Microarray analysis and draft genomes of two escherichia coli O157:H7 lineage II cattle isolates FRIK966 and FRIK2000 investigating lack of shiga toxin expression

Foodborne Pathogens and Disease

Volumn 7, Issue 7, 2010, Pages 763-773

  Dowd, Scot E ^a   Crippen, Tawni L ^b   Sun, Yan ^a   Gontcharova, Viktoria ^a   Youn, Eun ^c   Muthaiyan, Arunachalam ^d   Wolcott, Randall D ^a   Callaway, Todd R ^b   Ricke, Steven C ^d  

^a Research and Testing Laboratory   (United States)

^b SOUTHERN PLAINS AGRICULTURAL RESEARCH CENTER   (United States)

^c Texas Tech University   (United States)

^d UNIVERSITY OF ARKANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SHIGA TOXIN; TRANSPOSON; VEROTOXIN 2;

ARTICLE; BACTERIAL STRAIN; BACTERIOPHAGE; BACTERIUM ISOLATE; CATTLE; CONTROLLED STUDY; ESCHERICHIA COLI O157; GENE EXPRESSION; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSPOSON; ANIMAL; BACTERIAL GENOME; BIOLOGY; BOVINAE; CHEMISTRY; CHROMOSOME MAP; CLASSIFICATION; COMPARATIVE STUDY; DNA MICROARRAY; DNA SEQUENCE; ESCHERICHIA COLI INFECTION; FOODBORNE DISEASES; GENE EXPRESSION REGULATION; GENE REARRANGEMENT; GENETICS; HUMAN; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID DATABASE; PODOVIRIDAE; PROCEDURES; PROPHAGE; VALIDATION STUDY; VIROLOGY; VIRULENCE;

ANIMALS; CATTLE; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI O157; FOODBORNE DISEASES; GENE EXPRESSION REGULATION, BACTERIAL; GENE REARRANGEMENT; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PODOVIRIDAE; PROPHAGES; SEQUENCE ANALYSIS, DNA; SHIGA TOXIN 2; SHIGA TOXINS; VIRULENCE;

EID: 77954482977     PISSN: 15353141     EISSN: None     Source Type: Journal    
DOI: 10.1089/fpd.2009.0482     Document Type: Article

References (53)

1. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-29.
2. Ateba CN and Bezuidenhout CC. Characterisation of Escherichia coli O157 strains from humans, cattle and pigs in the North- West Province, South Africa. Int J Food Microbiol 2008;128: 181-188.
3. Basu I, Ferens WA, Stone DM, et al. Antiviral activity of shiga toxin requires enzymatic activity and is associated with increased permeability of the target cells. Infect Immun 2003; 71:327-334.
4. Benjamini Y and Hochberg Y. Controlling the false discovery rate: a practival and powerful approach to multiple testing. JR Stat Soc B 1995;57:289-300.
5. Bergstrom CT, McElhany P, and Real LA. Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens. Proc Natl Acad Sci USA 1999;96:5095-5100.
6. Blattner FR, Plunkett G III, Bloch CA, et al. The complete genome sequence of Escherichia coli K-12. Science 1997;277: 1453-1462.
7. Boerlin P, McEwen SA, Boerlin-Petzold F, et al. Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans. J Clin Microbiol 1999;37:497-503.
8. Campbell A, Berg DE, Botstein D, et al. Nomenclature of transposable elements in prokaryotes. Gene 1979;5:197-206. (Pubitemid 9161867)
9. Charbonnier Y, Gettler B, Francois P, et al. A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics 2005;6:95.
10. Cheng J, Wang Q, Wang W, et al. Characterization of E. coli O24 and O56 O antigen gene clusters reveals a complex evolutionary history of the O24 gene cluster. Curr Microbiol 2006; 53:470-476.
11. Datz M, Janetzki-Mittmann C, Franke S, et al. Analysis of the enterohemorrhagic Escherichia coli O157 DNA region containing lambdoid phage gene p and Shiga-like toxin structural genes. Appl Environ Microbiol 1996;62:791-797.
12. Dennis G Jr., Sherman BT, Hosack DA, et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 2003;4:3.
13. Donohue-Rolfe A, Jacewicz M, and Keusch GT. Isolation and characterization of functional Shiga toxin subunits and renatured holotoxin. Mol Microbiol 1989;3:1231-1236.
14. Donohue-Rolfe A, Keusch GT, Edson C, et al. Pathogenesis of Shigella diarrhea. IX. Simplified high yield purification of Shigella toxin and characterization of subunit composition and function by the use of subunit-specific monoclonal and polyclonal antibodies. J Exp Med 1984;160:1767-1781.
15. Donohue-Rolfe A, Kondova I, Oswald S, et al. Escherichia coli O157:H7 strains that express Shiga toxin (Stx) 2 alone are more neurotropic for gnotobiotic piglets than are isotypes producing only Stx1 or both Stx1 and Stx2. J Infect Dis 2000;181:1825- 1829.
16. Dowd SE. HTGOFAT: high throughput functional annotation toolkit. 2005. Available at http:==liru.ars.usda.gov=mainbio informatics.html.
17. Dowd SE and Ishizaki H. Microarray based comparison of two Escherichia coli O157:H7 lineages. BMC Microbiol 2006;6:30.
18. Dowd SE and Williams JB. Comparison of Shiga-like toxin II expression between two genetically diverse lineages of Escherichia coli O157:H7. J Food Prot 2008;71:1673-1678.
19. du-Bobie J, Frankel G, Bain C, et al. Detection of intimins alpha, beta, gamma, and delta, four intimin derivatives expressed by attaching and effacing microbial pathogens. J Clin Microbiol 1998;36:662-668.
20. Ferens WA, Cobbold R, and Hovde CJ. Intestinal Shiga toxinproducing Escherichia coli bacteria mitigate bovine leukemia virus infection in experimentally infected sheep. Infect Immun 2006;74:2906-2916.
21. Ferens WA and Hovde CJ. Antiviral activity of shiga toxin 1: suppression of bovine leukemia virus-related spontaneous lymphocyte proliferation. Infect Immun 2000;68:4462-4469.
22. Frankel G, Phillips AD, Rosenshine I, et al. Enteropathogenic and enterohaemorrhagic Escherichia coli: more subversive elements. Mol Microbiol 1998;30:911-921.
23. Hayashi T, Makino K, Ohnishi M, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001;8:11-22.
24. Hendrix RW, Smith MC, Burns RN, et al. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 1999;96:2192-2197.
25. Huang A, de GS, Friesen J, et al. Cloning and expression of the genes specifying Shiga-like toxin production in Escherichia coli H19. J Bacteriol 1986;166:375-379.
26. Jacewicz M, Clausen H, Nudelman E, et al. Pathogenesis of shigella diarrhea. XI. Isolation of a shigella toxin-binding glycolipid from rabbit jejunum and HeLa cells and its identification as globotriaosylceramide. J Exp Med 1986;163:1391-1404.
27. Johansen BK, Wasteson Y, Granum PE, et al. Mosaic structure of Shiga-toxin-2-encoding phages isolated from Escherichia coli O157:H7 indicates frequent gene exchange between lambdoid phage genomes. Microbiology 2001;147:1929-1936. (Pubitemid 32684934)
28. Karch H, Schmidt H, Janetzki-Mittmann C, et al. Shiga toxins even when different are encoded at identical positions in the genomes of related temperate bacteriophages. Mol Gen Genet 1999;262:600-607.
29. Kim J, Nietfeldt J, and Benson AK. Octamer-based genome scanning distinguishes a unique subpopulation of Escherichia coli O157:H7 strains in cattle. Proc Natl Acad Sci USA 1999;96:13288-13293.
30. Kobayashi H, Shimada J, Nakazawa M, et al. Prevalence and characteristics of shiga toxin-producing Escherichia coli from healthy cattle in Japan. Appl Environ Microbiol 2001;67:484-489.
31. Laing C, Pegg C, Yawney D, et al. Rapid determination of Escherichia coli O157:H7 lineage types and molecular subtypes by using comparative genomic fingerprinting. Appl Environ Microbiol 2008;74:6606-6615.
32. Laing CR, Buchanan C, Taboada EN, et al. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence. BMC Genomics 2009;10:287.
33. Lawrence JG and Ochman H. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 1998;95:9413-9417.
34. LeJeune JT, Abedon ST, Takemura K, et al. Human Escherichia coli O157:H7 genetic marker in isolates of bovine origin. Emerg Infect Dis 2004;10:1482-1485.
35. Lowe RM, Baines D, Selinger LB, et al. Escherichia coli O157:H7 strain origin, lineage, and Shiga toxin 2 expression affect colonization of cattle. Appl Environ Microbiol 2009;75:5074-5081.
36. Markowitz VM, Korzeniewski F, Palaniappan K, et al. The integrated microbial genomes (IMG) system. Nucleic Acids Res 2006;34:D344-D348.
37. Markowitz VM and Kyrpides NC. Comparative genome analysis in the integrated microbial genomes (IMG) system. Methods Mol Biol 2007;395:35-56.
38. Mellies JL, Elliott SJ, Sperandio V, et al. The Per regulon of enteropathogenic Escherichia coli: identification of a regulatory cascade and a novel transcriptional activator, the locus of enterocyte effacement (LEE)-encoded regulator (Ler). Mol Microbiol 1999;33:296-306.
39. Muhldorfer I, Hacker J, Keusch GT, et al. Regulation of the Shiga-like toxin II operon in Escherichia coli. Infect Immun 1996;64:495-502.
40. O'Brien AD, Newland JW, Miller SF, et al. Shiga-like toxinconverting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Science 1984;226: 694-696.
41. Ogata H, Goto S, Sato K, et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999;27:29-34.
42. Paton AW, Ratcliff RM, Doyle RM, et al. Molecular microbiological investigation of an outbreak of hemolytic-uremic syndrome caused by dry fermented sausage contaminated with Shiga-like toxin-producing Escherichia coli. J Clin Microbiol 1996;34:1622-1627.
43. Paton JC and Paton AW. Pathogenesis and diagnosis of Shiga toxin-producing Escherichia coli infections. Clin Microbiol Rev 1998;11:450-479.
44. Perna NT, Plunkett G III, Burland V, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 2001;409: 529-533. (Pubitemid 32144360)
45. Plunkett G III, Rose DJ, Durfee TJ, et al. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J Bacteriol 1999;181:1767-1778.
46. Riley LW, Remis RS, Helgerson SD, et al. Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med 1983;308:681-685.
47. Steele M, Ziebell K, Zhang Y, et al. Genomic regions conserved in lineage II Escherichia coli O157:H7 strains. Appl Environ Microbiol 2009;75:3271-3280.
48. Stephan R, Zhang W, Bielaszewska M, et al. Phenotypic and genotypic traits of Shiga toxin-negative E. coli O157:H7=H(-) bovine and porcine strains. Foodborne Pathog Dis 2009;6:235-243.
49. Tyler JS, Mills MJ, and Friedman DI. The operator and early promoter region of the Shiga toxin type 2-encoding bacteriophage 933W and control of toxin expression. J Bacteriol 2004; 186:7670-7679.
50. Unkmeir A and Schmidt H. Structural analysis of phage-borne stx genes and their flanking sequences in shiga toxin-producing Escherichia coli and Shigella dysenteriae type 1 strains. Infect Immun 2000;68:4856-4864.
51. Waddell T, Head S, Petric M, et al. Globotriosyl ceramide is specifically recognized by the Escherichia coli verocytotoxin 2. Biochem Biophys Res Commun 1988;152:674-679.
52. Wagner PL, Neely MN, Zhang X, et al. Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain. J Bacteriol 2001;183:2081-2085.
53. Yaron S, Kolling GL, Simon L, et al. Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. Appl Environ Microbiol 2000;66:4414-4420.