, General informationGoogle Scholar
  47. 47.
    Chapron CD, Ballester NA, Fontaine JH, Frades CN, Margolin AB (2000) Detection of astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface waters collected and evaluated by the information collection rule and an integrated cell culture-nested PCR procedure. Appl Environ Microbiol 66:2520–2525PubMedCrossRefGoogle Scholar
  48. 48.
    Charoenca N, Fujioka RS (1993) Assessment of Staphylococcus bacteria in Hawaii’s marine recreational waters. Water Sci Technol 27:283–289Google Scholar
  49. 49.
    Charoenca N, Fujioka RS (1995) Association of staphylococcal skin infections and swimming. Water Sci Technol 31:11–17Google Scholar
  50. 50.
    Chern EC, Tsai YL, Olson BH (2004) Occurrence of genes associated with enterotoxigenic and enterohemorrhagic Escherichia coli in agricultural waste lagoons. Appl Environ Microbiol 70:356–362PubMedCrossRefGoogle Scholar
  51. 51.
    Choi S, Jiang SC (2005) Real-time PCR quantification of human adenoviruses in urban rivers indicates genome prevalence but low infectivity. Appl Environ Microbiol 71:7426–7433PubMedCrossRefGoogle Scholar
  52. 52.
    Colford JM Jr, Wade TJ, Schiff KC, Wright CC, Griffith JF, Sandhu SK, Burns S, Sobsey M, Lovelace G, Weisberg SB (2007) Water quality indicators and the risk of illness at beaches with nonpoint sources of fecal contamination. Epidemiology 18:27–35PubMedCrossRefGoogle Scholar
  53. 53.
    Converse RR, Blackwood AD, Kirs M, Griffith JF, Noble RT (2009) Rapid QPCR-based assay for fecal Bacteroides spp. as a tool for assessing fecal contamination in recreational waters. Water Res 43:48–4837CrossRefGoogle Scholar
  54. 54.
    Davies CM, Long JA, Donald M, Ashbolt NJ (1995) Survival of fecal microorganisms in marine and freshwater sediments. Appl Environ Microbiol 61:1888–1896PubMedGoogle Scholar
  55. 55.
    DePaola A, Hopkins LH, Peeler JT, Wentz B, McPhearson RM (1990) Incidence of Vibrio parahaemolyticus in U.S. coastal waters and oysters. Appl Environ Microbiol 56:2299–2302PubMedGoogle Scholar
  56. 56.
    Desmarais TR, Solo-Gabriele HM, Palmer CJ (2002) Influence of soil on fecal indicator organisms in a tidally influenced subtropical environment. Appl Environ Microbiol 68:1165–1172PubMedCrossRefGoogle Scholar
  57. 57.
    Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16 S rRNA sequencing. PLoS Biol 6:e280PubMedCrossRefGoogle Scholar
  58. 58.
    Devriese LLA, van de Kerckhove A, Kilpper-Baelz R, Schleifer K (1987) Characterization and identification of Enterococcus species isolated from the intestines of animals. Int J Syst Bacteriol 37:257–259CrossRefGoogle Scholar
  59. 59.
    Dick LK, Field KG (2004) Rapid estimation of numbers of fecal Bacteroidetes by use of a quantitative PCR assay for 16 S rRNA genes. Appl Environ Microbiol 70:5695–5697PubMedCrossRefGoogle Scholar
  60. 60.
    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. Appl Environ Microbiol 71:3184–3191PubMedCrossRefGoogle Scholar
  61. 61.
    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 76:3255–3262PubMedCrossRefGoogle Scholar
  62. 62.
    Dickerson JW Jr, 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 41:3758–3770PubMedCrossRefGoogle Scholar
  63. 63.
    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 66:2572–2577PubMedCrossRefGoogle Scholar
  64. 64.
    Dorai-Raj S, O’Grady J, Colleran E (2009) Specificity and sensitivity evaluation of novel and existing Bacteroidales and Bifidobacteria-specific PCR assays on feces and sewage samples and their application for microbial source tracking in Ireland. Water Res 43:4980–4988PubMedCrossRefGoogle Scholar
  65. 65.
    Dufour AP (1984) Bacterial indicators of recreational water quality. Can J Public Health 75:49–56PubMedGoogle Scholar
  66. 66.
    Dufour AP, Schaub S (2007) The evolution of water quality criteria in the United Sates, 1922–2003. In: Wymer LJ (ed) Statistical framework for recreational water quality monitoring. Wiley, New YorkGoogle Scholar
  67. 67.
    Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638PubMedCrossRefGoogle Scholar
  68. 68.
    Eckner KF (1998) Comparison of membrane filtration and multiple-tube fermentation by the colilert and enterolert methods for detection of waterborne coliform bacteria, Escherichia coli, and enterococci used in drinking and bathing water quality monitoring in southern Sweden. Appl Environ Microbiol 64:3079–3083PubMedGoogle Scholar
  69. 69.
    Edge TA, Boehm AB (2011) Classical and molecular methods to measure fecal indicator bacteria. In: Sadowsky MJ, Whitman RL (eds) The fecal indicator bacteria. ASM Press, Washington, DCGoogle Scholar
  70. 70.
    Edwards DD, McFeters GA, Venkatesan MI (1998) Distribution of Clostridium perfringens and fecal sterols in a benthic coastal marine environment influenced by the sewage outfall from McMurdo Station, Antarctica. Appl Environ Microbiol 64:2596–2600PubMedGoogle Scholar
  71. 71.
    Emerson DJ, Cabelli VJ (1982) Extraction of Clostridium perfringens spores from bottom sediment samples. Appl Environ Microbiol 44:1144–1149PubMedGoogle Scholar
  72. 72.
    Field KG, Samadpour M (2007) Fecal source tracking, the indicator paradigm, and managing water quality. Water Res 41:3517–3538PubMedCrossRefGoogle Scholar
  73. 73.
    Field KG, Bernhard AE, Brodeur TJ (2003) Molecular approaches to microbiological monitoring: fecal source detection. Environ Monit Assess 81:313–326PubMedCrossRefGoogle Scholar
  74. 74.
    Fiksdal L, Maki JS, LaCroix SJ, Staley JT (1985) Survival and detection of Bacteroides spp., prospective indicator bacteria. Appl Environ Microbiol 49:148–150PubMedGoogle Scholar
  75. 75.
    Fogarty LR, Voytek MA (2005) Comparison of bacteroides-prevotella 16 S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol 71:5999–6007PubMedCrossRefGoogle Scholar
  76. 76.
    Fong T-T, Lipp EK (2005) Enteric viruses of humans and animals in aquatic environments: health risks, detection, and potential water quality assessment tools. Microbiol Mol Biol Rev 69:357–371PubMedCrossRefGoogle Scholar
  77. 77.
    Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 104:13780–13785PubMedCrossRefGoogle Scholar
  78. 78.
    Fremaux B, Gritzfeld J, Boa T, Yost CK (2009) Evaluation of host-specific Bacteroidales 16 S rRNA gene markers as a complementary tool for detecting fecal pollution in a prairie watershed. Water Res 43:4838–4849PubMedCrossRefGoogle Scholar
  79. 79.
    Fujioka RS (2001) Monitoring coastal marine waters for spore-forming bacteria of faecal and soil origin to determine point from non-point source pollution. Water Sci Technol 44:181–188PubMedGoogle Scholar
  80. 80.
    Fung DYC, Fujioka R, Vijayavel K, Sato D, Bishop D (2007) Evaluation of Fung double tube test for Clostridium perfringens and Easyphage test for F-specific RNA coliphages as rapid screening tests for fecal contamination in recreational waters of Hawaii (vol 15, pg 217, 2007). J Rapid Meth Aut Mic 15:411–411CrossRefGoogle Scholar
  81. 81.
    Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Dore J, Corthier G (2009) Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol 68:351–362PubMedCrossRefGoogle Scholar
  82. 82.
    Gast RJ, Moran D, Dennett MR, Wurtsbaugh WA, Amaral-Zettler LA (2011) Amoebae and Legionella pneumophila in saline environments. J Water Health 9:37–52PubMedCrossRefGoogle Scholar
  83. 83.
    Gauthier F, Neufeld JD, Driscoll BT, Archibald FS (2000) Coliform bacteria and nitrogen fixation in pulp and paper mill effluent treatment systems. Appl Environ Microbiol 66:5155–5160PubMedCrossRefGoogle Scholar
  84. 84.
    Gawler AH, Beecher JE, Brandao J, Carroll NM, Falcao L, Gourmelon M, Masterson B, Nunes B, Porter J, Rince A, Rodrigues R, Thorp M, Walters JM, Meijer WG (2007) Validation of host-specific Bacteriodales 16 S rRNA genes as markers to determine the origin of faecal pollution in Atlantic Rim countries of the European Union. Water Res 41:3780–3784PubMedCrossRefGoogle Scholar
  85. 85.
    Gerba CP, Rose JB, Haas CN, Crabtree KD (1996) Waterborne rotavirus: a risk assessment. Water Res 30:2929–2940CrossRefGoogle Scholar
  86. 86.
    Gersberg RM, Rose MA, Robles-Sikisaka R, Dhar AK (2006) Quantitative detection of hepatitis A virus and enteroviruses near the United States-Mexico border and correlation with levels of fecal indicator bacteria. Appl Environ Microbiol 72:7438–7444PubMedCrossRefGoogle Scholar
  87. 87.
    Gilpin B, James T, Nourozi F, Saunders D, Scholes P, Savill M (2003) The use of chemical and molecular microbial indicators for faecal source identification. Water Sci Technol 47:39–43PubMedGoogle Scholar
  88. 88.
    Goodwin KD, Pobuda M (2009) Performance of CHROMagar Staph aureus and CHROMagar MRSA for detection of Staphylococcus aureus in seawater and beach sand – comparison of culture agglutination, and molecular analyses. Water Res 43:4802–4811PubMedCrossRefGoogle Scholar
  89. 89.
    Gourmelon M, Caprais MP, Mieszkin S, Marti R, Wery N, Jarde E, Derrien M, Jadas-Hecart A, Communal PY, Jaffrezic A, Pourcher AM (2010) Development of microbial and chemical MST tools to identify the origin of the faecal pollution in bathing and shellfish harvesting waters in France. Water Res 44:4812–4824PubMedCrossRefGoogle Scholar
  90. 90.
    Graczyk TK, Sunderland D, Tamang L, Lucy FE, Breysse PN (2007) Bather density and levels of Cryptosporidium Giardia, and pathogenic microsporidian spores in recreational bathing water. Parasitol Res 101:1729–1731PubMedCrossRefGoogle Scholar
  91. 91.
    Griffin DW, Gibson CJ 3rd, Lipp EK, Riley K, Paul JH 3rd, Rose JB (1999) Detection of viral pathogens by reverse transcriptase PCR and of microbial indicators by standard methods in the canals of the Florida Keys. Appl Environ Microbiol 65:4118–4125PubMedGoogle Scholar
  92. 92.
    Griffin DW, Lipp EK, McLaughlin MR, Rose JB (2001) Marine recreation and public health microbiology: quest for the ideal indicator. Bioscience 51:817–825CrossRefGoogle Scholar
  93. 93.
    Griffith JF, Cao Y, McGee CD, Weisberg SB (2009) Evaluation of rapid methods and novel indicators for assessing microbiological beach water quality. Water Res 43:4900–4907PubMedCrossRefGoogle Scholar
  94. 94.
    Grimes DJ (1975) Release of sediment-bound fecal coliforms by dredging. Appl Microbiol 29:109–111PubMedGoogle Scholar
  95. 95.
    Haack SK, Duris JW, Fogarty LR, Kolpin DW, Focazio MJ, Furlong ET, Meyer MT (2009) Comparing wastewater chemicals, indicator bacteria concentrations, and bacterial pathogen genes as fecal pollution indicators. J Environ Qual 38:248–258PubMedCrossRefGoogle Scholar
  96. 96.
    Haake DA, Dundoo M, Cader R, Kubak BM, Hartskeerl RA, Sejvar JJ, Ashford DA (2002) Leptospirosis, water sports, and chemoprophylaxis. Clin Infect Dis 34:E40–E43PubMedCrossRefGoogle Scholar
  97. 97.
    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 65:5522–5531PubMedGoogle Scholar
  98. 98.
    Haile RW, Witte JS, Gold M, Cressey R, McGee C, Millikan RC, Glasser A, Harawa N, Ervin C, Harmon P, Harper J, Dermand J, Alamillo J, Barrett K, Nides M, Wang G (1999) The health effects of swimming in ocean water contaminated by storm drain runoff. Epidemiology 10:355–363PubMedCrossRefGoogle Scholar
  99. 99.
    Halbur PG, Kasorndorkbua C, Gilbert C, Guenette D, Potters MB, Purcell RH, Emerson SU, Toth TE, Meng XJ (2001) Comparative pathogenesis of infection of pigs with hepatitis E viruses recovered from a pig and a human. J Clin Microbiol 39:918–923PubMedCrossRefGoogle Scholar
  100. 100.
    Haley BJ, Cole DJ, Lipp EK (2009) Distribution, diversity, and seasonality of waterborne salmonellae in a rural watershed. Appl Environ Microbiol 75:1248–1255PubMedCrossRefGoogle Scholar
  101. 101.
    Hamilton MJ, Yan T, Sadowsky MJ (2006) Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways. Appl Environ Microbiol 72:4012–4019PubMedCrossRefGoogle Scholar
  102. 102.
    Harrison S, Kinra S (2004) Outbreak of Escherichia coli O157 associated with a busy beach. Commun Dis Public Health 7:47–50PubMedGoogle Scholar
  103. 103.
    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 31:1273–1278PubMedCrossRefGoogle Scholar
  104. 104.
    Harvey S, Greenwood JR, Pickett MJ, Mah RA (1976) Recovery of Yersinia enterocolitica from streams and lakes of California. Appl Environ Microbiol 32:352–354PubMedGoogle Scholar
  105. 105.
    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 66:3698–3704PubMedCrossRefGoogle Scholar
  106. 106.
    Haugland RA, Siefring SC, Wymer LJ, Brenner KP, Dufour AP (2005) Comparison of Enterococcus measurements in freshwater at two recreational beaches by quantitative polymerase chain reaction and membrane filter culture analysis. Water Res 39:559–568PubMedCrossRefGoogle Scholar
  107. 107.
    Hayashi H, Sakamoto M, Kitahara M, Benno Y (2006) Diversity of the Clostridium coccoides group in human fecal microbiota as determined by 16 S rRNA gene library. FEMS Microbiol Lett 257:202–207PubMedCrossRefGoogle Scholar
  108. 108.
    He J, Jiang S (2005) Quantification of enterococci and human adenoviruses in environmental samples by real-time PCR. Appl Environ Microbiol 71:2250–2255PubMedCrossRefGoogle Scholar
  109. 109.
    Higgins JA, Belt KT, Karns JS, Russell-Anelli J, Shelton DR (2005) tir- and stx-positive Escherichia coli in stream waters in a metropolitan area. Appl Environ Microbiol 71:2511–2519PubMedCrossRefGoogle Scholar
  110. 110.
    Hill RT, Straube WL, Palmisano AC, Gibson SL, Colwell RR (1996) Distribution of sewage indicated by Clostridium perfringens at a deep-water disposal site after cessation of sewage disposal. Appl Environ Microbiol 62:1741–1746PubMedGoogle Scholar
  111. 111.
    Hipsey MR, Antenucci JP, Brookes JD (2008) A generic, process-based model of microbial pollution in aquatic systems. Water Resour Res 44:26CrossRefGoogle Scholar
  112. 112.
    Horman A, Rimhanen-Finne R, Maunula L, von Bonsdorff C-H, Torvela N, Heikinheimo A, Hanninen M-L (2004) Campylobacter spp., Giardia spp., Cryptosporidium spp., Noroviruses, and indicator organisms in surface water in southwestern Finland, 2000–2001. Appl Environ Microbiol 70:87–95PubMedCrossRefGoogle Scholar
  113. 113.
    Hou D, Rabinovici SJM, Boehm AB (2006) Enterococci predictions from partial least squares regression models in conjunction with a single-sample standard improve the efficacy of beach management advisories. Environ Sci Technol 40:1737–1743PubMedCrossRefGoogle Scholar
  114. 114.
    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 61:3960–3966PubMedGoogle Scholar
  115. 115.
    Hussain MA, Ford R, Hill J (2010) Determination of fecal contamination indicator sterols in an Australian water supply system. Environ Monit Assess 165:147–157PubMedCrossRefGoogle Scholar
  116. 116.
    International Organization for Standardization (2000) Water quality – Detection and enumeration of intestinal enterococci ISO 7899–2:000Google Scholar
  117. 117.
    Ishii S, Ksoll WB, Hicks RE, Sadowsky MJ (2006) Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds. Appl Environ Microbiol 72:612–621PubMedCrossRefGoogle Scholar
  118. 118.
    Ishii S, Yan T, Shivley DA, Byappanahalli MN, Whitman RL, Sadowsky MJ (2006) Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan. Appl Environ Microbiol 72:4545–4553PubMedCrossRefGoogle Scholar
  119. 119.
    Jamieson R, Joy DM, Lee H, Kostaschuk R, Gordon R (2005) Transport and deposition of sediment-associated Escherichia coli in natural streams. Water Res 39:2665–2675PubMedCrossRefGoogle Scholar
  120. 120.
    Jamieson RC, Joy DM, Lee H, Kostaschuk R, Gordon RJ (2005) Resuspension of sediment-associated Escherichia coli in a natural stream. J Environ Qual 34:581–589PubMedCrossRefGoogle Scholar
  121. 121.
    Jeter SN, McDermott CM, Bower PA, Kinzelman JL, Bootsma MJ, Goetz GW, McLellan SL (2009) Bacteroidales diversity in ring-billed gulls (Laurus delawarensis) residing at Lake Michigan beaches. Appl Environ Microbiol 75:1525–1533PubMedCrossRefGoogle Scholar
  122. 122.
    Jiang SC, Chu W (2004) PCR detection of pathogenic viruses in southern California urban rivers. J Appl Microbiol 97:17–28PubMedCrossRefGoogle Scholar
  123. 123.
    Jiang S, Noble R, Chu W (2001) Human adenoviruses and coliphages in urban runoff-impacted coastal waters of Southern California. Appl Environ Microbiol 67:179–184PubMedCrossRefGoogle Scholar
  124. 124.
    Jiang SC, Nobel R, Chu W (2001) Human adenoviruses and coliphage in urban runoff-impacted coastal waters of southern California. Appl Environ Microbiol 67:179–184PubMedCrossRefGoogle Scholar
  125. 125.
    Jiang SC, Chu W, He JW (2007) Seasonal detection of human viruses and coliphage in Newport Bay, California. Appl Environ Microbiol 73:6468–6474PubMedCrossRefGoogle Scholar
  126. 126.
    Jofre J, Blasi M, Bosch A, Lucena F (1989) Occurrence of bacteriophages infecting Bacteroides-Fragilis and other viruses in polluted marine-sediments. Water Sci Technol 21:15–19Google Scholar
  127. 127.
    Johnson CN, Flowers AR, Noriea NF III, Zimmerman AM, Bowers JC, DePaola A, Grimes DJ (2010) Relationships between environmental factors and pathogenic Vibrios in the Northern Gulf of Mexico. Appl Environ Microbiol 76:7076–7084PubMedCrossRefGoogle Scholar
  128. 128.
    Johnston C, Ufnar JA, Griffith JF, Gooch JA, Stewart JR (2010) A real-time qPCR assay for the detection of the nifH gene of Methanobrevibacter smithii, a potential indicator of sewage pollution. J Appl Microbiol 109:1946–1956PubMedCrossRefGoogle Scholar
  129. 129.
    Keymer DP, Miller MC, Schoolnik GK, Boehm AB (2007) Genomic and phenotypic diversity of coastal Vibrio cholerae is explained by environmental factors. Appl Environ Microbiol 73:3705–3714PubMedCrossRefGoogle Scholar
  130. 130.
    Keymer DP, Lam L, Boehm AB (2009) Biogeographic patterns in genomic diversity among a large collection of Vibrio cholerae isolates. Appl Environ Microbiol 75:1658–1666PubMedCrossRefGoogle Scholar
  131. 131.
    Khatib LA, Tsai YL, Olson BH (2002) A biomarker for the identification of cattle fecal pollution in water using the LTIIa toxin gene from enterotoxigenic Escherichia coli. Appl Microbiol Biotechnol 59:97–104PubMedCrossRefGoogle Scholar
  132. 132.
    Khatib LA, Tsai YL, Olson BH (2003) A biomarker for the identification of swine fecal pollution in water, using the STII toxin gene from enterotoxigenic Escherichia coli. Appl Microbiol Biotechnol 63:231–238PubMedCrossRefGoogle Scholar
  133. 133.
    Kildare BJ, Leutenegger CM, McSwain BS, Bambic DG, Rajal VB, Wuertz S (2007) 16 S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach. Water Res 41:3701–3715PubMedCrossRefGoogle Scholar
  134. 134.
    Kinzelman J, McLellan SL, Daniels AD, Cashin S, Singh A, Gradus S, Bagley R (2004) Non-point source pollution: determination of replication versus persistence of Escherichia coli in surface water and sediments with correlation of levels to readily measurable environmental parameters. J Water Health 2:103–114PubMedGoogle Scholar
  135. 135.
    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 73:808–814PubMedCrossRefGoogle Scholar
  136. 136.
    Kreader CA (1995) Design and evaluation of Bacteroides DNA probes for the specific detection of human fecal pollution. Appl Environ Microbiol 61:1171–1179PubMedGoogle Scholar
  137. 137.
    Lamendella R, Domingo JW, Oerther DB, Vogel JR, Stoeckel DM (2007) Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16 S rRNA gene. FEMS Microbiol Ecol 59:651–660PubMedCrossRefGoogle Scholar
  138. 138.
    Layton A, McKay L, Williams D, Garrett V, Gentry R, Sayler G (2006) Development of Bacteroides 16 S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl Environ Microbiol 72:4214–4224PubMedCrossRefGoogle Scholar
  139. 139.
    Layton BA, Walters SP, Lam LH, Boehm AB (2010) Enterococcus species distribution among human and animal hosts using multiplex PCR. J Appl Microbiol 109:539–547PubMedGoogle Scholar
  140. 140.
    Leach MD, Broschat SL, Call DR (2008) A discrete, stochastic model and correction method for bacterial source tracking. Environ Sci Technol 42:524–529PubMedCrossRefGoogle Scholar
  141. 141.
    Leclerc H, Schwartzbrod L, Dei-Cas E (2002) Microbial agents associated with waterborne diseases. Crit Rev Microbiol 28:371–409PubMedCrossRefGoogle Scholar
  142. 142.
    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 82:311–318CrossRefGoogle Scholar
  143. 143.
    Lee DY, Weir SC, Lee H, Trevors JT (2010) Quantitative identification of fecal water pollution sources by TaqMan real-time PCR assays using Bacteroidales 16 S rRNA genetic markers. Appl Microbiol Biotechnol 88:1373–1383PubMedCrossRefGoogle Scholar
  144. 144.
    Lemarchand K, Lebaron P (2003) Occurrence of Salmonella spp. and Cryptosporidium spp. in a French coastal watershed: relationship with fecal indicators. FEMS Microbiol Lett 218:203–209PubMedCrossRefGoogle Scholar
  145. 145.
    Lemarchand K, Masson L, Brousseau R (2004) Molecular biology and DNA microarray technology for microbial quality monitoring of water. Crit Rev Microbiol 30:145–172PubMedCrossRefGoogle Scholar
  146. 146.
    Leung HD, Chen G, Sharma K (2005) Effect of detached/re-suspended solids from sewer sediment on the sewage phase bacterial activity. Water Sci Technol 52:147–152PubMedGoogle Scholar
  147. 147.
    Lipp EK, Huq A, Colwell RR (2002) Effects of global climate on infectious disease: the cholera model. Clin Microbiol Rev 15:757–770PubMedCrossRefGoogle Scholar
  148. 148.
    Lynch PA, Gilpin BJ, Sinton LW, Savill MG (2002) The detection of Bifidobacterium adolescentis by colony hybridization as an indicator of human faecal pollution. J Appl Microbiol 92:526–533PubMedCrossRefGoogle Scholar
  149. 149.
    Mac Kenzie WR, Hoxie NJ, Proctor ME, Gradus MS, Blair KA, Peterson DE, Kazmierczak JJ, Addiss DG, Fox KR, Rose JB et al (1994) A massive outbreak in Milwaukee of cryptosporidium infection transmitted through the public water supply. N Engl J Med 331:161–167PubMedCrossRefGoogle Scholar
  150. 150.
    Malinen E, Rinttila T, Kajander K, Matto J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A (2005) Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol 100:373–382PubMedCrossRefGoogle Scholar
  151. 151.
    Mallin MA, Williams KE, Esham EC, Lowe RP (2000) Effect of human development on bacteriological water quality in coastal watersheds. Ecol Appl 10:1047–1056CrossRefGoogle Scholar
  152. 152.
    Marshall MM, Naumovitz D, Ortega Y, Sterling CR (1997) Waterborne protozoan pathogens. Clin Microbiol Rev 10:67–85PubMedGoogle Scholar
  153. 153.
    Matsuki T, Watanabe K, Fujimoto J, Miyamoto Y, Takada T, Matsumoto K, Oyaizu H, Tanaka R (2002) Development of 16 S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 68:5445–5451PubMedCrossRefGoogle Scholar
  154. 154.
    Matsuki T, Watanabe K, Fujimoto J, Kado Y, Takada T, Matsumoto K, Tanaka R (2004) Quantitative PCR with 16 S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl Environ Microbiol 70:167–173PubMedCrossRefGoogle Scholar
  155. 155.
    Matsuki T, Watanabe K, Fujimoto J, Takada T, Tanaka R (2004) Use of 16 S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol 70:7220–7228PubMedCrossRefGoogle Scholar
  156. 156.
    McBride GB, Salmond CE, Bandaranayake DR, Turner SJ, Lewis GD, Till DG (1998) Health effects of marine bathing in New Zealand. Int J Environ Health Res 8:173–189CrossRefGoogle Scholar
  157. 157.
    McLaughlin MR, Rose JB (2006) Application of Bacteroides fragilis phage as an alternative indicator of sewage pollution in Tampa Bay, Florida. Estuar Coast 29:246–256CrossRefGoogle Scholar
  158. 158.
    McLellan SL, Daniels AD, Salmore AK (2001) Clonal populations of thermotolerant Enterobacteriaceae in recreational water and their potential interference with fecal Escherichia coli counts. Appl Environ Microbiol 67:4934–4938PubMedCrossRefGoogle Scholar
  159. 159.
    McLellan SL, Daniels AD, Salmore AK (2003) Genetic characterization of Escherichia coli populations from host sources of fecal pollution by using DNA fingerprinting. Appl Environ Microbiol 69:2587–2594PubMedCrossRefGoogle Scholar
  160. 160.
    McLellan SL, Hollis EJ, Depas MM, Van Dyke M, Harris J, Scopel CO (2007) Distribution and fate of Escherichia coli in Lake Michigan following contamination with urban stormwater and combined sewer overflows. J Great Lakes Res 33:566–580CrossRefGoogle Scholar
  161. 161.
    McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML (2010) Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12:378–392PubMedCrossRefGoogle Scholar
  162. 162.
    McQuaig SM, Scott TM, Harwood VJ, Farrah SR, Lukasik JO (2006) Detection of human-derived fecal pollution in environmental waters by use of a PCR-based human polyomavirus assay. Appl Environ Microbiol 72:7567–7574PubMedCrossRefGoogle Scholar
  163. 163.
    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 75:3379–3388PubMedCrossRefGoogle Scholar
  164. 164.
    Medema GJ, Bahar M, Schets FM (1997) Survival of Cryptosporidium parvum, Escherichia coli, faecal enterococci and Clostridium perfringens in river water: influence of temperature and autochthonous microorganisms. Water Sci Technol 35:249–252Google Scholar
  165. 165.
    Mieszkin S, Yala JF, Joubrel R, Gourmelon M (2010) Phylogenetic analysis of Bacteroidales 16 S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR. J Appl Microbiol 108:974–984PubMedCrossRefGoogle Scholar
  166. 166.
    Miller WA, Miller MA, Gardner IA, Atwill ER, Byrne BA, Jang S, Harris M, Ames J, Jessup D, Paradies D, Worcester K, Melli A, Conrad PA (2006) Salmonella spp., Vibrio spp., Clostridium perfringens, and Plesiomonas shigelloides in marine and freshwater invertebrates from coastal California ecosystems. Microb Ecol 52:198–206PubMedCrossRefGoogle Scholar
  167. 167.
    Mocé-Llivina L, Lucena F, Jofre J (2005) Enteroviruses and bacteriophages in bathing waters. Appl Environ Microbiol 71:6838–6844PubMedCrossRefGoogle Scholar
  168. 168.
    Moe C (2002) Waterborne transmission of infectious agents. In: Hurst CJ, Crawfod RL, Knudsen GR, McInerney MJ, Stetzenbach LD (eds) Manual of environmental microbiology, 2nd edn. ASM Press, Washington, DC, pp 184–204Google Scholar
  169. 169.
    Mueller-Spitz SR, Stewart LB, Klump JV, McLellan SL (2010) Freshwater suspended sediments and sewage are reservoirs for enterotoxin-positive Clostridium perfringens. Appl Environ Microbiol 76:5556–5562PubMedCrossRefGoogle Scholar
  170. 170.
    Mumy KL, Findlay RH (2004) Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR. J Microbiol Methods 57:259–268PubMedCrossRefGoogle Scholar
  171. 171.
    Muniesa M, Jofre J, Garcia-Aljaro C, Blanch AR (2006) Occurrence of Escherichia coli O157:H7 and other enterohemorrhagic Escherichia coli in the environment. Environ Sci Technol 40:7141–7149PubMedCrossRefGoogle Scholar
  172. 172.
    Muniesa M, Payan A, Moce-Llivina L, Blanch AR, Jofre J (2009) Differential persistence of F-specific RNA phage subgroups hinders their use as single tracers for faecal source tracking in surface water. Water Res 43:1559–1564PubMedCrossRefGoogle Scholar
  173. 173.
    Nebra Y, Bonjoch X, Blanch AR (2003) Use of Bifidobacterium dentium as an indicator of the origin of fecal water pollution. Appl Environ Microbiol 69:2651–2656PubMedCrossRefGoogle Scholar
  174. 174.
    Nevers MB, Boehm AB (2010) Modeling fate and transport of fecal bacteria in surface water. In: Sadowsky MJ, Whitman RL (eds) The fecal indicator bacteria. ASM Press, Washington, DCGoogle Scholar
  175. 175.
    Newton RJ, VandeWalle JL, Borchardt MA, Gorelick MH, McLellan SL (2011) Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor. Appl Environ Microbiol 77:6972–6981PubMedCrossRefGoogle Scholar
  176. 176.
    Nichols PD, Leeming R, Rayner MS, Latham V, Ashbolt NJ, Turner C (1993) Comparison of the abundance of the fecal sterol soprostanol and fecal bacerial groups in inner-shlef waters and sediments near Sydney, Australia. J Chromatogr 643:189–195PubMedCrossRefGoogle Scholar
  177. 177.
    Niemela SI, Vaatanen P (1982) Survival in lake water of Klebsiella pneumoniae discharged by a paper mill. Appl Environ Microbiol 44:264–269PubMedGoogle Scholar
  178. 178.
    Noble RT, Fuhrman JD (2001) Enteroviruses detected by reverse transcriptase polymerase chain reaction from the coastal waters of Santa Monica Bay, California: low correlation to bacterial indicator levels. Hydrobiologia 460:175–183CrossRefGoogle Scholar
  179. 179.
    Noble RT, Allen SM, Blackwood AD, Chu W, Jiang SC, Lovelace GL, Sobsey MD, Stewart JR, Wait DA (2003) Use of viral pathogens and indicators to differentiate between human and non-human fecal contamination in a microbial source tracking comparison study. J Water Health 1:195–207PubMedGoogle Scholar
  180. 180.
    Noble RT, Moore DF, Leecaster MK, McGee CD, Weisberg SB (2003) Comparison of total coliform, fecal coliform, and enterococcus bacterial indicator response for ocean recreational water quality testing. Water Res 37:1637–1643PubMedCrossRefGoogle Scholar
  181. 181.
    Noble RT, Griffith JF, Blackwood AD, Fuhrman JA, Gregory JB, Hernandez X, Liang X, Bera AA, Schiff K (2006) Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California. Appl Environ Microbiol 72:1604–1612PubMedCrossRefGoogle Scholar
  182. 182.
    Noble RT, Blackwood AD, Griffith JF, McGee CD, Weisberg SB (2010) Comparison of rapid quantitative PCR-based and conventional culture-based methods for enumeration of Enterococcus spp. and Escherichia coli in recreational waters. Appl Environ Microbiol 76:7437–7443PubMedCrossRefGoogle Scholar
  183. 183.
    Obiri-Danso K, Jones K (2000) Intertidal sediments as reservoirs for hippurate negative campylobacters, salmonellae and faecal indicators in three EU recognized bathing waters in North West England. Water Res 34:519–527CrossRefGoogle Scholar
  184. 184.
    Okabe S, Shimazu Y (2007) Persistence of host-specific Bacteroides-Prevotella 16 S rRNA genetic markers in environmental waters: effects of temperature and salinity. Appl Microbiol Biotechnol 76:935–944PubMedCrossRefGoogle Scholar
  185. 185.
    Okabe S, Okayama N, Savichtcheva O, Ito T (2007) Quantification of host-specific Bacteroides-Prevotella 16 S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl Microbiol Biotechnol 74:890–901PubMedCrossRefGoogle Scholar
  186. 186.
    Palmer CJ, Tsai YL, Paszko-Kolva C, Mayer C, Sangermano LR (1993) Detection of Legionella species in sewage and ocean water by polymerase chain reaction, direct fluorescent- antibody, and plate culture methods. Appl Environ Microbiol 59:3618–3624PubMedGoogle Scholar
  187. 187.
    Panicker G, Myers ML, Bej AK (2004) Rapid detection of Vibrio vulnificus in shellfish and Gulf of Mexico water by real-time PCR. Appl Environ Microbiol 70:498–507PubMedCrossRefGoogle Scholar
  188. 188.
    Parveen S, Murphree RL, Edmiston L, Kaspar CW, Portier KM, Tamplin ML (1997) Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay. Appl Environ Microbiol 63:2607–2612PubMedGoogle Scholar
  189. 189.
    Parveen S, Hodge NC, Stall RE, Farrah SR, Tamplin ML (2001) Phenotypic and genotypic characterization of human and nonhuman Escherichia coli. Water Res 35:379–386PubMedCrossRefGoogle Scholar
  190. 190.
    Payan A, Ebdon J, Taylor H, Gantzer C, Ottoson J, Papageorgiou GT, Blanch AR, Lucena F, Jofre J, Muniesa M (2005) Method for isolation of Bacteroides bacteriophage host strains suitable for tracking sources of fecal pollution in water. Appl Environ Microbiol 71:5659–5662PubMedCrossRefGoogle Scholar
  191. 191.
    Payment P, Franco E (1993) Clostridium perfringens and somatic coliphages as indicators of the efficiency of drinking water treatment for viruses and protozoan cysts. Appl Environ Microbiol 59:2418–2424PubMedGoogle Scholar
  192. 192.
    Pianetti A, Sabatini L, Bruscolini F, Chiaverini F, Cecchetti G (2004) Faecal contamination indicators, salmonella, vibrio and aeromonas in water used for the irrigation of agricultural products. Epidemiol Infect 132:231–238CrossRefGoogle Scholar
  193. 193.
    Pina S, Puig M, Lucena F, Jofre J, Girones R (1998) Viral pollution in the environment and in shellfish: human adenovirus detection by PCR as an index of human viruses. Appl Environ Microbiol 64:3376–3382PubMedGoogle Scholar
  194. 194.
    Pinto R, Abad F, Gajardo R, Bosch A (1996) Detection of infectious astroviruses in water. Appl Environ Microbiol 62:1811–1813PubMedGoogle Scholar
  195. 195.
    Pruss A (1998) Review of epidemiological studies on health effects from exposure to recreational water. Int J Epidemiol 27:1–9PubMedCrossRefGoogle Scholar
  196. 196.
    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 65:1772–1776PubMedGoogle Scholar
  197. 197.
    Rabinovici SJM, Bernknopf RL, Wein AM, Coursey DL, Whitman RL (2004) Economic and health risk trade-offs of swim closures at a Lake Michigan beach. Environ Sci Technol 38:2737–2745PubMedCrossRefGoogle Scholar
  198. 198.
    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 41:1411–1422PubMedCrossRefGoogle Scholar
  199. 199.
    Rajal VB, McSwain BS, Thompson DE, Leutenegger CM, Wuertz S (2007) Molecular quantitative analysis of human viruses in California stormwater. Water Res 41:4287–4298PubMedCrossRefGoogle Scholar
  200. 200.
    Ram JL, Thompson B, Turner C, Nechvatal JM, Sheehan H, Bobrin J (2007) Identification of pets and raccoons as sources of bacterial contamination of urban storm sewers using a sequence-based bacterial source tracking method. Water Res 41:3605–3614PubMedCrossRefGoogle Scholar
  201. 201.
    Resnick IG, Levin MA (1981) Assessment of bifidobacteria as indicators of human fecal pollution. Appl Environ Microbiol 42:433–438PubMedGoogle Scholar
  202. 202.
    Rose JB, Mullinax RL, Singh SN, Yates MV, Gerba CP (1987) Occurrence of rotaviruses and enteroviruses in recreational waters of Oak Creek, Arizona. Water Resour 21:1375–1381Google Scholar
  203. 203.
    Saha ML, Khan MR, Ali M, Hoque S (2009) Bacterial load and chemical pollution level of the River Buriganga, Dhaka, Bangladesh. Bangladesh J Botany 38:87–91Google Scholar
  204. 204.
    Sambrook J, Russell D (2001) Molecular cloning: a labortory manual, 3rd edn. Cold Spring Harbor Laboratory, New YorkGoogle Scholar
  205. 205.
    Sandery M, Stinear T, Kaucner C (1996) Detection of pathogenic Yersinia enterocolitica in environmental waters by PCR. J Appl Bacteriol 80:327–332PubMedCrossRefGoogle Scholar
  206. 206.
    Santo Domingo JW, Bambic DG, Edge TA, Wuertz S (2007) Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. Water Res 41:3539–3552PubMedCrossRefGoogle Scholar
  207. 207.
    Santoro AE, Boehm AB (2007) Frequent occurrence of the human-specific Bacteroides fecal marker at an open coast marine beach: relationship to waves, tides and traditional indicators. Environ Microbiol 9:2038–2049PubMedCrossRefGoogle Scholar
  208. 208.
    Savichtcheva O, Okayama N, Okabe S (2007) Relationships between Bacteroides 16 S rRNA genetic markers and presence of bacterial enteric pathogens and conventional fecal indicators. Water Res 41:3615–3628PubMedCrossRefGoogle Scholar
  209. 209.
    Schriewer A, Miller WA, Byrne BA, Miller MA, Oates S, Conrad PA, Hardin D, Yang HH, Chouicha N, Melli A, Jessup D, Dominik C, Wuertz S (2010) Presence of Bacteroidales as a predictor of pathogens in surface waters of the central California coast. Appl Environ Microbiol 76:5802–5814PubMedCrossRefGoogle Scholar
  210. 210.
    Schulz CJ, Childers GW (2011) Fecal Bacteroidales diversity and decay in response to temperature and salinity. Appl Environ Microbiol 77:2563–2572PubMedCrossRefGoogle Scholar
  211. 211.
    Scott TM, Rose JB, Jenkins TM, Farrah SR, Lukasik J (2002) Microbial source tracking: current methodology and future directions. Appl Environ Microbiol 68:5796–5803PubMedCrossRefGoogle Scholar
  212. 212.
    Scott TM, Jenkins TM, Lukasik J, Rose JB (2005) Potential use of a host associated molecular marker in Enterococcus faecium as an index of human fecal pollution. Environ Sci Technol 39:283–287PubMedCrossRefGoogle Scholar
  213. 213.
    Sedmak G, Bina D, MacDonald J (2003) Assessment of an enterovirus sewage surveillance system by comparison of clinical isolates with sewage isolates from Milwaukee, Wisconsin, collected August 1994 to December 2002. Appl Environ Microbiol 69:7181–7187PubMedCrossRefGoogle Scholar
  214. 214.
    Sedmak G, Bina D, Macdonald J, Couillard L (2005) Nine-year study of the occurrence of culturable viruses in source water for two drinking water treatment plants and the influent and effluent of a wastewater treatment plant in Milwaukee, Wisconsin (August 1994 through July 2003). Appl Environ Microbiol 71:1042–1050PubMedCrossRefGoogle Scholar
  215. 215.
    Semel JD, Trenholme G (1990) Aeromonas hydrophila water-associated traumatic wound infections: a review. J Trauma 30:324–327PubMedCrossRefGoogle Scholar
  216. 216.
    Sercu B, Van De Werfhorst LC, Murray J, Holden PA (2009) Storm drains are sources of human fecal pollution during dry weather in three urban Southern California watersheds. Environ Sci Technol 43:293–298PubMedCrossRefGoogle Scholar
  217. 217.
    Seurinck S, Verstraete W, Siciliano SD (2003) Use of 16 S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources. Appl Environ Microbiol 69:4942–4950PubMedCrossRefGoogle Scholar
  218. 218.
    Seurinck S, Defoirdt T, Verstraete W, Siciliano SD (2005) Detection and quantification of the human-specific HF183 Bacteroides 16 S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environ Microbiol 7:249–259PubMedCrossRefGoogle Scholar
  219. 219.
    Sghir A, Gramet G, Suau A, Rochet V, Pochart P, Dore J (2000) Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 66:2263–2266PubMedCrossRefGoogle Scholar
  220. 220.
    Shanks OC, Santo Domingo JW, Lamendella R, Kelty CA, Graham JE (2006) Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples. Appl Environ Microbiol 72:4054–4060PubMedCrossRefGoogle Scholar
  221. 221.
    Shanks OC, Domingo JW, Lu J, Kelty CA, Graham JE (2007) Identification of bacterial DNA markers for the detection of human fecal pollution in water. Appl Environ Microbiol 73:2416–2422PubMedCrossRefGoogle Scholar
  222. 222.
    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 74:745–752PubMedCrossRefGoogle Scholar
  223. 223.
    Shanks OC, Kelty CA, Sivaganesan M, Varma M, Haugland RA (2009) Quantitative PCR for genetic markers of human fecal pollution. Appl Environ Microbiol 75:5507–5513PubMedCrossRefGoogle Scholar
  224. 224.
    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 76:1359–1366PubMedCrossRefGoogle Scholar
  225. 225.
    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 44:6281–6288PubMedCrossRefGoogle Scholar
  226. 226.
    Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML (2011) Community structure of cattle fecal bacteria from different animal feeding operations. Appl Environ Microbiol 77:2992–3001PubMedCrossRefGoogle Scholar
  227. 227.
    Shibata T, Solo-Gabriele HM, Fleming LE, Elmir S (2004) Monitoring marine recreational water quality using multiple microbial indicators in an urban tropical environment. Water Res 38:3119–3131PubMedCrossRefGoogle Scholar
  228. 228.
    Silkie SS, Nelson KL (2009) Concentrations of host-specific and generic fecal markers measured by quantitative PCR in raw sewage and fresh animal feces. Water Res 43:4860–4871PubMedCrossRefGoogle Scholar
  229. 229.
    Sinton LW, Hall CH, Lynch PA, Davies-Colley RJ (2002) Sunlight inactivation of fecal indicator bacteria and bacteriophages from waste stabilization pond effluent in fresh and saline waters. Appl Environ Microbiol 68:1122–1131PubMedCrossRefGoogle Scholar
  230. 230.
    Sivaganesan M, Seifring S, Varma M, Haugland RA, Shanks OC (2008) A Bayesian method for calculating real-time quantitative PCR calibration curves using absolute plasmid DNA standards. BMC Bioinformatics 9:120PubMedCrossRefGoogle Scholar
  231. 231.
    Sivaganesan M, Haugland RA, Chern EC, Shanks OC (2010) Improved strategies and optimization of calibration models for real-time PCR absolute quantification. Water Res 44:4726–4735PubMedCrossRefGoogle Scholar
  232. 232.
    Soller JA, Bartrand T, Ashbolt NJ, Ravenscroft J, Wade TJ (2010) Estimating the primary etiologic agents in recreational freshwaters impacted by human sources of faecal contamination. Water Res 44:4736–4747PubMedCrossRefGoogle Scholar
  233. 233.
    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 44:4674–4691PubMedCrossRefGoogle Scholar
  234. 234.
    Steets BM, Holden PA (2003) A mechanistic model of runoff-associated fecal coliform fate and transport through a coastal lagoon. Water Res 37:589–608PubMedCrossRefGoogle Scholar
  235. 235.
    Stewart JR, Ellender RD, Gooch JA, Jiang S, Myoda SP, Weisberg SB (2003) Recommendations for microbial source tracking: lessons from a methods comparison study. J Water Health 1:225–231PubMedGoogle Scholar
  236. 236.
    Stewart JR, Gast RJ, Fujioka RS, Solo-Gabriele HM, Meschke JS, Amaral-Zettler LA, Del Castillo E, Polz MF, Collier TK, Strom MS, Sinigalliano CD, Moeller PD, Holland AF (2008) The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs. Environ Health 7(Suppl 2):S3PubMedCrossRefGoogle Scholar
  237. 237.
    Stoeckel DM, Harwood VJ (2007) Performance, design, and analysis in microbial source tracking studies. Appl Environ Microbiol 73:2405–2415PubMedCrossRefGoogle Scholar
  238. 238.
    Stoeckel DM, Stelzer EA, Dick LK (2009) Evaluation of two spike-and-recovery controls for assessment of extraction efficiency in microbial source tracking studies. Water Res 43:4820–4827PubMedCrossRefGoogle Scholar
  239. 239.
    Sullivan D, Brooks P, Tindale N, Chapman S, Ahmed W (2010) Faecal sterols analysis for the identification of human faecal pollution in a non-sewered catchment. Water Sci Technol 61:1355–1361PubMedCrossRefGoogle Scholar
  240. 240.
    Tartera C, Lucena F, Jofre J (1989) Human origin of Bacteroides fragilis bacteriophages present in the environment. Appl Environ Microbiol 55:2696–2701PubMedGoogle Scholar
  241. 241.
    Teng LJ, Hsueh PR, Huang YH, Tsai JC (2004) Identification of Bacteroides thetaiotaomicron on the basis of an unexpected specific amplicon of universal 16 S ribosomal DNA PCR. J Clin Microbiol 42:1727–1730PubMedCrossRefGoogle Scholar
  242. 242.
    Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484PubMedCrossRefGoogle Scholar
  243. 243.
    Ufnar JA, Wang SY, Christiansen JM, Yampara-Iquise H, Carson CA, Ellender RD (2006) Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters. J Appl Microbiol 101:44–52PubMedCrossRefGoogle Scholar
  244. 244.
    Ufnar JA, Ufnar DF, Wang SY, Ellender RD (2007) Development of a swine-specific fecal pollution marker based on host differences in methanogen mcrA genes. Appl Environ Microbiol 73:5209–5217PubMedCrossRefGoogle Scholar
  245. 245.
    Ufnar JA, Wang SY, Ufnar DF, Ellender RD (2007) Methanobrevibacter ruminantium as an indicator of domesticated-ruminant fecal pollution in surface waters. Appl Environ Microbiol 73:7118–7121PubMedCrossRefGoogle Scholar
  246. 246.
    Unno T, Jang J, Han D, Kim JH, Sadowsky MJ, Kim OS, Chun J, Hur HG (2010) Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds. Environ Sci Technol 44:7777–7782PubMedCrossRefGoogle Scholar
  247. 247.
    USEPA (2000) Improved enumeration methods for recreational water quality indicators: Enterococci and Escherichia coli. EPA 821/R-97/004. US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  248. 248.
    USEPA (2002) Method 1603: Escherichia coli (E. coli) in water by membrane filtration using modified membrane-thermotolerant Escherichia coli agar (modified mTEC) EPA-821-R-02-023. US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  249. 249.
    USEPA (2002) Method 1604: total coliforms and Escherichia coli in water by membrane filtration using a simultaneous detection technique (MI Medium). US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  250. 250.
    USEPA (2006) Method 1600: Enterococci in Water by Membrane Filtration Using MEMBRANE-Enterococus Indoxyl-B-D-Glucoside agar (mEI) EPA-821-R-06-009. US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  251. 251.
    USEPA (2007) Critical path science plan for the development of new or revised recreational water quality criteria. 823-R-08-002. US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  252. 252.
    USEPA (2009) National water quality inventory: report to congress 2004 reporting cycle. EPA 841-R-08-001. US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  253. 253.
    USEPA (2010) Method A: Enterococci in water by TaqMan® quantitative polymerase chain reaction (qPCR) assay. US Environmental Protection Agency Office of Water, Washington, DCGoogle Scholar
  254. 254.
    Viau EJ, Goodwin KD, Yamahara KM, Layton BA, Sassoubre LM, Burns S, Tong H-I, Wong SHC, Boehm AB (2011) Human bacterial pathogens and fecal indicators in tropical streams discharging to Hawaiian coastal waters. Water Res 45:3279–3290PubMedCrossRefGoogle Scholar
  255. 255.
    Volkmann H, Schwartz T, Kirchen S, Stofer C, Obst U (2007) Evaluation of inhibition and cross-reaction effects on real-time PCR applied to the total DNA of wastewater samples for the quantification of bacterial antibiotic resistance genes and taxon-specific targets. Mol Cell Probes 21:125–133PubMedCrossRefGoogle Scholar
  256. 256.
    Wade TJ, Pai N, Eisenberg JN, Colford JM Jr (2003) Do U.S. Environmental Protection Agency water quality guidelines for recreational waters prevent gastrointestinal illness? A systematic review and meta-analysis. Environ Health Perspect 111:1102–1109PubMedCrossRefGoogle Scholar
  257. 257.
    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. Environ Health Perspect 114:24–28PubMedCrossRefGoogle Scholar
  258. 258.
    Wade TJ, Calderon RL, Brenner KP, Sams E, Beach M, Haugland R, Wymer L, Dufour AP (2008) High sensitivity of children to swimming-associated gastrointestinal illness: results using a rapid assay of recreational water quality. Epidemiol 19:375–383CrossRefGoogle Scholar
  259. 259.
    Wade TJ, Sams E, Brenner KP, Haugland R, Chern E, Beach M, Wymer L, Rankin CC, Love D, Li Q, Noble R, Dufour AP (2010) Rapidly measured indicators of recreational water quality and swimming-associated illness at marine beaches: a prospective cohort study. Environ Health 9:66PubMedCrossRefGoogle Scholar
  260. 260.
    Walters SP, Gannon VPJ, 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 41:1856–1862PubMedCrossRefGoogle Scholar
  261. 261.
    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 43:4929–4939PubMedCrossRefGoogle Scholar
  262. 262.
    Walters SP, Thebo AL, Boehm AB (2011) Impact of urbanization and agriculture on the occurrence of bacterial pathogens and stx genes in coastal waterbodies of central California. Water Res 45:1752–1762PubMedCrossRefGoogle Scholar
  263. 263.
    Westrell T, Teunis P, van den Berg H, Lodder W, Ketelaars H, Stenstrom TA, de Roda Husman AM (2006) Short- and long-term variations of norovirus concentrations in the Meuse river during a 2-year study period. Water Res 40:2613–2620PubMedCrossRefGoogle Scholar
  264. 264.
    Wetz JJ, Blackwood AD, Fries JS, Williams ZF, Noble RT (2008) Trends in total Vibrio spp. and Vibrio vulnificus concentrations in the eutrophic Neuse River Estuary, North Carolina, during storm events. Aquat Microb Ecol 53:141–149CrossRefGoogle Scholar
  265. 265.
    Whitman RL, Nevers MB (2003) Foreshore sand as a source of Escherichia coli in nearshore water of a Lake Michigan beach. Appl Environ Microbiol 69:5555–5562PubMedCrossRefGoogle Scholar
  266. 266.
    Whitman RL, Nevers MB, Korinek GC, Byappanahalli MN (2004) Solar and temporal effects on Escherichia coli concentration at a Lake Michigan swimming beach. Appl Environ Microbiol 70:4276–4285PubMedCrossRefGoogle Scholar
  267. 267.
    Whitman RL, Ge Z, Nevers MB, Boehm AB, Chern EC, Haugland RA, Lukasik AM, Molina M, Przybyla-Kelly K, Shively DA, White EM, Zepp RG, Byappanahalli MN (2010) Relationship and variation of qPCR and culturable Enterococci estimates in ambient surface waters are predictable. Environ Sci Technol 44:5049–5054PubMedCrossRefGoogle Scholar
  268. 268.
    Wiedenmann A, Kruger P, Dietz K, Lopez-Pila JM, Szewzyk R, Botzenhart K (2006) A randomized controlled trial assessing infectious disease risks from bathing in fresh recreational waters in relation to the concentration of Escherichia coli, intestinal enterococci, Clostridium perfringens, and somatic coliphages. Environ Health Perspect 114:228–236PubMedCrossRefGoogle Scholar
  269. 269.
    Wiggins BA (1996) Discriminant analysis of antibiotic resistance patterns in fecal streptococci, a method to differentiate human and animal sources of fecal pollution in natural waters. Appl Environ Microbiol 62:3997–4002PubMedGoogle Scholar
  270. 270.
    Wilkes G, Edge T, Gannon V, Jokinen C, Lyautey E, Medeiros D, Neumann N, Ruecker N, Topp E, Lapen DR (2009) Seasonal relationships among indicator bacteria, pathogenic bacteria, Cryptosporidium oocysts, Giardia cysts, and hydrological indices for surface waters within an agricultural landscape. Water Res 43:2209–2223PubMedCrossRefGoogle Scholar
  271. 271.
    Wong M, Kumar L, Jenkins TM, Xagoraraki I, Phanikumar MS, Rose JB (2009) Evaluation of public health risks at recreational beaches in Lake Michigan via detection of enteric viruses and a human-specific bacteriological marker. Water Res 43:1137–1149PubMedCrossRefGoogle Scholar
  272. 272.
    Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, Hazen TC, Holden PA, Andersen GL (2010) Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One 5:e11285PubMedCrossRefGoogle Scholar
  273. 273.
    Wyn-Jones AP, Carducci A, Cook N, D’Agostino M, Divizia M, Fleischer J, Gantzer C, Gawler A, Girones R, Höller C, Husman AM, Kay D, Kozyra I, López-Pila J, Muscillo M, Nascimento MS, Papageorgiou G, Rutjes S, Sellwood J, Szewzyk R, Wyer M (2011) Surveillance of adenoviruses and noroviruses in European recreational waters. Water Res 45:1025–1038PubMedCrossRefGoogle Scholar
  274. 274.
    Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074–2076PubMedCrossRefGoogle Scholar
  275. 275.
    Yamahara KM, Layton BA, Santoro AE, Boehm AB (2007) Beach sands along the California coast are diffuse sources of fecal bacteria to coastal waters. Environ Sci Technol 41:4515–4521PubMedCrossRefGoogle Scholar
  276. 276.
    Yamahara KM, Walters SP, Boehm AB (2009) Growth of enterococci in unaltered, unseeded beach sands subjected to tidal wetting. Appl Environ Microbiol 75:1517–1524PubMedCrossRefGoogle Scholar
  277. 277.
    Yampara-Iquise H, Zheng G, Jones JE, Carson CA (2008) Use of a Bacteroides thetaiotaomicron-specific alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water. J Appl Microbiol 105:1686–1693PubMedCrossRefGoogle Scholar
  278. 278.
    Young TA, Heidler J, Matos-Perez CR, Sapkota A, Toler T, Gibson KE, Schwab KJ, Halden RU (2008) Ab initio and in situ comparison of caffeine, triclosan, and triclocarban as indicators of sewage-derived microbes in surface waters. Environ Sci Technol 42:3335–3340PubMedCrossRefGoogle Scholar
  279. 279.
    Zheng G, Yampara-Iquise H, Jones JE, Carson CA (2009) Development of Faecalibacterium 16 S rRNA gene marker for identification of human faeces. J Appl Microbiol 106:634–641PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Sandra L. McLellan
    • 1
    Email author
  • Alexandria B. Boehm
    • 2
  • Orin C. Shanks
    • 3
  1. 1.School of Freshwater SciencesUniversity of Wisconsin-MilwaukeeMilwaukeeUSA
  2. 2.Environmental and Water Studies, Department of Civil and Environmental EngineeringStanford UniversityStanfordUSA
  3. 3.National Risk Management Research LaboratoryUnited States Environmental Protection AgencyCincinnatiUSA

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