Use of 16S-23S rRNA intergenic spacer region PCR and repetitive extragenic palindromic PCR analyses of Escherichia coli isolates to identify nonpoint fecal sources

Applied and Environmental Microbiology

Volumn 69, Issue 8, 2003, Pages 4942-4950

  Seurinck, Sylvie ^a   Verstraete, Willy ^a   Siciliano, Steven D ^a,b  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY OF SASKATCHEWAN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI; RNA;

PRIMERS;

MICROBIOLOGY;

PALINDROMIC RNA; RNA; RNA 16S; RNA 23S; SPACER RNA; UNCLASSIFIED DRUG; WATER;

POLYMERASE CHAIN REACTION;

ANALYTIC METHOD; ARTICLE; BIRD; BOX SEQUENCE; COW; DOG; ENVIRONMENTAL MONITORING; ESCHERICHIA COLI; FECES; FINGERPRINT STABILITY; HORSE; JACKKNIFE TEST; MANURE; MOLECULAR STABILITY; NONHUMAN; POLYMERASE CHAIN REACTION; RNA FINGERPRINTING; RNA SEQUENCE; SAMPLE SIZE; SEWAGE; SIMULATION; SPECIES DIVERSITY; TECHNIQUE; WATER POLLUTION;

ANIMALS; DNA FINGERPRINTING; DNA, RIBOSOMAL SPACER; ESCHERICHIA COLI; FECES; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S; SEWAGE;

ANIMALIA; AVES; CANIS FAMILIARIS; EQUIDAE; EQUUS CABALLUS; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0042529200     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.8.4942-4950.2003     Document Type: Article

References (49)

1. Anderson, S. A., S. J. Turner, and G. D. Lewis. 1997. Enterococci in the New Zealand environment: implications for water quality monitoring. Water Sci. Technol. 35:325-331.
2. Anton, A. I., A. J. Martinez-Murcia, and F. Rodriguez-Valera. 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. Evolution. 47:62-72.
3. Baker, K. H., and D. S. Herson. 1999. Detection and occurrence of indicator organisms and pathogens. Water Environ. Res. 71:530-551.
4. Baudart, J., J. Grabulos, J. P. Barusseau, and P. Lebaron. 2000. Salmonella spp. and fecal coliform loads in coastal waters from a point vs. nonpoint source of pollution. J. Environ. Qual. 29:241-250.
5. Bennet, A. F., and R. E. Lenski. 1993. Evolutionary adaptation to temperature. II. Thermal niches of experimental lines of Escherichia coli. Evolution 47:1-12.
6. Buchan, A., M. Alber, and R. E. Hodson. 2001. Strain-specific differentiation of environmental Escherichia coli isolates via denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S intergenic spacer region. FEMS Microbiol. Ecol. 35:313-321.
7. Carson, C. A., B. L. Shear, M. R. Ellersieck, and A. Asfaw. 2001. Identification of fecal Escherichia coli from humans and animals by ribotyping. Appl. Environ. Microbiol. 67:1503-1507.
8. Chao, A. 1987. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43:783-791.
9. Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11:265-270.
10. Condon, C., J. Philips, Z. Fu, C. Squires, and C. L. Squires. 1992. Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli. EMBO J. 11:4175-4185.
11. Cornuet, J., S. Piry, G. Luikart, A. Estoup, and M. Solignac. 1999. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989-2000.
12. Danovaro, R., E. Manini, and A. Dell'Anno. 2002. Higher abundance of bacteria than of viruses in deep Mediterranean sediments. Appl. Environ. Microbiol. 68:1468-1472.
13. Dice, L. R. 1945. Measures of the amount of ecologic association between species. Ecology 26:297-302.
14. Dionisio, L. P. C., M. Joao, V. S. Ferreiro, M. L. Fidalgo, M. E. Garcia, and J. J. Borrego. 2000. Occurrence of Salmonella spp in estuarine and coastal waters of Portugal. Antonie von Leeuwenhoek Int. J. Genet. 78:99-106.
15. Dombek, P. E., L. K. Johnson, S. T. Zimmerley, and M. J. Sadowsky. 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Environ. Microbiol. 66:2572-2577.
16. Freter, R. 1983. Factors affecting conjugal plasmid transfer in natural communities, p. 105-114. In M. J. Klug and C. A. Reddy (ed.), Current perspectives in microbial ecology. Academic Press, New York, N.Y.
17. Fromin, N., W. Achouak, J. M. Thiery, and T. Heulin. 2001. The genotypic diversity of Pseudomonas brassicacearum populations isolated from roots of Arabidopsis thaliana: influence of plant genotype. Fems Microbiol. Ecol. 37:21-29.
18. Gordon, D. M. 2001. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiology 147:1079-1085.
19. Gordon, D. M., S. Bauer, and J. R. Johnson. 2002. The genetic structure of Escherichia coli populations in primary and secondary habitats. Microbiology 148:1513-1522.
20. Gostin, L. O., Z. Lazzarini, V. S. Neslund, and M. T. Osterholm. 2000. Water quality laws and waterborne diseases: Cryptosporidium and other emerging pathogens. Am. J. Public Health 90:847-853.
21. Graves, A. K., C. Hagedorn, A. Teetor, M. Mahal, A. M. Booth, and R. B. Reneau. 2002. Antibiotic resistance profiles to determine sources of fecal contamination in a rural Virginia watershed. J. Environ. Qual. 31:1300-1308.
22. Griffin, D. W., E. K. Lipp, M. R. McLaughlin, and J. B. Rose. 2001. Marine recreation and public health microbiology: quest for the ideal indicator. BioScience 51:817-825.
23. Hagedorn, C., S. L. Robinson, J. R. Filtz, S. M. Grubbs, T. A. Angier, and R. B. Reneau. 1999. Determining sources of fecal pollution in a rural Virginia watershed with antibiotic resistance patterns in fecal streptococci. Appl. Environ. Microbiol. 65:5522-5531.
24. Hambly, E., F. Tetart, C. Desplats, W. H. Wilson, H. M. Krisch, and N. H. Mann. 2001. A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc. Natl. Acad. Sci. USA 98:11411-11416.
25. Hartel, P. G., J. D. Summer, J. H. Hill, J. V. Collins, J. A. Entry, and W. I. Segars. Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia. J. Environ. Qual. 31:1273-1278.
26. Harwood, V. J., J. Whitlock, and V. Withington. 2000. Classification of antibiotic resistance patterns of indicator bacteria by discriminant analysis: use in predicting the source of fecal contamination in subtropical waters. Appl. Environ. Microbiol. 66:3698-3704.
27. Havelaar, A. H., W. M. Pot-Hogeboom, K. Furuse, R. Pot, and M. P. Hormann. 1990. F-specific RNA bacteriophages and sensitive host strains in faeces and wastewater of human and animal origin. J. Appl. Bacteriol. 69:30-37.
28. Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. M. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
29. Hulton, C. S. J., C. F. Higgins, and P. M. Sharp. 1991. ERIC sequences: a novel family of repetitive elements in the genome of Escherichia coli, Salmonella typhimurium and other enteric bacteria. Mol. Microbiol. 5:825-834.
30. Jagals, P., W. O. K. Grabow, and J. C. Devilliers. 1995. Evaluation of indicators for assessment of human and animal fecal pollution of surface runoff. Water Sci. Technol. 31:235-241.
31. Jensen, M. A., J. A. Webster, and N. Straus. 1993. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol. 59:945-952.
32. Khatib, L. A., Y. L. Tsai, and B. H. Olson. 2002. A biomarker for the identification of cattle fecal pollution in water with the LTIIa toxin gene from enterotoxigenic Escherichia coli. Appl. Microbiol. Biot. 59:97-104.
33. Krieg, N. R., and J. G. Holt. 1984. Bergey's manual of systematic bacteriology, vol. 1. Williams & Wilkins, Baltimore, Md.
34. Livermore, D. M., M. Warner, L. M. C. Hall, V. I. Enne, S. J. Projan, P. M. Dunman, S. L. Wooster, and G. Harrison. 2001. Antibiotic resistance in bacteria from magpies (Pica pica) and rabbits (Oryctolagus cuniculus) from west Wales. Environ. Microbiol. 3:658-661.
35. Martin, B., O. Humbert, M. Camara, E. Guenzi, J. Walker, T. Mitchell, P. Andrew, M. Prudhomme, G. Alloing, R. Hakenbeck, D. A. Morrison, G. J. Boulnois, and J.-P Claverys. 1992. A highly conserved repeated DNA element in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res. 20:3479-3483.
36. Muyzer, G., E. C. de Wall, and A. G. Uitterlinden. 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. 59:695-700.
37. Naas, T., M. Blot, W. M. Fitch, and W. Arber. 1995. Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol. Biol. Evol. 12:198-207.
38. Parveen, S., N. C. Hodge, R. E. Stall, S. R. Farrah, and M. L. Tamplin. 2001. Phenotypic and genotypic characterization of human and nonhuman Escherichia coli. Water Res. 35:379-386.
39. Parveen, S., M. Portier, K. Robinson, L. Edmiston, M. L. Tamplin. 1999. Discriminant analysis of ribotype profiles of Escherichia coli for differentiating human and nonhuman sources of fecal pollution. Appl. Environ. Microbiol. 65:3142-3147.
40. Rademaker, J. L. W., and F. J. de Bruijn. 1997. Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer-assisted pattern analysis, p. 151-171. In G. Caetano-Anollés and P. M. Gresshoff (ed.), DNA markers: protocols, application, and overviews. J. Wiley and Sons, New York, N.Y.
41. Souza, V., M. Rocha, A. Valera, and L. E. Eguiarte. 1999. Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Appl. Environ Microbiol. 65:3373-3385.
42. Stern, M. J., G. F.-L. Ames, N. H. Smith, E. C. Robinson, and C. F. Higgins. 1984. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37:1015-1026.
43. Vernozy-Rozand, C., M. P. Montet, and S. Ray-Gueniot. 2002. E. coli O157:H7 in water: a public health problem. Rev. Med. Vet. Toulouse 153:235-242.
44. Versalovic, J., T. Koeuth, and J. R. Lupski. 1991. Distribution of repetitive DNA-sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19:6823-6831.
45. Versalovic, J., M. Schneider, F. J. de Bruijn, and J. R. Lupski. 1994. Genomic fingerprinting of bacteria with repetitive sequence-based polymerase chain reaction. Methods Cell Biol. 5:25-40.
46. Whiley, R. A., B. Duke, J. M. Hardie, and L. M. C. Hall. 1995. Heterogeneity among 16S-23S rRNA intergenic spacers of species within the Streptococcus milleri group. Microbiology 141:1461-1467.
47. Whittam, T. S. 1989. Clonal dynamics of Escherichia coli in its natural habitat. Antonie van Leeuwenhoek J. Microbiol. 55:23-32.
48. 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. Appl. Environ. Microbiol. 62:3997-4002.
49. Wommack, K. E., and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.