Comparative efficacy of five different rep-PCR methods to discriminate Escherichia coli populations in aquatic environments

Water Science and Technology

Volumn 58, Issue 3, 2008, Pages 537-547

  Mohapatra, B R ^a   Mazumder, A ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

(GTG)5 PCR; DNA fingerprinting; Escherichia coli; Microbial source tracking; Molecular typing; Rep PCR

Indexed keywords

CONTAMINATION; ESCHERICHIA COLI; PLANNING; STRATEGIC PLANNING; WATER POLLUTION;

(GTG)5-PCR; DNA FINGERPRINTING; MICROBIAL SOURCE TRACKING; MOLECULAR TYPING; REP-PCR;

COSMIC RAYS;

AQUATIC ENVIRONMENT; CLUSTER ANALYSIS; COMPARATIVE STUDY; DIGESTIVE SYSTEM DISORDER; DISEASE TRANSMISSION; DNA FINGERPRINTING; FECAL COLIFORM; FECES; POLYMERASE CHAIN REACTION; WATER POLLUTION; WATERSHED;

AQUATIC ENVIRONMENT; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CONTROLLED STUDY; ESCHERICHIA COLI; INTERMETHOD COMPARISON; POLYMERASE CHAIN REACTION; WASTE WATER MANAGEMENT; WATER CONTAMINATION;

BACTERIAL TYPING TECHNIQUES; BRITISH COLUMBIA; CLUSTER ANALYSIS; DNA FINGERPRINTING; ESCHERICHIA COLI; FRESH WATER; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

BRITISH COLUMBIA; CANADA; LAKELSE LAKE; NORTH AMERICA; OKANAGAN LAKE;

ESCHERICHIA COLI;

EID: 52949122499     PISSN: 02731223     EISSN: None     Source Type: Book Series    
DOI: 10.2166/wst.2008.424     Document Type: Article

References (25)

1. Anderson, K. L., Whitlock, J. E. & Harwood, V. J. 2005 Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Appl. Environ. Microbiol. 71, 3041-3048.
2. ASM 2004 Response to: water quality criteria for bacteria for coastal and Great Lakes waters. American Society of Microbiology (online), http://www.asm.org/Policy/index. asp?bid = 29781 (accessed 13 December 2006).
3. Baldy-Chudzik, K., Niedbach, J. & Stosik, M. 2003 Rep-PCR fingerprinting as a tool for the analysis of genomic diversity in Escherichia coli strains isolated from an aqueous/freshwater environment. Cell. Mol. Biol. Lett. 8, 793-798.
4. Borges, L. G. A., Vechia, V. D. & Corção, G. 2003 Characterization and genetic diversity via REP-PCR of Escherichia coli isolates from polluted waters in southern Brazil. FEMS Microbiol. Ecol. 45, 173-180.
5. 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. Appl. Environ. Microbiol. 69, 1836-1839.
6. Chen, J. & Griffiths, M. W. 1998 PCR differentiation of Escherichia coli from other Gram-negative bacteria using primers derived from the nucleotide sequences flanking the gene encoding the universal stress protein. Lett. Appl. Microbiol. 27, 369-371.
7. Clesceri, L. S., Greenberg, A. E. & Eaton, A. D. 1998 Standard Methods for the Examination of Water and Wastewater, 20th edition. American Public Health Association, Washington, DC, USA.
8. 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, 2572-2577.
9. Gevers, D., Huys, G. & Swings, J. 2001 Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 205, 31-36.
10. Holt, J. G., Krieg, N. R., Sneath, P. H. A., Staley, J. T. & Williams, S. T. 1994 Bergey's Manual of Determinative Bacteriology, 9th edition. Williams and Wilkins, Hagerstown, MD, USA.
11. Hunter, P. R. & Gaston, M. A. 1988 Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26, 2465-2466.
12. 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. Appl. Environ. Microbiol. 70, 4478-4485.
13. 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 Microbiol. Ecol. 47, 111-119.
14. McLellan, S. L. 2004 Genetic diversity of Escherichia coli isolated from urban rivers and beach water. Appl. Environ. Microbiol. 70, 4658-4665.
15. Meays, C. L., Broersma, K., Nordin, R. & Mazumder, A. 2004 Source tracking fecal bacteria in water: a critical review of current methods. J. Environ. Manage. 73, 71-79.
16. Mohapatra, B. R., Broersma, K., Nordin, R. & Mazumder, A. 2007 Evaluation of repetitive extragenic palindromic-PCR for discrimination of fecal Escherichia coli from humans, and different domestic-and wild-animals. Microbiol. Immunol. 51, 733-740.
17. Rademaker, J. L. W. & de Bruijn, F. J. 1997 Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer-assisted pattern analysis. In: Caetano-Anollés, G. & Gresshoff, P. M. (eds) DNA markers: protocols, applications, and overviews. Wiley and Sons, New York, USA, pp. 151-171.
18. Rasschaert, G., Houf, K., Imberechts, H., Grijspeerdt, K., De Zutter, L. & Heyndrickx, M. 2005 Comparison of five repetitive-sequence-based PCR typing methods for molecular discrimination of Salmonella enterica isolates. J. Clin. Microbiol. 43, 3615-3623.
19. Savageau, M. A. 1983 Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122, 732-734.
20. Scott, T. M., Rose, J. B., Jenkins, T. M., Farrah, S. R. & Lukasik, J. 2002 Microbial source tracking: current methodology and future directions. Appl. Environ. Microbiol. 68, 5796-5803.
21. Simpson, J. M., Domingo, J. W. S. & Reasoner, D. J. 2002 Microbial source tracking: state of the science. Environ. Sci. Technol. 36, 5279-5288.
22. Somarelli, J. A., Makarewicz, J. C., Sia, R. & Simon, R. 2007 Wildlife identified as major source of Escherichia coli in agriculturally dominated watersheds by BOX A1R-derived genetic fingerprints. J. Environ. Manage. 82, 60-65.
23. 5-PCR for identification of Enterococcus spp. FEMS Microbiol. Lett. 247, 59-63.
24. Versalovic, J., Schneider, M., de Bruijn, F. J. & Lupski, J. R. 1994 Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5, 25-40.
25. WHO 2003 Emerging issues in water and infectious diseases. World Health Organization, Geneva (online), http://www.who.int/ water_sanitation_health/ emerging/en/emerging.pdf, accessed 13 December 2006.