Optimization and validation of rep-PCR genotypic libraries for microbial source tracking of environmental Escherichia coli isolates

Canadian Journal of Microbiology

Volumn 56, Issue 1, 2010, Pages 8-17

  Lyautey, Emilie ^a   Lu, Zexun ^a   Lapen, David R ^a   Berkers, Tanya E ^a   Edge, Thomas A ^b   Topp, Edward ^a  

^a AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^b ENVIRONMENT CANADA   (Canada)

Author keywords

Escherichia coli; Fecal source; Genotypic library; Microbial source tracking

Indexed keywords

AGRICULTURAL LANDSCAPES; AVERAGE RATE; COMMUNITY COMPOSITION; ENVIRONMENTAL ISOLATES; FECAL CONTAMINATION; FECAL SAMPLES; FECAL SOURCE; FECAL SOURCES; K-NEAREST NEIGHBOURS; LOSS OF ACCURACY; MICROBIAL SOURCE TRACKING; ONTARIO; PATTERN-MATCHING ALGORITHM; PER UNIT; REP-PCR; SENSITIVITY AND SPECIFICITY; TEMPORAL SHIFTS;

LIBRARIES; POLYMERASE CHAIN REACTION;

ESCHERICHIA COLI;

ACCURACY ASSESSMENT; AGRICULTURAL LAND; ALGORITHM; BIOINDICATOR; COLIFORM BACTERIUM; FECES; GENOTYPE; ISOLATED POPULATION; MICROBIAL ACTIVITY; OPTIMIZATION; POLLUTANT SOURCE; POLLUTION MONITORING; POLYMERASE CHAIN REACTION;

ACCURACY; AGRICULTURAL LAND; ARTICLE; BACTERIAL GENE; BACTERIUM CONTAMINATION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CANADA; CLASSIFICATION ALGORITHM; CLONE; ENTEROBACTER; ENVIRONMENTAL MONITORING; ESCHERICHIA COLI; FECES ANALYSIS; GENE LIBRARY; GENOTYPE; MICROBIAL COMMUNITY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

ANIMALS; BACTERIAL TYPING TECHNIQUES; DNA, BACTERIAL; ESCHERICHIA COLI; FECES; FRESH WATER; GENE LIBRARY; GENOTYPE; HUMANS; ONTARIO; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; WATER MICROBIOLOGY;

ENTEROBACTERIACEAE; ESCHERICHIA COLI;

EID: 76749134780     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/W09-113     Document Type: Article

References (40)

1. Albert, J.M., Munakata-Marr, J., Tenorio, L., and Siegrist, R.L. 2003. Statistical evaluation of bacterial source tracking data obtained by rep-PCR DNA fingerprinting of Escherichia coli. Environ. Sci. Technol. 37(20): 4554-4560. doi:10.1021/es034211q. PMID:14594360.
2. Apajalahti, J.H.A., Kettunen, A., Bedford, M.R., and Holben, W.E. 2001. Percent G+C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens. Appl. Environ. Microbiol. 67(12): 5656-5667. doi:10. 1128/AEM.67.12.5656-5667.2001. PMID:11722920.
3. Buchan, A., Alber, M., and Hodson, R.E. 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(3): 313-321. PMID:11311442.
4. Casarez, E.A., Pillai, S.D., Mott, J.B., Vargas, M., Dean, K.E., and Di Giovanni, G.D. 2007. Direct comparison of four bacterial source tracking methods and use of composite data sets. J. Appl. Microbiol. 103(2): 350-364. doi:10.1111/j.1365-2672. 2006.03246.x. PMID:17650195.
5. Ciebin, B.W., Brodsky, M.H., Eddington, R., Horsnell, G., Choney, A., Palmateer, G., et al. 1995. Comparative evaluation of modified m-FC and m-TEC media for membrane filter enumeration of Escherichia coli in water. Appl. Environ. Microbiol. 61(11): 3940-3942. PMID:8526507.
6. Dombek, P.E., Johnson, L.K., Zimmerley, S.T., and 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(6): 2572-2577. doi:10. 1128/AEM.66.6.2572-2577.2000. PMID:10831440.
7. Duriez, P., and Topp, E. 2007. Temporal dynamics and impact of manure storage on antibiotic resistance patterns and population structure of Escherichia coli isolates from a commercial swine farm. Appl. Environ. Microbiol. 73(17): 5486-5493. doi:10. 1128/AEM.00218-07. PMID:17616622.
8. Farber, J.M. 1996. An introduction of the hows and whys of molecular typing. J. Food Prot. 59: 1091-1101.
9. Field, K.G., Chern, E.C., Dick, L.K., Furhman, J., Griffith, J., Holden, P.A., et al. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Water Res. 1: 181-194.
10. Gordon, D.M. 2001. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiology, 147(Pt 5): 1079-1085. PMID: 11320111.
11. Gordon, D.M., Bauer, S., and Johnson, J.R. 2002. The genetic structure of Escherichia coli populations in primary and secondary habitats. Microbiology, 148(Pt 5): 1513-1522. PMID: 11988526.
12. Hartel, P.G., Summer, J.D., Hill, J.L., Collins, J.V., Entry, J.A., and Segars, W.I. 2002. Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia. J. Environ. Qual. 31(4): 1273-1278. PMID:12175046.
13. Harwood, V.J., Whitlock, J., and 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(9): 3698-3704. doi:10.1128/AEM.66.9.3698-3704. 2000. PMID:10966379.
14. Harwood, V.J., Wiggins, B., Hagedorn, C., Ellender, R.D., Gooch, J., Kern, J., et al. 2003. Phenotypic library-based microbial source tracking methods: efficacy in the California collaborative study. J. Water Health, 1(4): 153-166. PMID:15382721.
15. Health Canada. 2002. From source to tap: the multi-barrier approach to safe drinking water [online]. Available from www.hcsc. gc.ca/ewh-semt/water-eau/ drink-potab/multi-barrier/index--e.html [accessed March 2009.]
16. International Joint Commission. 2004. 12th Biennial report on Great Lakes water quality [online]. Available from www.ijc. org/php/publications/html/12br/ english/report/index.html. [accessed 24 December 2004].
17. Johnson, L.K., Brown, M.B., Carruthers, E.A., Ferguson, J.A., Dombek, P.E., and 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(8): 4478-4485. doi:10.1128/AEM.70.8.4478-4485. 2004. PMID:15294775.
18. Khatib, L.A., Tsai, Y.L., and Olson, B.H. 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(2): 231-238. doi:10.1007/s00253-003-1373-9. PMID:13680204.
19. Kon, T., Weir, S.C., Howell, E.T., Lee, H., and Trevors, J.T. 2009. Repetitive element (REP)-polymerase chain reaction (PCR) analysis of Escherichia coli isolates from recreational waters of southeastern Lake Huron. Can. J. Microbiol. 55(3): 269-276. doi:10.1139/W08-123. PMID:19370070.
20. Kruse, H., and Sørum, H. 1994. Transfer of multiple drug resistance plasmids between bacteria of diverse origins in natural microenvironments. Appl. Environ. Microbiol. 60(11): 4015-4021. PMID:11865872.
21. Leung, K.T., Mackereth, R., Tien, Y.C., and 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(1): 111-119. doi:10.1016/S0168-6496(03) 00254-X. PMID:19712352.
22. Lu, Z., Lapen, D., Scott, A., Dang, A., and Topp, E. 2005. Identifying host sources of fecal pollution: diversity of Escherichia coli in confined dairy and swine production systems. Appl. Environ. Microbiol. 71(10): 5992-5998. doi:10.1128/AEM.71.10. 5992-5998.2005. PMID:16204513.
23. Lyautey, E., Lapen, D.R., Wilkes, G., McCleary, K., Pagotto, F., Tyler, K., et al. 2007. Distribution and characteristics of Listeria monocytogenes isolates from surface waters of the South Nation River watershed, Ontario, Canada. Appl. Environ. Microbiol. 73(17): 5401-5410. doi:10.1128/AEM.00354-07. PMID: 17630309.
24. McLellan, S.L., Daniels, A.D., and Salmore, A.K. 2003. Genetic characterization of Escherichia coli populations from host sources of fecal pollution by using DNA fingerprinting. Appl. Environ. Microbiol. 69(5): 2587-2594. doi:10.1128/AEM.69.5. 2587-2594.2003. PMID:12732525.
25. Meays, C.L., Broersma, K., Nordin, R., and Mazumder, A. 2004. Source tracking fecal bacteria in water: a critical review of current methods. J. Environ. Manag. 73(1): 71-79. doi:10.1016/j. jenvman.2004.06.001. PMID:15327848.
26. Mohapatra, B.R., Broersma, K., and Mazumder, A. 2007. Comparison of five rep-PCR genomic fingerprinting methods for differentiation of fecal Escherichia coli from humans, poultry and wild birds. FEMS Microbiol. Lett. 277(1): 98-106. doi:10.1111/ j.1574-6968.2007.00948.x. PMID:17986090.
27. Myoda, S.P., Carson, C.A., Fuhrmann, J.J., Hahm, B.K., Hartel, P.G., Yampara-Lquise, H., et al. 2003. Comparison of genotypic-based microbial source tracking methods requiring a host origin database. J. Water Health, 1(4): 167-180. PMID: 15382722.
28. Ritter, K.J., Carruthers, E., Carson, C.A., Ellender, R.D., Harwood, V.J., Kingsley, K., et al. 2003. Assessment of statistical methods used in library-based approaches to microbial source tracking. J. Water Health, 1(4): 209-223. PMID:15382725.
29. Robinson, B.J., Ritter, K.J., and Ellender, R.D. 2007. A statistical appraisal of disproportional versus proportional microbial source tracking libraries. J. Water Health, 5(4): 503-509. doi:10.2166/ wh.2007.044. PMID:17878563.
30. Ruecker, N.J., Braithwaite, S.L., Topp, E., Edge, T., Lapen, D.R., Wilkes, G., et al. 2007. Tracking host sources of Cryptosporidium spp. in raw water for improved health risk assessment. Appl. Environ. Microbiol. 73(12): 3945-3957. doi:10.1128/ AEM.02788-06. PMID:17483276.
31. Russell, J.B., Diez-Gonzalez, F., and Jarvis, G.N. 2000. Invited review: effects of diet shifts on Escherichia coli in cattle. J. Dairy Sci. 83(4): 863-873. PMID:10791804.
32. Schwemmer, P., Garthe, S., and Mundry, R. 2008. Area utilization of gulls in a coastal farmland landscape: habitat mosaic supports niche segregation of opportunistic species. Landsc. Ecol. 23(3): 355-367. doi:10.1007/s10980- 008-9194-y.
33. 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. Appl. Environ. Microbiol. 69(2): 1089-1092. doi:10.1128/AEM.69.2.1089-1092.2003. PMID:12571033.
34. Stoeckel, D.M., and Harwood, V.J. 2007. Performance, design, and analysis in microbial source tracking studies. Appl. Environ. Microbiol. 73(8): 2405-2415. doi:10.1128/AEM.02473-06. PMID: 17308193.
35. U.S. Environmental Protection Agency. 2000. Improved enumeration methods for the recreational water quality indicator: enterococci and Escherichia coli [online]. U.S. EPA Doc. No. EPA/ 821/R-97/004. Available from www.epa.gov/microbes/RecManv. pdf [accessed December 2009].
36. U.S. Environmental Protection Agency. 2005. Microbial source tracking guide document [online]. U.S. EPA Doc. No. EPA-600/R-05/064. Available from www.epa.gov/nrmrl/pubs/ 600r05064/600r05064.pdf [accessed December 2009].
37. Versalovic, J., Koeuth, T., and Lupski, J.R. 1991. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 19(24): 6823-6831. doi:10.1093/nar/19.24.6823. PMID:1762913.
38. Versalovic, J., Schneider, M., De Bruijn, F.J., and Lupski, J.R. 1994. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol. Cell. Biol. 5: 25-40.
39. 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(11): 3997-4002. PMID:8899986.
40. Wilkes, G., Edge, T., Gannon, V., Jokinen, C., Lyautey, E., Medeiros, D., et al. 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(8): 2209-2223. doi:10.1016/j. watres.2009.01.033. PMID:19339033.