Exploration of biases that affect the interpretation of restriction fragment patterns produced by pulsed-field gel electrophoresis

Journal of Clinical Microbiology

Volumn 42, Issue 12, 2004, Pages 5502-5511

  Singer, Randall S ^a,b   Sischo, William M ^a   Carpenter, Tim E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RESTRICTION ENDONUCLEASE;

ARTICLE; BACTERIUM ISOLATE; COMPUTER SIMULATION; CONTROLLED STUDY; ESCHERICHIA COLI K 12; GENE MUTATION; GENE SEQUENCE; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RESTRICTION FRAGMENT; SPECIES COMPARISON;

BACTERIAL TYPING TECHNIQUES; BIAS (EPIDEMIOLOGY); COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DISEASE OUTBREAKS; DNA RESTRICTION ENZYMES; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI K12; MUTATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; ESCHERICHIA COLI K12; NEGIBACTERIA;

EID: 10844279752     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.12.5502-5511.2004     Document Type: Article

References (32)

1. Barrett, T. J., H. Lior, J. H. Green, R. Khakhria, J. G. Wells, B. P. Bell, K. D. Greene, J. Lewis, and P. M. Griffin. 1994. Laboratory investigation of a multistate food-borne outbreak of Escherichia coli O157:H7 by using pulsed-field gel electrophoresis and phage typing. J. Clin. Microbiol. 32:3013-3017.
2. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
3. Bourhy, H., B. Kissi, N. Tordo, H. Badrane, and D. Sacramento. 1995. Molecular epidemiological tools and phylogenetic analysis of bacteria and viruses with special emphasis on lyssaviruses. Prev. Vet. Med. 25:161-181.
4. Bustamante, C., S. Gurrieri, and S. B. Smith. 1993. Towards a molecular description of pulsed-field gel electrophoresis. Trends Biotechnol. 11:23-30.
5. Cardinali, G., and A. Martini. 1999. Critical observations on computerized analysis of banding patterns with commercial software packages. J. Clin. Microbiol. 37:876-877.
6. Davis, M. A., D. D. Hancock, T. E. Besser, and D. R. Call. 2003. Evaluation of pulsed-field gel electrophoresis as a tool for determining the degree of genetic relatedness between strains of Escherichia coli O157:H7. J. Clin. Microbiol. 41:1843-1849.
7. Dice, L. R. 1945. Measures of the amount of ecological association between species. Ecology 26:297-302.
8. Diekema, D. J., J. Barr, L. D. Boyken, B. J. Buschelman, R. N. Jones, M. A. Pfaller, and L. A. Herwaldt. 1997. A cluster of serious Escherichia coli infections in a neonatal intensive-care unit. Infect. Control Hosp. Epidemiol. 18:774-776.
9. Drake, J. W. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88:7160-7164.
10. Duck, W. M., C. D. Steward, S. N. Banerjee, J. E. McGowan, Jr., and F. C. Tenover. 2003. Optimization of computer software settings improves accuracy of pulsed-field gel electrophoresis macrorestriction fragment pattern analysis. J. Clin. Microbiol. 41:3035-3042.
11. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
12. Gerner-Smidt, P., L. M. Graves, S. Hunter, and B. Swaminathan. 1998. Computerized analysis of restriction fragment length polymorphism patterns: comparative evaluation of two commercial software packages. J. Clin. Microbiol. 36:1318-1323.
13. Izumiya, H., J. Terajima, A. Wada, Y. Inagaki, K. I. Itoh, K. Tamura, and H. Watanabe. 1997. Molecular typing of enterohemorrhagic Escherichia coli O157:H7 isolates in Japan by using pulsed-field gel electrophoresis. J. Clin. Microbiol. 35:1675-1680.
14. Kariuki, S., C. Gilks, J. Kimari, A. Obanda, J. Muyodi, P. Waiyaki, and C. A. Hart. 1999. Genotype analysis of Escherichia coli strains isolated from children and chickens living in close contact. Appl. Environ. Microbiol. 65:472-476.
15. Kudva, I. T., P. S. Evans, N. T. Perna, T. J. Barrett, F. M. Ausubel, F. R. Blattner, and S. B. Calderwood, 2002. Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J. Bacteriol. 184:1873-1879.
16. Lenski, R. E., C. L. Winkworth, and M. A. Riley. 2003. Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations. J. Mol. Evol. 56:498-508.
17. Manly, B. F. J. 1997. Randomization, bootstrap and Monte Carlo methods in biology. Chapman & Hall, London, United Kingdom.
18. Matsuda, J., Y. Hirakata, F. Iori, C. Mochida, Y. Ozaki, M. Nakano, K. Izumikawa, T. Yamaguchi, R. Yoshida, Y. Miyazaki, S. Maesaki, K. Tomono, Y. Yamada, S. Kohno, and S. Kamihira. 1998. Genetic relationship between blood and nonblood isolates from bacteremic patients determined by pulsed-field gel electrophoresis. J. Clin. Microbiol. 36:3081-3084.
19. Oprea, S. F., N. Zaidi, S. M. Donabedian, M. Balasubramaniam, E. Hershberger, and M. J. Zervos. 2004. Molecular and clinical epidemiology of vancomycin-resistant Enterococcus faecalis. J. Antimicrob. Chemother. 53:626-630.
20. Page, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12:357-358.
21. Payne, R. E., M. D. Lee, D. W. Dreesen, and H. M. Barnhart. 1999. Molecular epidemiology of Campylobacter jejuni in broiler flocks using randomly amplified polymorphic DNA-PCR and 23S rRNA-PCR and role of litter in its transmission. Appl. Environ. Microbiol. 65:260-263.
22. Samadpour, M. 1995. Molecular epidemiology of Escherichia coli O157:H7 by restriction fragment length polymorphism using Shiga-like toxin genes. J. Clin. Microbiol. 33:2150-2154.
23. Singer, R. S., J. S. Jeffrey, T. E. Carpenter, C. L. Cooke, E. R. Atwill, W. O. Johnson, and D. C. Hirsh. 2000. Persistence of cellulitis-associated E. coli DNA fingerprints in successive broiler chicken flocks. Vet. Microbiol. 75:59-71.
24. Singer, R. S., J. S. Jeffrey, T. E. Carpenter, C. L. Cooke, R. P. Chin, and D. C. Hirsh. 1999. Spatial heterogeneity of Escherichia coli isolated from avian cellulitis lesions in broilers. Avian Dis. 43:756-762.
25. Sonntag, A. K., R. Prager, M. Bielaszewska, W. Zhang, A. Fruth, H. Tschape, and H. Karch. 2004. Phenotypic and genotypic analyses of enterohemorrhagic Escherichia coli O145 strains from patients in Germany. J. Clin. Microbiol. 42:954-962.
26. Swaminathan, B., T. J. Barrett, S. B. Hunter, and R. V. Tauxe. 2001. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg. Infect. Dis. 7:382-389.
27. Tenover, F. C., R. D. Arbeit, and R. V. Goering, 1997. How to select and interpret molecular strain typing methods for epidemiological studies of bacterial infections: a review for healthcare epidemiologists. Infect. Control Hosp. Epidemiol. 18:426-439.
28. Tenover, F. C., R. D. Arbeit, R. V. Goering, P. A. Mickelsen, B. E. Murray, D. H. Persing, and B. Swaminathan. 1995. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33:2233-2239.
29. Traub, W. H., A. Eiden, B. Leonhard, and D. Bauer. 1996. Typing of nosocomial strains of Serratia marcescens: comparison of restriction enzyme cleaved genomic DNA fragment (PFGE) analysis with bacteriocin typing, biochemical profiles and serotyping. Zentbl. Bakteriol. Parasitenkd. Infektkrankh. Hyg. Abt. 1 Orig. 284:93-106.
30. van Belkum, A., W. van Leeuwen, M. E. Kaufmann, B. Cookson, F. Forey, J. Etienne, R. Goering, F. Tenover, C. Steward, F. O'Brien, W. Grubb, P. Tassios, N. Legakis, A. Morvan, N. El Solh, R. de Ryck, M. Struelens, S. Salmenlinna, J. Vuopio-Varkila, M. Kooistra, A. Talens, W. Witte, and H. Verbrugh. 1998. Assessment of resolution and intercenter reproducibility of results of genotyping Staphylococcus aureus by pulsed-field gel electrophoresis of SmaI macrorestriction fragments: a multicenter study. J. Clin. Microbiol. 36:1653-1659.
31. Vautor, E., G. Abadie, J. M. Guibert, C. Huard, and M. Pepin. 2003. Genotyping of Staphylococcus aureus isolated from various sites on farms with dairy sheep using pulsed-field gel electrophoresis. Vet. Microbiol. 96:69-79.
32. Wassenaar, T. M., B. Geilhausen, and D. G. Newell. 1998. Evidence of genomic instability in Campylobacter jejuni isolated from poultry. Appl. Environ. Microbiol. 64:1816-1821.