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Determining Sources of Fecal Bacteria in Waterways

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Abstract

The microbiological contamination of waterways by pathogenic microbes has been, and is still, a persistent public safety concern in the United States and in most countries of the world. As most enteric pathogens are transmitted through the fecal–oral route, fecal pollution is generally regarded as the major contributor of pathogens to waterways. Fecal pollution of waterways can originate from wastewater treatment facilities, septic tanks, domestic- and wild-animal feces, and pets. Because enteric pathogens are derived from human or animal sources, techniques capable of identifying and apportioning fecal sources have been intensively investigated for use in remediation efforts and to satisfy regulatory concerns. Pollution of human origin is of the most concern, since human feces is more likely to contain human-specific enteric pathogens. Fecal indicator bacteria have been used successfully as the primary tool for microbiologically based risk assessment. However measurement of fecal indicator bacteria does not define what pathogens are present, or define the sources of these bacteria. Microbial source tracking (MST) methods that have the ability to differentiate among sources of fecal pollution are currently under development. These methods will ultimately be useful for risk assessment purposes and to aid regulatory agencies in developing strategies to remediate microbiologically impaired waterways.

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References

  • Albert, J. M., Munakata-Marr, J., Tenorio, L., & Siegrist, R. L. (2003). Statistical evaluation of bacterial source tracking data obtained by rep-PCR DNA fingerprinting of Escherichia coli. Environmental Science and Technology, 37(20), 4554–4560.

    Article  CAS  Google Scholar 

  • Alexander, L. M., Heaven, A., Tennant, A., & Morris, R. (1992). Symptomatology of children in contact with sea water contaminated with sewage. Journal of Epidemiology and Community Health, 46(4), 340–344.

    CAS  Google Scholar 

  • Barrett, T. J., Lior, H., Green, J. H., Khakhria, R., Wells, J. G., Bell, B. P., et al. (1994). Laboratory investigation of a multistate food-borne outbreak of Escherichia coli O157:H7 by using pulsed-field gel electrophoresis and phage typing. Journal of Clinical Microbiology, 32(12), 3013–17.

    CAS  Google Scholar 

  • Bernhard, A. E., & Field, K. G. (2000a). 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.

    Article  CAS  Google Scholar 

  • Bernhard, A. E., & Field, K. G. (2000b). 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.

    Article  CAS  Google Scholar 

  • Bettelheim, K. A., Ismail, N., Shinebaum, R., Shooter, R. A., Moorhouse, E., & Farrell, W. (1976). The distribution of serotypes of Escherichia coli in cow-pats and other animal material compared with serotypes of E. coli isolated from human sources. Journal of Hygiene (London), 76(3), 403–406.

    CAS  Google Scholar 

  • Blears, M. J., De Grandis, S. A., Lee, H., & Trevors, J. T. (1998). Amplified fragment length polymorphism (AFLP): A review of the procedure and its applications. Journal of Industrial Microbiology and Biotechnology, 21(3), 99–114.

    Article  CAS  Google Scholar 

  • Carson, C. A., Shear, B. L., Ellersieck, M. R., & Asfaw, A. (2001). Identification of fecal Escherichia coli from humans and animals by ribotyping. Applied and Environmental Microbiology, 67(4), 1503–1507.

    Article  CAS  Google Scholar 

  • Carson, C. A., Shear, B. L., Ellersieck, M. R., & Schnell, J. D. (2003). Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals. Applied and Environmental Microbiology, 69(3), 1836–1839.

    Article  CAS  Google Scholar 

  • Craun, G. F., Nwachuku, N., Calderon, R. L., & Craun, M. F. (2002). Outbreaks in drinking-water systems, 1991–1998. Journal of Environmental Health, 65(1), 16–23.

    CAS  Google Scholar 

  • De Bruijn, F. J. (1992). Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Applied and Environmental Microbiology, 58(7), 2180–2187.

    Google Scholar 

  • De Motes, C. M., Clemente-Casares, P., Hundesa, A., Martin, M., & Girones, R. (2004). Detection of bovine and porcine adenoviruses for tracing the source of fecal contamination. Applied and Environmental Microbiology, 70(3), 1448–1454.

    Article  CAS  Google Scholar 

  • Dick, L. K., & Field, K. G. (2004). 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.

    Article  CAS  Google Scholar 

  • Dick, L. K., Simonich, M. T., & Field, K. G. (2005). Microplate subtractive hybridization to enrich for Bacteroidales genetic markers for fecal source identification. Applied and Environmental Microbiology, 71(6), 3179–3183.

    Article  CAS  Google Scholar 

  • Dombek, P. E., Johnson, L. K., Zimmerley, S. T., & Sadowsky, M. J. (2000). Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Applied and Environmental Microbiology, 66(6), 2572–2577.

    Article  CAS  Google Scholar 

  • Furuse, K., Ando, A., Osawa, S., & Watanabe, I. (1981). Distribution of ribonucleic acid coliphages in raw sewage from treatment plants in Japan. Applied and Environmental Microbiology, 41(5), 1139–1143.

    CAS  Google Scholar 

  • Geldreich, E. E., & Kenner, B. A. (1969). Concepts of fecal streptococci in stream pollution. Journal Water Pollution Control Federation, 41, R336–R352.

    Google Scholar 

  • Gerba, C. P., Goyal, S. M., LaBelle, R. L., Cech, I., & Bodgan, G. F. (1979). Failure of indicator bacteria to reflect the occurrence of enteroviruses in marine waters. American Journal of Public Health, 69(11), 1116–1119.

    Article  CAS  Google Scholar 

  • Gonzalez, E. A., & Blanco, J. (1989). Serotypes and antibiotic resistance of verotoxigenic (VTEC) and necrotizing (NTEC) Escherichia coli strains isolated from calves with diarrhea. FEMS Microbiology Letters, 60(1), 31–6.

    Article  CAS  Google Scholar 

  • Grimont, F., & Grimont, P. A. D. (1986). Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Annales de l’Institut Pasteur. Microbiology, 137B(2), 165–175.

    CAS  Google Scholar 

  • Guan, S., Xu, R., Chen, S., Odumeru, J., & Gyles, C. (2002). Development of a procedure for discriminating among Escherichia coli isolates from animal and human sources. Applied and Environmental Microbiology, 68(6), 2690–2698.

    Article  CAS  Google Scholar 

  • Hagedorn, C., Crozier, J. B., Mentz, K. A., Booth, A. M., Graves, A. K., Nelson, N. J., et al. (2003). Carbon source utilization profiles as a method to identify sources of faecal pollution in water. Journal of Applied Microbiology, 94(5), 792–799.

    Article  CAS  Google Scholar 

  • Hagedorn, C., Robinson, S. L., Filtz, J. R., Grubbs, S. M., Angier, T. A., & Reneau, R. B., Jr. (1999). Determining sources of fecal pollution in a rural virginia watershed with antibiotic resistance patterns in fecal streptococci. Applied and Environmental Microbiology, 65(12), 5522–5531.

    CAS  Google Scholar 

  • Hartel, P. G., Summer, J. D., Hill, J. L., Collins, J. V., Entry, J. A., & Segars, W. I. (2002). Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia. Journal of Environmental Quality, 31(4), 1273–1278.

    CAS  Google Scholar 

  • Hartley, C. L., Howe, K., Linton, A. H., Linton, K. B., & Richmond, M. H. (1975). Distribution of R plasmids among the O-antigen types of Escherichia coli isolated from human and animal sources. Antimicrobial Agents and Chemotherapy, 8(2), 122–131.

    CAS  Google Scholar 

  • Harwood, V. J., 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. Applied and Environmental Microbiology, 66(9), 3698–3704.

    Article  CAS  Google Scholar 

  • Havelaar, A. H., Pot-Hogeboom, W. M., Furuse, K., Pot, R., & Hormann, M. P. (1990). F-specific RNA bacteriophages and sensitive host strains in feces and wastewater of human and animal origin. Journal of Applied Bacteriology, 69(1), 30–37.

    CAS  Google Scholar 

  • Hsu, F.-C., Shieh, Y. S. C., van Duin, J., Beekwilder, M. J., & Sobsey, M. D. (1995). Genotyping male-specific RNA coliphages by hybridization with oligonucleotide probes. Applied and Environmental Microbiology, 61(11), 3960–3966.

    CAS  Google Scholar 

  • Iyoda, S., Wada, A., Weller, J., Flood, S. J. A., Schreiber, E., Tucker, B., et al. (1999). Evaluation of AFLP, A high-resolution DNA fingerprinting method, as a tool for molecular subtyping of enterohemorrhagic Escherichia coli O157:H7 isolates. Microbiology and Immunology, 43(8), 803–806.

    CAS  Google Scholar 

  • Janssen, P., & Dijkshoorn, L. (1996). High resolution DNA fingerprinting of Acinetobacter outbreak strains. FEMS Microbiology Letters, 142(2–3), 191–194.

    Article  CAS  Google Scholar 

  • Jenkins, M. B., Hartel, P. G., Olexa, T. J., & Stuedemann, J. A. (2003). Putative temporal variability of Escherichia coli ribotypes from yearling steers. Journal of Environmental Quality, 32(1), 305–309.

    Article  CAS  Google Scholar 

  • Jiang, S., Noble, R., & Chu, W. (2001). Human adenoviruses and coliphages in urban runoff-impacted coastal waters of Southern California. Applied and Environmental Microbiology, 67(1), 179–184.

    Article  CAS  Google Scholar 

  • Jiménez-Clavero, M. A., Fernández, C., Ortiz, J. A., Pro, J., Carbonell, G., Tarazona, J. V., et al. (2003). Teschoviruses as indicators of porcine fecal contamination of surface water. Applied and Environmental Microbiology, 69(10), 6311–6315.

    Article  CAS  Google Scholar 

  • Jofre, J., Bosch, A., Lucena, F., Girones, R., & Tartera, C. (1986). Evaluation of Bacteroides fragilis bacteriophages as indicators of the virological quality of water. Water Science and Technology, 18(10), 167–173.

    CAS  Google Scholar 

  • Johnson, L. K., Brown, M. B., Carruthers, E. A., Ferguson, J. A., Dombek, P. E., & Sadowsky, M. J. (2004). Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Applied and Environmental Microbiology, 70(8), 4478–4485.

    Article  CAS  Google Scholar 

  • Johnson, J. Y. M., Thomas, J. E., Graham, T. A., Townshend, I., Byrne, J., Selinger, L. B., et al. (2003). Prevalence of Escherichia coli O157:H7 and Salmonella spp. in surface waters of southern Alberta and its relation to manure sources. Canadian Journal of Microbiology, 49(5), 326–335.

    Article  CAS  Google Scholar 

  • Kariuki, S., Gilks, C., Kimari, J., Obanda, A., Muyodi, J., Waiyaki, P., & Hart, C. A. (1999). Genotype analysis of Escherichia coli strains isolated from children and chickens living in close contact. Applied and Environmental Microbiology, 65(2), 472–476.

    CAS  Google Scholar 

  • Krumperman, P. H. (1983). Multiple antibiotic resistance indexing of Escherichia coli to identify high-risk sources of fecal contamination of foods. Applied and Environmental Microbiology, 46(1), 165–170.

    CAS  Google Scholar 

  • Leung, K. T., Mackereth, R., Tien, Y.-C., & Topp, E. (2004). A comparison of AFLP and ERIC-PCR analyses for discriminating Escherichia coli from cattle, pig and human sources. FEMS Microbiology Ecology, 47(1), 111–119.

    Article  CAS  Google Scholar 

  • Levy, S. B., FitzGerald, G. B., & Macone, A. B. (1976). Changes in intestinal flora of farm personnel after introduction of a tetracycline-supplemented feed on a farm. New England Journal of Medicine, 295(11), 583–588.

    Article  CAS  Google Scholar 

  • Ley, V., Higgins, J., & Fayer, R. (2002). Bovine enteroviruses as indicators of fecal contamination. Applied and Environmental Microbiology, 68(7), 3455–3461.

    Article  CAS  Google Scholar 

  • Liu, B. L., Lambden, P. R., Gunther, H., Otto, P., Elschner, M., & Clarke, I. N. (1999). Molecular characterization of a bovine enteric calicivirus: relationship to the Norwalk-like viruses. Journal of Virology, 73(1), 819–825.

    CAS  Google Scholar 

  • Malakoff, D. (2002). Water quality: Microbiologists on the trail of polluting bacteria. Science, 295(5564), 2352–2353.

    Article  CAS  Google Scholar 

  • Mara, D. D., & Oragui, J. I. (1983). Sorbitol-fermenting bifidobacteria as specific indicators of human faecal pollution. Journal of Applied Bacteriology, 55(2), 349–357.

    CAS  Google Scholar 

  • Martin, B., Humbert, O., Camara, M., Guenzi, E., Walker, J., Mitchell, T., et al. (1992). A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Research, 20(13), 3479–3483.

    Article  CAS  Google Scholar 

  • McLellan, S. L., Daniels, A. D., & Salmore, A. K. (2003). Genetic characterization of Escherichia coli populations from host sources of fecal pollution by using DNA fingerprinting. Applied and Environmental Microbiology, 69(5), 2587–2594.

    Article  CAS  Google Scholar 

  • Parveen, S., Hodge, N. C., Stall, R. E., Farrah, S. R., & Tamplin, M. L. (2001). Phenotypic and genotypic characterization of human and nonhuman Escherichia coli. Water Research, 35(2), 379–386.

    Article  CAS  Google Scholar 

  • Parveen, S., Portier K. M., Robinson, K., Edmiston, L., & Tamplin, M. L. (1999). Discriminant analysis of ribotype profiles of Escherichia coli for differentiating human and nonhuman sources of fecal pollution. Applied and Environmental Microbiology, 65(7), 3142–3147.

    CAS  Google Scholar 

  • Parveen, S., Murphree, R. L., Edmiston, L., Kaspar, C. W., Portier, K. M., & Tamplin, M. L. (1997). Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay. Applied and Environmental Microbiology, 63(7), 2607–2612.

    CAS  Google Scholar 

  • 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. Applied and Environmental Microbiology, 64(9), 3376–3382.

    CAS  Google Scholar 

  • Pourcher, A. M., Devriese, L. A., Hernandez, J. F., & Delattre, J. M. (1991). Enumeration by a miniaturized method of E. coli, Streptococcus bovis, and enterococci as indicators of the origin of faecal pollution in waters. Journal of Applied Bacteriology, 65, 1772–1776.

    Google Scholar 

  • 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. Applied and Environmental Microbiology, 65(4), 1772–1776.

    CAS  Google Scholar 

  • Resnick, I. G., & Levin, M. A. (1981). Assessment of bifidobacteria as indicators of human fecal pollution. Applied and Environmental Microbiology, 42(3), 433–438.

    CAS  Google Scholar 

  • Rhodes, M. W., & Kator, H. (1999). Sorbitol-fermenting bifidobacteria as indicators of diffuse human fecal pollution in estuarine watersheds. Journal of Applied Microbiology, 87(4), 528–535.

    Article  CAS  Google Scholar 

  • Rodgers, P., Soulsby, C., Hunter, C., & Petry, J. (2003). Spatial and temporal bacterial quality of a lowland agricultural stream in northeast Scotland. Science of the Total Environment, 314–316, 289–302.

    Article  CAS  Google Scholar 

  • Sadowsky, M. J., Kinkel, L. L., Bowers, J. H., & Schottel, J. L. (1996). Use of repetitive intergenic DNA sequences to classify pathogenic and disease-suppressive Streptomyces strains. Applied and Environmental Microbiology, 62(9), 3489–3493.

    CAS  Google Scholar 

  • Schwartz, D. C., & Cantor, C. R. (1984). Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67–75.

    Article  CAS  Google Scholar 

  • Scott, T. M., Parveen, S., Portier, K. M., Rose, J. B., Tamplin, M. L., Farrah, S. R., et al. (2003). Geographical variation in ribotype profiles of Escherichia coli isolates from humans, swine, poultry, beef, and dairy cattle in Florida. Applied and Environmental Microbiology, 69(2), 1089–1092.

    Article  CAS  Google Scholar 

  • Scott, T. M., Rose, J. B., Jenkins, T. M., Farrah, S. R., & Lukasik, J. (2002). Microbial source tracking: current methodology and future directions. Applied and Environmental Microbiology, 68(12), 5796–5803.

    Article  CAS  Google Scholar 

  • Simpson, J. M., Santo Domingo, J. W., & Reasoner, D. J. (2002). Microbial source tracking: state of the science. Environmental Science and Technology, 36(24), 5279–5288.

    Article  CAS  Google Scholar 

  • Stull, T. L., LiPuma, J. J., & Edlind, T. D. (1988). A broad-spectrum probe for molecular epidemiology of bacteria: ribosomal RNA. Journal of Infectious Diseases, 157(2), 280–286.

    CAS  Google Scholar 

  • Szewzyk, U., Szewzyk, R., Manz, W., & Schleifer, K. H. (2000). Microbiological safety of drinking water. Annual Review of Microbiology, 54, 81–127.

    Article  CAS  Google Scholar 

  • Tarkka, E., Ahman, H., & Siitonen, A. (1994). Ribotyping as an epidemiologic tool for Escherichia coli. Epidemiology and Infection, 112(2), 263–274.

    Article  CAS  Google Scholar 

  • Tartera, C., & Jofre, J. (1987). Bacteriophages active against Bacteroides fragilis in sewage-polluted waters. Applied and Environmental Microbiology, 53(7), 1632–1637.

    CAS  Google Scholar 

  • Tartera, C., Lucena, F., & Jofre, J. (1989). Human origin of Bacteroides fragilis bacteriophages present in the environment. Applied and Environmental Microbiology, 55(10), 2696–2701.

    CAS  Google Scholar 

  • USCDC (1997). Outbreak of Vibrio parahaemolyticus infections associated with eating raw oysters – pacific northwest. Atlanta, Georgia, USA: U. S. Center for Disease Control.

    Google Scholar 

  • USEPA (2000). National Water Quality Inventory: 1998 Report to Congress. Washington, DC.

  • Versalovic, J., Koeuth, T., & Lupski, J. R. (1991). Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Research, 19(24), 6823–31.

    Article  CAS  Google Scholar 

  • Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., et al. (1995). AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 23(21), 4407–4414.

    Article  CAS  Google Scholar 

  • WHO (2004). Water, sanitation and hygiene links to health: Facts and figures. Geneva: World Health Organization.

    Google Scholar 

  • Wiggins, B. A. (1996). Discriminant analysis of antibiotic resistance patterns in fecal streptococci, a method to differentiate human and animal sources of fecal pollution in natural waters. Applied and Environmental Microbiology, 62(11), 3997–4002.

    CAS  Google Scholar 

  • Wiggins, B. A., Andrews, R. W., Conway, R. A., Corr, C. L., Dobratz, E. J., Dougherty, D. P., et al. (1999). Use of antibiotic resistance analysis to identify nonpoint sources of fecal pollution. Applied and Environmental Microbiology, 65(8), 3483–3486.

    CAS  Google Scholar 

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Yan, T., Sadowsky, M.J. Determining Sources of Fecal Bacteria in Waterways. Environ Monit Assess 129, 97–106 (2007). https://doi.org/10.1007/s10661-006-9426-z

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