Simultaneous analysis of multiple enzymes increases accuracy of pulsed-field gel electrophoresis in assigning genetic relationships among homogeneous Salmonella strains

Journal of Clinical Microbiology

Volumn 49, Issue 1, 2011, Pages 85-94

  Zheng, Jie ^a,c   Keys, Christine E ^a   Zhao, Shaohua ^a   Ahmed, Rafiq ^b   Meng, Jianghong ^c   Brown, Eric W ^a  

^a CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^b Public Health Agency of Canada   (Canada)

^c UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BLNI PROTEI; ENZYME; NOTI PROTEIN; PACI PROTEIN; PROTEIN; SFII PROTEIN; SPEI PROTEIN; UNCLASSIFIED DRUG; XBAI PROTEIN;

ACCURACY; ARTICLE; BACTERIAL STRAIN; CLUSTER ANALYSIS; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; ENZYME ANALYSIS; MOLECULAR PHYLOGENY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SALMONELLA ENTERICA; SALMONELLA ENTERITIDIS; SALMONELLA TYPHIMURIUM;

ANIMALS; DNA RESTRICTION ENZYMES; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENOTYPE; HUMANS; MOLECULAR TYPING; SALMONELLA ENTERITIDIS; SALMONELLA INFECTIONS; SALMONELLA INFECTIONS, ANIMAL; SALMONELLA TYPHIMURIUM;

SALMONELLA; SALMONELLA ENTERICA; SALMONELLA ENTERITIDIS;

EID: 78650862588     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00120-10     Document Type: Article

References (41)

1. Amavisit, P., P. F. Markham, D. Lightfoot, K. G. Whithear, and G. F. Browning. 2001. Molecular epidemiology of Salmonella Heidelberg in an equine hospital. Vet. Microbiol. 80:85-98.
2. Baumler, A. J., R. M. Tsolis, T. A. Ficht, and L. G. Adams. 1998. Evolution of host adaptation in Salmonella enterica. Infect. Immun. 66:4579-4587.
3. Boxrud, D., K. Pederson-Gulrud, J. Wotton, C. Medus, E. Lyszkowicz, J. Besser, and J. M. Bartkus. 2007. Comparison of multiple-locus variable-number tandem repeat analysis, pulsed-field gel electrophoresis, and phage typing for subtype analysis of Salmonella enterica serotype Enteritidis. J. Clin. Microbiol. 45:536-543.
4. Boyd, D., G. A. Peters, A. Cloeckaert, K. S. Boumedine, E. Chaslus-Dancla, H. Imberechts, and M. R. Mulvey. 2001. Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona. J. Bacteriol. 183:5725-5732.
5. Brown, E. W., M. L. Kotewicz, and T. A. Cebula. 2002. Detection of recombination among Salmonella enterica strains using the incongruence length difference test. Mol. Phylogenet. Evol. 24:102-120.
6. Brown, E. W., J. E. LeClerc, M. L. Kotewicz, and T. A. Cebula. 2001. Three R's of bacterial evolution: how replication, repair, and recombination frame the origin of species. Environ. Mol. Mutagen. 38:248-260.
7. Brown, E. W., J. E. LeClerc, B. Li, W. L. Payne, and T. A. Cebula. 2001. Phylogenetic evidence for horizontal transfer of mutS alleles among naturally occurring Escherichia coli strains. J. Bacteriol. 183:1631-1644.
8. Brown, E. W., M. K. Mammel, J. E. LeClerc, and T. A. Cebula. 2003. Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens. Proc. Natl. Acad. Sci. U. S. A. 100:15676-15681.
9. Bull, J. J., J. P. Huelsenbeck, C. W. Cunningham, D. L. Swofford, and P. J. Wadell. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
10. 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.
11. Dykhuizen, D. E., and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:7257-7268.
12. Farris, J. S., M. Kallersjo, A. G. Kluge, and C. Bult. 1995. Testing significance of incongruence. Cladistics 10:315-319.
13. Foley, S. L., D. G. White, P. F. McDermott, R. D. Walker, B. Rhodes, P. J. Fedorka-Cray, S. Simjee, and S. Zhao. 2006. Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. J. Clin. Microbiol. 44:3569-3577.
14. Forey, P. L., C. J. Humphries, I. Kitching, R. W. Scotland, D. J. Siebert, and D. Williams. 1992. Cladistics, a practical course in systematics. Clarendon Press, Oxford, United Kingdom.
15. Gadagkar, S. R., M. S. Rosenberg, and S. Kumar. 2005. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J. Exp. Zool. B Mol. Dev. Evol. 304:64-74.
16. Guerra, B., P. Schrors, and M. C. Mendoza. 2000. Application of PFGE performed with XbaI to an epidemiological and phylogenetic study of Salmonella serotype Typhimurium. Relations between genetic types and phage types. New Microbiol. 23:11-20.
17. Hillis, D. M., and J. P. Huelsenbeck. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. J. Hered. 83:189-195.
18. Hudson, C. R., M. Garcia, R. K. Gast, and J. J. Maurer. 2001. Determination of close genetic relatedness of the major Salmonella Enteritidis phage types by pulsed-field gel electrophoresis and DNA sequence analysis of several Salmonella virulence genes. Avian Dis. 45:875-886.
19. Hyytia-Trees, E., S. C. Smole, P. A. Fields, B. Swaminathan, and E. M. Ribot. 2006. Second generation subtyping: a proposed PulseNet protocol for multiple-locus variable-number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 (STEC O157). Foodborne Pathog. Dis. 3:118-131.
20. Jakobsen, I. B., and S. A. Eastal. 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput. Appl. Biosci. (Cambridge) 12:291-295.
21. Keim, P., M. N. Van Ert, T. Pearson, A. J. Vogler, L. Y. Huynh, and D. M. Wagner. 2004. Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect. Genet. Evol. 4:205-213.
22. Kingsley, R. A., and A. J. Baumler. 2000. Host adaptation and the emergence of infectious disease: the Salmonella paradigm. Mol. Microbiol. 36:1006-1014.
23. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
24. Lukinmaa, S., U. M. Nakari, M. Eklund, and A. Siitonen. 2004. Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens. APMIS 112:908-929.
25. Mead, P. S., L. Slutsker, V. Dietz, L. F. McCaig, J. S. Bresee, C. Shapiro, P. M. Griffin, and R. V. Tauxe. 1999. Food-related illness and death in the United States. Emerg. Infect. Dis. 5:607-625.
26. Nesse, L. L., K. Nordby, E. Heir, B. Bergsjoe, T. Vardund, H. Nygaard, and G. Holstad. 2003. Molecular analyses of Salmonella enterica isolates from fish feed factories and fish feed ingredients. Appl. Environ. Microbiol. 69:1075-1081.
27. Olsen, J. E., M. N. Skov, E. J. Threlfall, and D. J. Brown. 1994. Clonal lines of Salmonella enterica serotype Enteritidis documented by IS200-, ribo-, pulsed-field gel electrophoresis and RFLP typing. J. Med. Microbiol. 40:15-22.
28. Porwollik, S., and M. McClelland. 2003. Lateral gene transfer in Salmonella. Microbes Infect. 5:977-989.
29. Ribot, E. M., M. A. Fair, R. Gautom, D. N. Cameron, S. B. Hunter, B. Swaminathan, and T. J. Barrett. 2006. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog. Dis. 3:59-67.
30. Ridley, A. M., E. J. Threlfall, and B. Rowe. 1998. Genotypic characterization of Salmonella Enteritidis phage types by plasmid analysis, ribotyping, and pulsed-field gel electrophoresis. J. Clin. Microbiol. 36:2314-2321.
31. Saeed, A. M., S. T. Walk, M. Arshad, and T. S. Whittam. 2006. Clonal structure and variation in virulence of Salmonella Enteritidis isolated from mice, chickens, and humans. J. AOAC Int. 89:504-511.
32. Sandvang, D., F. M. Aarestrup, and L. B. Jensen. 1998. Characterisation of integrons and antibiotic resistance genes in Danish multiresistant Salmonella enterica Typhimurium DT104. FEMS Microbiol. Lett. 160:37-41.
33. Selander, R. K., J. Li, and K. Nelson. 1996. Evolutionary genetics of Salmonella enterica, p. 2691-2707. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, DC.
34. Shinkai, A., P. H. Patel, and L. A. Loeb. 2001. The conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable. J. Biol. Chem. 276:18836-18842.
35. Stanley, J., M. Goldsworthy, and E. J. Threlfall. 1992. Molecular phylogenetic typing of pandemic isolates of Salmonella enteritidis. FEMS Microbiol. Lett. 69:153-160.
36. 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.
37. Swofford, D. L. 1999. Phylogenetic analysis using parsimony (PAUP* v. 4.03b) program and documentation. The Smithsomian Institution, Washington, DC.
38. Ward, L. R., J. D. de Sa, and B. Rowe. 1987. A phage-typing scheme for Salmonella Enteritidis. Epidemiol. Infect. 99:291-294.
39. Whittam, T. S., and T. M. Bergholz. 2007. Molecular subtyping, source tracking, and food safety, p. 93-136. In J. W. Santo Domingo and M. J. Sadowsky (ed.), Microbial source tracking. American Society for Microbiology, Washington, DC.
40. Xi, M., J. Zheng, S. Zhao, E. W. Brown, and J. Meng. 2008. An enhanced discriminatory pulsed-field gel electrophoresis scheme for subtyping Salmonella serotypes Heidelberg, Kentucky, SaintPaul, and Hadar. J. Food Prot. 71:2067-2072.
41. Zheng, J., C. E. Keys, S. Zhao, J. Meng, and E. W. Brown. 2007. Enhanced subtyping scheme for Salmonella Enteritidis. Emerg. Infect. Dis. 13:1932-1935.