• [1]
    Geldreich, E.E. (1966) Sanitary significance of fecal coliform in the environment. In: Water Pollution Control Research Series, publication WP-20-3. Federal Water Pollution Control Administration, US Department of the Interior, Cincinnati, OH.
  • [2]
    Orskov, F. and Orskov, L. (1981) Enterobacterioaceae. In: Medical Microbiology and Infectious Diseases (Broude, A.I., Ed.), pp. 340–352. W.B. Saunders Co., Philadelphia, PA.
  • [3]
    Olsen, J.E., Brown, D.J., Baggesen, D.L., Bisgaard, M. (1992) Biochemical and molecular characterization of Salmonella enterica serovar berta, and comparison of methods for typing. Epidemiol. Infect. 108, 243260.
  • [4]
    Parveen, S., Murphree, R.L., Edmiston, L., Kasper, C.W., Portier, K.M., Tamplin, M.L. (1997) Association of multiple-antibiotic-resistance profiles with point and non-point sources of Escherichia coli in Apalachicola Bay. Appl. Environ. Microbiol. 63, 26072612.
  • [5]
    Zierdt, C.H., Robertson, E.A., Williams, R.L., MacLowry, J.D. (1980) Computer analysis of Staphylococcus aureus phage typing from 1957 to 1975, citing epidemiological trends and natural evolution within phage typing system. Appl. Environ. Microbiol. 39, 623629.
  • [6]
    Geldreich, E.E., Kenner, B.A. (1969) Concepts of fecal streptococci in stream pollution. J. Water Pollut. Conf. Fed. 41, R336R352.
  • [7]
    Stull, T.L., LiPuma, J.J., Edlind, T.D. (1988) A broad-spectrum probe for molecular epidemiology of bacteria: ribosomal RNA. J. Infect. Dis. 157, 280286.
  • [8]
    Wiggens, B.A., Andrews, R.W., Conway, R.A., Corr, C.L., Dobratz, E.J., Dougherty, D.P., Eppard, J.R., Knupp, S.R., Limjoco, M.C., Mettenburg, J.M., Rinehardt, J.M., Sonsino, J., Torrijos, R.L., Zimmerman, M.E. (1999) Use of antibiotic resistance analysis to identify nonpoint sources of fecal pollution. Appl. Environ. Microbiol. 65, 34833486.
  • [9]
    Freter, R. (1983) Factors affecting conjugal plasmid transfer in natural bacteria communities. In: Current Perspectives in Microbial Ecology (Klug, M.J. and Reddy, C.A., Eds.), pp. 105–114. American Society for Microbiology, Washington, DC.
  • [10]
    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. Appl. Environ. Microbiol. 66, 25722577.
  • [11]
    Farnleitner, A.H., Kreuzinger, N., Kavka, G.G., Grillenberger, S., Rath, J., Mach, R.L. (2000) Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the β-D-glucuronidase gene. Appl. Environ. Microbiol. 66, 13401346.
  • [12]
    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. Appl. Environ. Microbiol. 65, 31423147.
  • [13]
    Gürtler, V., Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 316.
  • [14]
    Whiley, R.A., Duke, B., Hardie, J.M., Hall, L.M.C. (1995) Heterogeneity among 16S-23S rRNA intergenic spacers of species within the ‘Streptococcus milleri’ group. Microbiology 141, 14611467.
  • [15]
    Woese, C.R. (1987) Bacterial evolution. Microbiol. Rev. 51, 221227.
  • [16]
    Condon, C., Philips, J., Fu, Z., Squires, C., Squires, C.L. (1992) Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli. EMBO J. 11, 41754185.
  • [17]
    Antón, A.I., Martı́nez-Murcia, A.J., Rodrı́guez-Valera, F. (1998) Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J. Mol. Evol. 47, 6272.
  • [18]
    Jensen, J.A., Webster, J.A., Straus, N. (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59, 945952.
  • [19]
    Van Belkum, A., Maas, H., Verbrugh, H., Van Leeuwen, N. (1996) Serotyping, ribotyping, PCR-mediated ribosomal 16S-23S spacer analysis and arbitrarily primed PCR for epidemiological studies on Legionella pneumophila. Res. Microbiol. 147, 405413.
  • [20]
    Dolzani, L., Tonin, E., Lagatolla, C., Monti-Bragadin, C. (1994) Typing of Staphylococcus aureus by amplification of the 16S-23S rRNA intergenic spacer sequences. FEMS Microbiol. Lett. 119, 167174.
  • [21]
    Dolzani, L., Tonin, E., Lagatolla, C., Prandin, L., Monti-Bragadin, C. (1995) Identification of Acinetobacter isolates in the A. calcoaceticus-A. baumannii complex by restriction analysis of the 16S-23S rRNA intergenic spacer sequences. J. Clin. Microbiol. 133, 11081113.
  • [22]
    Bourque, S.N., Valero, J.R., Lavoie, M.C., Levesque, R.C. (1995) Comparative analysis of the 16S to 23S ribosomal intergenic spacer sequences of Bacillus thuringiensis strains and subspecies and of closely related species. Appl. Environ. Microbiol. 61, 16231626.
  • [23]
    Abed, Y., Bollet, C., de Micco, P. (1995) Identification and strain differentiation of Mycobacterium species on the basis of DNA 16S-23S spacer region polymorphism. Res. Microbiol. 146, 405413.
  • [24]
    Fischer, S.G., Lerman, L.S. (1979) Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell 16, 191200.
  • [25]
    Myers, R.M., Maniatis, T., Lerman, L.S. (1987) Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods Enzymol. 155, 501527.
  • [26]
    K.M. MillerT.J. MingA.D. SchulzeR.E. Withler Denaturing gradient gel electrophoresis (DGGE): A rapid and sensitive technique to screen nucleotide sequence variation in populations, Biotechniques, 27 1999 1016.
  • [27]
    Langefors, A., Lohm, J., von Schantz, T., Grahn, M. (2000) Screening of Mhc variation in Atlantic salmon (Salmo salar): a comparison of restriction fragment length polymorphism (RFLP), denaturing gradient gel electrophoresis (DGGE) and sequencing. Mol. Ecol. 9, 215219.
  • [28]
    Reiseberg, L.H. (1996) Homology among RAPD fragments in interspecific comparisons. Mol. Ecol. 5, 99105.
  • [29]
    van Oppen, M.J.H., Klerk, H., de Graaf, M., Stam, W.T., Olsen, J.L. (1996) Assessing the limits of random amplified polymorphic DNAs (RAPDs) in seaweed biogeography. J. Phycol. 32, 433444.
  • [30]
    Garcı́a-Martı́nez, J., Martı́nez-Murcia, A., Antón, A.I., Rodrı́guez-Valera, F.R. (1996) Comparison of the small 16S to 23S intergenic spacer region (ISR) of the rRNA operons of some Escherichia coli strains of the ECOR collection and E. coli K-12. J. Bacteriol. 178, 63746377.
  • [31]
    Ochman, H., Selander, R.K. (1984) Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157, 690693.
  • [32]
    de Olivieri, V.M., Coutinho, H.L.C., Sobral, B.W.S., Guimaraes, C.T., Van Elsas, J.D., Manfio, G.P. (1999) Discrimination of Rhizobium tropici and R. leguminosarum strains by PCR-specific amplification of 16S-23S rDNA spacer region fragments and denaturing gradient gel electrophoresis (DGGE). Lett. Appl. Microbiol. 28, 137141.
  • [33]
    Greensberg, A.E., Connors, J.J., Jenkins, D. and Franson, M.A.H. (Eds.) (1992) Standard Methods for the Examination of Water and Wastewater, 15th Edn. American Public Health Association, American Water Works Association, and Water Pollution Control Federation, Washington, DC.
  • [34]
    Holt, J.G. (Ed.) (1993) Bergey's Manual of Determinative Bacteriology, 9th Edn. Williams and Wilkins, Baltimore, MD.
  • [35]
    Madico, G., Akopyants, N.S., Berg, D.E. (1995) Arbitrarily primed PCR DNA fingerprinting of Escherichia coli O157:H7 strains by using templates from boiled cultures. J. Clin. Microbiol. 33, 15341536.
  • [36]
    Muyzer, G., de Wall, E.C., Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695700.
  • [37]
    Mills, A.L., Wassel, R.A. (1980) Aspects of diversity measurement for microbial communities. Appl. Environ. Microbiol. 40, 578586.
  • [38]
    Swofford, D.L. (1993) PAUP: Phylogenetic analysis using parsimony. Illinois Natural History Survey, Champaign, IL.
  • [39]
    Souza, V., Rocha, M., Valera, A., Eguiarte, L.E. (1999) Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Appl. Environ. Microbiol. 65, 33733385.
  • [40]
    Jarvis, G.N., Kizoulis, M.G., Dize-Gonzalez, F., Russel, J.B. (2000) The genetic diversity of predominant Escherichia coli strains isolated from cattle fed various amounts of hay and grain. FEMS Microbiol. Ecol. 32, 225233.
  • [41]
    Milkman, R. (1997) Recombination and population structure in Escherichia coli. Genetics 146, 745750.
  • [42]
    Hagedorn, C., Robinson, S.L., Filtz, J.R., Grubbs, S.M., Angier, T.A., Reneau, R.B. (1999) Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci. Appl. Environ. Microbiol. 65, 55225531.
  • [43]
    Wilkinson, J., Jenkins, A., Wyer, M., Kay, D. (1995) Modeling fecal coliform dynamics in streams and rivers. Water Res. 29, 847855.
  • [44]
    Whittam, T.S. (1989) Clonal dynamics of Escherichia coli in its natural habitat. Antonie van Leeuwenhoek 55, 2332.
  • [45]
    Flint, K.P. (1987) The long-term survival of Escherichia coli in river water. J. Appl. Bacteriol. 63, 261270.
  • [46]
    Gurijala, V., Alexander, M. (1980) Explanation for the decline of bacteria introduced into lake water. Microbiol. Ecol. 20, 231244.
  • [47]
    Davies, C.M., Long, L.A., Donald, M., Ashbolt, N.J. (1995) Survival of fecal microorganisms in marine and freshwater sediments. Appl. Environ. Microbiol. 61, 18881896.
  • [48]
    Müldorfer, I., Hacker, J. (1994) Genetic aspects of E. coli virulence. Microbiol. Pathogen 16, 171181.