Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray

Journal of Bacteriology

Volumn 185, Issue 2, 2003, Pages 553-563

  Chan, Kaman ^b   Baker, Stephen ^a   Kim, Charles C ^b   Detweiler, Corrella S ^b   Dougan, Gordon ^a   Falkow, Stanley ^b  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ADAPTATION; ARTICLE; BACTERIAL GENOME; DISEASE COURSE; DNA MICROARRAY; ENZYME ELECTROPHORESIS; NONHUMAN; PATHOGENICITY; PHYLOGENY; PRIORITY JOURNAL; SALMONELLA; SALMONELLA BONGORI; SALMONELLA ENTERICA; SALMONELLA TYPHIMURIUM; SEROTYPE;

BACTERIAL PROTEINS; GENOME, BACTERIAL; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA TYPHIMURIUM; SENSITIVITY AND SPECIFICITY; SEROTYPING;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; SALMONELLA BONGORI; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM; SALMONELLA TYPHIMURIUM; TYPHIMURIUM;

EID: 0037224655     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.2.553-563.2003     Document Type: Article

References (58)

1. Affolter, M., C. Parent-Vaugeois, and A. Anderson. 1983. Curing and induction of the Fels 1 and Fels 2 prophages in the Ames mutagen tester strains of Samonella typhimurium. Mutat. Res. 110:243-262.
2. Ausubel, F. M. 1995. Preparation of genomic DNA from bacteria, p. 2.11-2.22. In F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.), Short protocols in molecular biology, 3rd ed. John Wiley & Sons, Inc., New York, N.Y.
3. 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.
4. Baumler, A. J., R. M. Tsolis, and F. Heffron. 1996. Contribution of fimbrial operons to attachment to and invasion of epithelial cell lines by Salmonella typhimurium. Infect. Immun. 64:1862-1865.
5. Baumler, A. J., R. M. Tsolis, and F. Heffron. 1996. The lpf fimbrial operon mediates adhesion of Salmonella typhimurium to murine Peyer's patches. Proc. Natl. Acad. Sci. USA 93:279-283.
6. Beltran, P., J. M. Musser, R. Helmuth, J. J. Farmer III, W. M. Frerichs, I. K. Wachsmuth, K. Ferris, A. C. McWhorter, J. G. Wells, A. Cravioto, et al. 1988. Toward a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S. choleraesuis, S. derby, S. dublin, S. enteritidis, S. heidelberg, S. infantis, S. newport, and S. typhimurium. Proc. Natl. Acad. Sci. USA 85:7753-7757.
7. Beltran, P., S. A. Plock, N. H. Smith, T. S. Whittam, D. C. Old, and R. K. Selander. 1991. Reference collection of strains of the Salmonella typhimurium complex from natural populations. J. Gen. Microbiol. 137(Pt. 3): 601-606.
8. Boyd, E. F., and D. L. Hartl. 1998. Salmonella virulence plasmid: modular acquisition of the spv virulence region by an F-plasmid in Salmonella enterica subspecies I and insertion into the chromosome of subspecies II, IIIa, IV and VII isolates. Genetics 149:1183-1190.
9. Boyd, E. F., F. S. Wang, P. Beltran, S. A. Plock, K. Nelson, and R. K. Selander. 1993. Salmonella reference collection B (SARB): strains of 37 serovars of subspecies I. J. Gen. Microbiol. 139(Pt. 6):1125-1132.
10. Boyd, E. F., F. S. Wang, T. S. Whittam, and R. K. Selander. 1996. Molecular genetic relationships of the salmonellae. Appl. Environ. Microbiol. 62:804-808.
11. Canvin, J., P. R. Langford, K. E. Wilks, and J. S. Kroll. 1996. Identification of sodC encoding periplasmic [Cu,Zn]-superoxide dismutase in Salmonella. FEMS Microbiol. Lett. 136:215-220.
12. Collier-Hyams, L. S., H. Zeng, J. Sun, A. D. Tomlinson, Z. Q. Bao, H. Chen, J. L. Madara, K. Orth, and A. S. Neish. 2002. Cutting edge: Salmonella AvrA effector inhibits the key proinflammatory, anti-apoptotic NF-κB pathway. J. Immunol. 169:2846-2850.
13. Crosa, J. H., D. J. Brenner, W. H. Ewing, and S. Falkow. 1973. Molecular relationships among the salmonellae. J. Bacteriol. 115:307-315.
14. Edwards, R. A., G. J. Olsen, and S. R. Maloy. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol. 10:94-99.
15. Eisen, M. B., and P. O. Brown. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303:179-205.
16. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868.
17. Fang, F. C., M. A. DeGroote, J. W. Foster, A. J. Baumler, U. Ochsner, T. Testerman, S. Bearson, J. C. Giard, Y. Xu, G. Campbell, and T. Laessig. 1999. Virulent Salmonella typhimurium has two periplasmic Cu,Zn-superoxide dismutases. Proc. Natl. Acad. Sci. USA 96:7502-7507.
18. Farrant, J. L., A. Sansone, J. R. Canvin, M. J. Pallen, P. R. Langford, T. S. Wallis, G. Dougan, and J. S. Kroll. 1997. Bacterial copper- and zinc-cofactored superoxide dismutase contributes to the pathogenesis of systemic salmonellosis. Mol. Microbiol. 25:785-796.
19. Fierer, J., and D. G. Guiney. 2001. Diverse virulence traits underlying different clinical outcomes of Salmonella infection. J. Clin. Investig. 107:775-780.
20. Figueroa-Bossi, N., E. Coissac, P. Netter, and L. Bossi. 1997. Unsuspected prophage-like elements in Salmonella typhimurium. Mol. Microbiol. 25:161-173.
21. Figueroa-Bossi, N., S. Uzzau, D. Maloriol, and L. Bossi. 2001. Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Mol. Microbiol. 39:260-271.
22. Fitzgerald, J. R., and J. M. Musser. 2001. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 9:547-553.
23. Groisman, E. A., and H. Ochman. 1996. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87:791-794.
24. Hall, M. L., and B. Rowe. 1992. Salmonella arizonae in the United Kingdom from 1966 to 1990. Epidemiol. Infect. 108:59-65.
25. Hansen-Wester, I., and M. Hensel. 2001. Salmonella pathogenicity islands encoding type III secretion systems. Microbes Infect. 3:549-559.
26. Hardt, W. D., and J. E. Galan. 1997. A secreted Salmonella protein with homology to an avirulence determinant of plant pathogenic bacteria. Proc. Natl. Acad. Sci. USA 94:9887-9892.
27. Joyce, E. A., K. Chan, N. Salama, and S. Falkow. 2002. Redefining bacterial populations: a post-genomic reformation. Nat. Rev. Genet. 3:462-473.
28. Kim, C. C., E. A. Joyce, K. Chan, and S. Falkow. 2002. Improved analytical methods for microarray-based genome-composition analysis. Genome Biol. 3:RESEARCH0065.
29. Lawrence, J. G., and J. R. Roth. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860.
30. Leach, J. E., and F. F. White. 1996. Bacterial avirulence genes. Annu. Rev. Phytopathol. 64:156-179.
31. Le Minor, L., M. Y. Popoff, B. Laurent, and D. Hermant. 1986. Characterization of a 7th subspecies of Salmonella: S. choleraesuis subsp. indica subsp. nov. Ann. Inst. Pasteur Microbiol. 137B:211-217.
32. Le Minor, L., M. Veron, and M. Popoff. 1982. The taxonomy of Salmonella. Ann. Microbiol. 133:223-243.
33. Li, J., N. H. Smith, K. Nelson, P. B. Crichton, D. C. Old, T. S. Whittam, and R. K. Selander. 1993. Evolutionary origin and radiation of the avian-adapted non-motile salmonellae. J. Med. Microbiol. 38:129-139.
34. Libby, S. J., M. Lesnick, P. Hasegawa, M. Kurth, C. Belcher, J. Fierer, and D. G. Guiney. 2002. Characterization of the spv locus in Salmonella enterica serovar Arizona. Infect. Immun. 70:3290-3294.
35. Marcus, S. L., J. H. Brumell, C. G. Pfeifer, and B. B. Finlay. 2000. Salmonella pathogenicity islands: big virulence in small packages. Microbes Infect. 2:145-156.
36. McClelland, M., K. E. Sanderson, J. Spieth, S. W. Clifton, P. Latreille, L. Courtney, S. Porwollik, J. Ali, M. Dante, F. Du, S. Hou, D. Layman, S. Leonard, C. Nguyen, K. Scott, A. Holmes, N. Grewal, E. Mulvaney, E. Ryan, H. Sun, L. Florea, W. Miller, T. Stoneking, M. Nhan, R. Waterston, and R. K. Wilson. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
37. Ochman, H., and E. A. Groisman. 1996. Distribution of pathogenicity islands in Salmonella spp. Infect. Immun. 64:5410-5412.
38. Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
39. Orth, K. 2002. Function of the Yersinia effector YopJ. Curr. Opin. Microbiol. 5:38-43.
40. Parkhill, J., G. Dougan, K. D. James, N. R. Thomson, D. Pickard, J. Wain, C. Churcher, K. L. Mungall, S. D. Bentley, M. T. Holden, M. Sebaihia, S. Baker, D. Basham, K. Brooks, T. Chillingworth, P. Connerton, A. Cronin, P. Davis, R. M. Davies, L. Dowd, N. White, J. Farrar, T. Feltwell, N. Hamlin, A. Haque, T. T. Hien, S. Holroyd, K. Jagels, A. Krogh, T. S. Larsen, S. Leather, S. Moule, P. O'Gaora, C. Parry, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848-852.
41. Porwollik, S., R. M. Wong, and M. McClelland. 2002. Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:8956-8961.
42. Prager, R., S. Mirold, E. Tietze, U. Strutz, B. Knuppel, W. Rabsch, W. D. Hardt, and H. Tschape. 2000. Prevalence and polymorphism of genes encoding translocated effector proteins among clinical isolates of Salmonella enterica. Int. J. Med. Microbiol. 290:605-617.
43. Rabsch, W., H. L. Andrews, R. A. Kingsley, R. Prager, H. Tschape, L. G. Adams, and A. J. Baumler. 2002. Salmonella enterica serotype Typhimurium and its host-adapted variants. Infect. Immun. 70:2249-2255.
44. Raetz, C. R. H. 1996. Bacterial lipopolysaccharides: a remarkable family of bioactive macroamphiphiles, p. 1035-1063. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 1. ASM Press, Washington, D.C.
45. Reeves, M. W., G. M. Evins, A. A. Heiba, B. D. Plikaytis, and J. J. Farmer III. 1989. Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov. J. Clin. Microbiol. 27:313-320.
46. Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132:365-386.
47. Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacterpylori strains. Proc. Natl. Acad. Sci. USA 97:14668-14673.
48. Salzberg, S. L., A. L. Delcher, S. Kasif, and O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:544-548.
49. Sanderson, K. E., A. Hessel, and B. A. D. Stocker. 1996. Strains of Salmonella typhimurium and other Salmonella species used in genetic analysis, p. 2496-2503. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
50. Sansone, A., P. R. Watson, T. S. Wallis, P. R. Langford, and J. S. Kroll. 2002. The role of two periplasmic copper- and zinc-cofactored superoxide dismutases in the virulence of Salmonella choleraesuis. Microbiology 148:719-726.
51. Selander, R. K., P. Beltran, N. H. Smith, R. Helmuth, F. A. Rubin, D. J. Kopecko, K. Ferris, B. D. Tall, A. Cravioto, and J. M. Musser. 1990. Evolutionary genetic relationships of clones of Salmonella serovars that cause human typhoid and other enteric fevers. Infect. Immun. 58:2262-2275.
52. Selander, R. K., D. A. Caugant, H. Ochman, J. M. Musser, M. N. Gilmour, and T. S. Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51:873-884.
53. Selander, R. K., L. J., and K. Nelson. 1996. Evolutionary genetics of Salmonella enterica, p. 2691-2707. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
54. Sherlock, G., T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J. C. Matese, S. S. Dwight, M. Kaloper, S. Weng, H. Jin, C. A. Ball, M. B. Eisen, P. T. Spellman, P. O. Brown, D. Botstein, and J. M. Cherry. 2001. The Stanford microarray database. Nucleic Acids Res. 29:152-155.
55. Smith, B. P., M. Reina-Guerra, S. K. Hoiseth, B. A. Stocker, F. Habasha, E. Johnson, and F. Merritt. 1984. Aromatic-dependent Salmonella typhimurium as modified live vaccines for calves. Am. J. Vet. Res. 45:59-66.
56. Sulkin, S. E., and J. C. Willett. 1940. A triple sugar-ferrous sulfate medium for use in identification of enteric organisms. J. Lab. Clin. Med. 25:649-653.
57. Townsend, S. M., N. E. Kramer, R. Edwards, S. Baker, N. Hamlin, M. Simmonds, K. Stevens, S. Maloy, J. Parkhill, G. Dougan, and A. J. Baumler. 2001. Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences. Infect. Immun. 69:2894-2901.
58. Weiss, S. H., M. J. Blaser, F. P. Paleologo, R. E. Black, A. C. McWhorter, M. A. Asbury, G. P. Carter, R. A. Feldman, and D. J. Brenner. 1986. Occurrence and distribution of serotypes of the Arizona subgroup of Salmonella strains in the United States from 1967 to 1976. J. Clin. Microbiol. 23:1056-1064.