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Chapter 2 : Understanding the Model and the Menace: a Postgenomic View of

Authors: Roy R. Chaudhuri1, Gavin H. Thomas2
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Affiliations: 1: Division of Immunity and Infection, IBR West, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; 2: Department of Biology, Area 10, University of York, P.O. Box 373, York YO10 5YW, United Kingdom
Content Type: Monograph
Publication Year: 2007

Category: Genomics and Bioinformatics; Bacterial Pathogenesis

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Abstract:

This chapter discusses the insights into pathogenicity and the wider processes of genome evolution that have resulted from the sequencing of the K-12 genome, and, more recently, those from a number of pathogenic strains, including several from the related “genus” . It also discusses the available resources for genomics and the progress that has been made in recent years toward a complete understanding of biology. Genes that are acquired by horizontal transfer subsequently undergo a process of amelioration as their base composition becomes acclimatized to the new host. Programs such as BLAST can be used to identify unexpected similarities between genes in phylogenetically distinct species, although it should be noted that BLAST results do not necessarily correspond to those from more robust phylogenetic analyses. Interestingly, strains classified as group B2 are rarely found as human commensals, and the group includes many strains with extraintestinal pathogenic (ExPEC) virulence determinants. As with enterohemorrhagic (EHEC) O157:H7, serotype 2a was an obvious target for whole-genome sequencing because of its importance as a pathogen. The processes of genome evolution are clear from the genome sequences already available.

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
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Understanding the Model and the Menace: a Postgenomic View of Escherichia coli
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Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
/content/10.1128/9781555815530.ch02.ch02fig01
FIGURE 1
Phylogenetic relationships between the strains in the ECOR collection, as assessed by MLEE ( ). Data were obtained from http://foodsafe.msu.edu/whittam, and a neighbor-joining tree was generated by neighbor, part of the PHYLIP package. The tree was rooted using group B2 as an outgroup ( ).
10.1128/9781555815530/f0026-01_thmb.gif
10.1128/9781555815530/f0026-01.gif
Image of FIGURE 1
FIGURE 1

Phylogenetic relationships between the strains in the ECOR collection, as assessed by MLEE ( ). Data were obtained from http://foodsafe.msu.edu/whittam, and a neighbor-joining tree was generated by neighbor, part of the PHYLIP package. The tree was rooted using group B2 as an outgroup ( ).

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
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References

/content/book/10.1128/9781555815530.ch02
1. Abbott, J. C.,, D. M. Aanensen,, K. Rutherford,, S. Butcher, and, B. G. Spratt. 2005. WebACT—an online companion for the Artemis Comparison Tool. Bioinformatics 21: 3665– 3666.
2. Aiba, H.,, T. Baba,, K. Hayashi,, T. Inada,, K. Isono,, T. Itoh,, H. Kasai,, K. Kashimoto,, S. Kimura,, M. Kitakawa,, M. Kitagawa,, K. Makino,, T. Miki,, K. Mizobuchi,, H. Mori,, T. Mori,, K. Motomera,, S. Nakade,, Y. Nakamura,, H. Nashimoto,, Y. Nishio,, T. Oshima,, N. Saito,, G. Sampei, and, T. Horiuchi. 1996. A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0–40.1 min region on the linkage map (supplement). DNA Res. 3: 435– 440.
3. Altschul, S. F.,, T. L. Madden,, A. A. Schaffer,, J. Zhang,, Z. Zhang,, W. Miller, and, D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389– 3402.
4. Anjum, M. F.,, S. Lucchini,, A. Thompson,, J. C. Hinton, and, M. J. Woodward. 2003. Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens. Infect. Immun. 71: 4674– 4683.
5. Arnold, C.,, L. Metherell,, G. Willshaw,, A. Maggs, and, J. Stanley. 1999. Predictive fluorescent amplified-fragment length polymorphism analysis of Escherichia coli: high-resolution typing method with phylogenetic significance. J. Clin. Microbiol. 37: 1274– 1279.
6. Baba, T.,, T. Ara,, M. Hasegawa,, Y. Takai,, Y. Okumura,, M. Baba,, K. A. Datsenko,, M. Tomita,, B. L. Wanner, and, H. Mori. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2: 2006.0008.
7. Bachmann, B. J. 1996. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, p. 2460–2488. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, DC.
8. Beinke, C.,, S. Laarmann,, C. Wachter,, H. Karch,, L. Greune, and, M. A. Schmidt. 1998. Diffusely adhering Escherichia coli strains induce attaching and effacing phenotypes and secrete homologs of Esp proteins. Infect. Immun. 66: 528– 539.
9. Bergthorsson, U., and, H. Ochman. 1998. Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol. Biol. Evol. 15: 6– 16.
10. Bergthorsson, U., and, H. Ochman. 1995. Heterogeneity of genome sizes among natural isolates of Escherichia coli. J. Bacteriol. 177: 5784– 5789.
11. Bingen, E.,, B. Picard,, N. Brahimi,, S. Mathy,, P. Desjardins,, J. Elion, and, E. Denamur. 1998. Phylogenetic analysis of Escherichia coli strains causing neonatal meningitis suggests horizontal gene transfer from a predominant pool of highly virulent B2 group strains. J. Infect. Dis. 177: 642– 650.
12. Blattner, F. R. 1983. Biological frontiers. Science 222: 719– 720.
13. Blattner, F. R.,, V. Burland,, G. Plunkett III,, H. J. Sofia, and, D. L. Daniels. 1993. Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 21: 5408– 5417.
14. 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. May-hew,, 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.
15. Boyd, E. F., and, D. L. Hartl. 1998. Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J. Bacteriol. 180: 1159– 1165.
16. Brenner, D. J.,, G. R. Fanning,, F. J. Skerman, and, S. Falkow. 1972. Polynucleotide sequence divergence among strains of Escherichia coli and closely related organisms. J. Bacteriol. 109: 953– 965.
17. Burland, V.,, G. Plunkett III,, D. L. Daniels, and, F. R. Blattner. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16: 551– 561.
18. Burland, V.,, G. Plunkett III,, H. J. Sofia,, D. L. Daniels, and, F. R. Blattner. 1995. Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res. 23: 2105– 2119.
19. Burland, V.,, Y. Shao,, N. T. Perna,, G. Plunkett,, H. J. Sofia, and, F. R. Blattner. 1998. The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res. 26: 4196– 4204.
20. Carver, T. J.,, K. M. Rutherford,, M. Berriman,, M. A. Rajandream,, B. G. Barrell, and, J. Parkhill. 2005. ACT: the Artemis comparison tool. Bioinformatics 21: 3422– 3423.
21. Casalino, M.,, M. C. Latella,, G. Prosseda, and, B. Colonna. 2003. CadC is the preferential target of a convergent evolution driving enteroinvasive Escherichia coli toward a lysine decarboxylase-defective phenotype. Infect. Immun. 71: 5472– 5479.
22. Chaudhuri, R. R.,, A. M. Khan, and, M. J. Pallen. 2004. coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Res. 32 (Database issue): D296– D299.
23. Chaudhuri, R. R., and, M. J. Pallen. 2006. xBASE, a collection of online databases for bacterial comparative genomics. Nucleic Acids Res. 34: D335– D337.
24. Chen, S. L.,, C. S. Hung,, J. Xu,, C. S. Reigstad,, V. Magrini,, A. Sabo,, D. Blasiar,, T. Bieri,, R. R. Meyer,, P. Ozersky,, J. R. Armstrong,, R. S. Fulton,, J. P. Latreille,, J. Spieth,, T. M. Hooton,, E. R. Mardis,, S. J. Hultgren, and, J. I. Gordon. 2006. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. USA 103: 5977– 5982.
25. Clermont, O.,, S. Bonacorsi, and, E. Bingen. 2001. The Yersinia high-pathogenicity island is highly predominant in virulence-associated phylogenetic groups of Escherichia coli. FEMS Microbiol. Lett. 196: 153– 157.
26. Czeczulin, J. R.,, T. S. Whittam,, I. R. Henderson,, F. Navarro-Garcia, and, J. P. Nataro. 1999. Phylogenetic analysis of enteroaggregative and diffusely adherent Escherichia coli. Infect. Immun. 67: 2692– 2699.
27. Daniels, D. L.,, G. Plunkett III,, V. Burland, and, F. R. Blattner. 1992. Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257: 771– 778.
28. Day, W. A., Jr.,, R. E. Fernandez, and, A. T. Maurelli. 2001. Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp. Infect. Immun. 69: 7471– 7480.
29. Delcher, A. L.,, A. Phillippy,, J. Carlton, and, S. L. Salzberg. 2002. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30: 2478– 2483.
30. Dho-Moulin, M., and, J. M. Fairbrother. 1999. Avian pathogenic Escherichia coli (APEC). Vet. Res. 30: 299– 316.
31. Diamant, E.,, Y. Palti,, R. Gur-Arie,, H. Cohen,, E. M. Hallerman, and, Y. Kashi. 2004. Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci. Appl. Environ. Microbiol. 70: 2464– 2473.
32. Dixon, B. 1998. E. coli’s double life. ASM News 64: 616– 617.
33. Dobrindt, U.,, F. Agerer,, K. Michaelis,, A. Janka,, C. Buchrieser,, M. Samuelson,, C. Svanborg,, G. Gottschalk,, H. Karch, and, J. Hacker. 2003. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J. Bacteriol. 185: 1831– 1840.
34. Duriez, P.,, O. Clermont,, S. Bonacorsi,, E. Bingen,, A. Chaventre,, J. Elion,, B. Picard, and, E. Denamur. 2001. Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Micro-biology 147: 1671– 1676.
35. Escherich, T. 1885. Die Darmbakterien des Neugeborenen und Säuglings. Fortsch. Med. 3: 515– 522, 547– 554.
36. Escherich, T. 1989. The intestinal bacteria of the neonate and breast-fed infant. 1885. Rev. Infect. Dis. 11: 352– 356.
37. Escobar-Paramo, P.,, O. Clermont,, A. B. Blanc-Potard,, H. Bui,, C. Le Bouguenec, and, E. Denamur. 2004. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21: 1085– 1094.
38. Escobar-Paramo, P.,, C. Giudicelli,, C. Parsot, and, E. Denamur. 2003. The evolutionary history of Shigella and enteroinvasive Escherichia coli revised. J. Mol. Evol. 57: 140– 148.
39. Florea, L.,, M. McClelland,, C. Riemer,, S. Schwartz, and, W. Miller. 2003. EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae. Nucleic Acids Res. 31: 3527– 3532.
40. Fujita, N.,, H. Mori,, T. Yura, and, A. Ishihama. 1994. Systematic sequencing of the Escherichia coli genome: analysis of the 2.4–4.1 min (110, 917– 193, 643 bp) region. Nucleic Acids Res. 22: 1637– 1639.
41. Fukiya, S.,, H. Mizoguchi,, T. Tobe, and, H. Mori. 2004. Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J. Bacteriol. 186: 3911– 3921.
42. Glasner, J. D.,, P. Liss,, G. Plunkett III,, A. Darling,, T. Prasad,, M. Rusch,, A. Byrnes,, M. Gilson,, B. Biehl,, F. R. Blattner, and, N. T. Perna. 2003. ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31: 147– 151.
43. Hall, B. G.,, L. L. Parker,, P. W. Betts,, R. F. Du-Bose,, S. A. Sawyer, and, D. L. Hartl. 1989. IS103, a new insertion element in Escherichia coli: characterization and distribution in natural populations. Genetics 121: 423– 431.
44. Hall, B. G., and, P. M. Sharp. 1992. Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates. Mol. Biol. Evol. 9: 654– 665.
45. Hartleib, S.,, R. Prager,, I. Hedenstrom,, S. Lofdahl, and, H. Tschape. 2003. Prevalence of the new, SPI1-like, pathogenicity island ETT2 among Escherichia coli. Int. J. Med. Microbiol. 292: 487– 493.
46. Hayashi, K.,, N. Morooka,, Y. Yamamoto,, K. Fujita,, K. Isono,, S. Choi,, E. Ohtsubo,, T. Baba,, B. L. Wanner,, H. Mori, and, T. Horiuchi. 2006. Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Sys. Biol. 2: E1– E5.
47. Hayashi, T.,, K. Makino,, M. Ohnishi,, K. Kurokawa,, K. Ishii,, K. Yokoyama,, C. G. Han,, E. Ohtsubo,, K. Nakayama,, T. Murata,, M. Tanaka,, T. Tobe,, T. Iida,, H. Takami,, T. Honda,, C. Sasakawa,, N. Ogasawara,, T. Ya-sunaga,, S. Kuhara,, T. Shiba,, M. Hattori, and, H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8: 11– 22.
48. Henderson, I. R.,, J. Czeczulin,, C. Eslava,, F. Noriega, and, J. P. Nataro. 1999. Characterization of Pic, a secreted protease of Shigella flexneri and enteroaggregative Escherichia coli. Infect. Immun. 67: 5587– 5596.
49. Herzer, P. J.,, S. Inouye,, M. Inouye, and, T. S. Whittam. 1990. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J. Bacteriol. 172: 6175– 6181.
50. Hill, C. W.,, G. Feulner,, M. S. Brody,, S. Zhao,, A. B. Sadosky, and, C. H. Sandt. 1995. Correlation of Rhs elements with Escherichia coli population structure. Genetics 141: 15– 24.
51. Hill, C. W., and, B.W. Harnish. 1981. Inversions between ribosomal RNA genes of Escherichia coli. Proc. Natl. Acad. Sci. USA 78: 7069– 7072.
52. Hinton, J. C. 1997. The Escherichia coli genome sequence: the end of an era or the start of the FUN? Mol. Microbiol. 26: 417– 422.
53. Ideses, D.,, U. Gophna,, Y. Paitan,, R. R. Chaudhuri,, M. J. Pallen, and, E. Z. Ron. 2005. A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis. J. Bacteriol. 187: 8164– 8171.
54. Itoh, T.,, H. Aiba,, T. Baba,, K. Hayashi,, T. Inada,, K. Isono,, H. Kasai,, S. Kimura,, M. Kitakawa,, M. Kitagawa,, K. Makino,, T. Miki,, K. Mizobuchi,, H. Mori,, T. Mori,, K. Motomura,, S. Nakade,, Y. Nakamura,, H. Nashimoto,, Y. Nishio,, T. Oshima,, N. Saito,, G. Sampei,, Y. Seki, and, T. Horiuchi. 1996. A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1–50.0 min region on the linkage map (supplement). DNA Res. 3: 441– 445.
55. Jin, Q.,, Z. Yuan,, J. Xu,, Y. Wang,, Y. Shen,, W. Lu,, J. Wang,, H. Liu,, J. Yang,, F. Yang,, X. Zhang,, J. Zhang,, G. Yang,, H. Wu,, D. Qu,, J. Dong,, L. Sun,, Y. Xue,, A. Zhao,, Y. Gao,, J. Zhu,, B. Kan,, K. Ding,, S. Chen,, H. Cheng,, Z. Yao,, B. He,, R. Chen,, D. Ma,, B. Qiang,, Y. Wen,, Y. Hou, and, J. Yu. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30: 4432– 4441.
56. Johnson, J. R., and, M. Kuskowski. 2000. Clonal origin, virulence factors, and virulence. Infect. Immun. 68: 424– 425.
57. Kaper, J. B.,, J. P. Nataro, and, H. L. Mobley. 2004. Pathogenic Escherichia coli. Nat. Rev. Micro-biol. 2: 123– 140.
58. Karp, P. D.,, M. Riley,, M. Saier,, I. T. Paulsen,, J. Collado-Vides,, S. M. Paley,, A. Pellegrini-Toole,, C. Bonavides, and, S. Gama-Castro. 2002. The EcoCyc Database. Nucleic Acids Res. 30: 56– 58.
59. Koski, L. B., and, G. B. Golding. 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52: 540– 542.
60. Koski, L. B.,, R. A. Morton, and, G. B. Golding. 2001. Codon bias and base composition are poor indicators of horizontally transferred genes. Mol. Biol. Evol. 18: 404– 412.
61. Kroger, M., and, R. Wahl. 1998. Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC. Nucleic Acids Res. 26: 46– 49.
62. Kyaw, C. M.,, C. R. De Araujo,, M. R. Lima,, E. G. Gondim,, M. M. Brigido, and, L. G. Giugliano. 2003. Evidence for the presence of a type III secretion system in diffusely adhering Escherichia coli (DAEC). Infect. Genet. Evol. 3: 111– 117.
63. Labat, F.,, O. Pradillon,, L. Garry,, M. Peuchmaur,, B. Fantin, and, E. Denamur. 2005. Mutator phenotype confers advantage in Escherichia coli chronic urinary tract infection pathogenesis. FEMS Immunol. Med. Microbiol. 44: 317– 321.
64. Lan, R.,, M. C. Alles,, K. Donohoe,, M. B. Martinez, and, P. R. Reeves. 2004. Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp. Infect. Immun. 72: 5080– 5088.
65. Lan, R., and, P. R. Reeves. 2002. Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect. 4: 1125– 1132.
66. Lawrence, J. G., and, H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44: 383– 397.
67. Lawrence, J. G., and, H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95: 9413– 9417.
68. Lawrence, J. G., and, H. Ochman. 2002. Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10: 1– 4.
69. Lawrence, J. G.,, H. Ochman, and, D. L. Hartl. 1991. Molecular and evolutionary relationships among enteric bacteria. J. Gen. Microbiol. 137(Pt. 8): 1911– 1921.
70. Lecointre, G.,, L. Rachdi,, P. Darlu, and, E. Denamur. 1998. Escherichia coli molecular phylogeny using the incongruence length difference test. Mol. Biol. Evol. 15: 1685– 1695.
71. Lederberg, J. 2004. E. coli K-12. Microbiology Today 31: 116.
72. Makino, K.,, K. Ishii,, T. Yasunaga,, M. Hattori,, K. Yokoyama,, C. H. Yutsudo,, Y. Kubota,, Y. Yamaichi,, T. Iida,, K. Yamamoto,, T. Honda,, C. G. Han,, E. Ohtsubo,, M. Kasamatsu,, T. Hayashi,, S. Kuhara, and, H. Shinagawa. 1998. Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak. DNA Res. 5: 1– 9.
73. Makino, S.,, T. Tobe,, H. Asakura,, M. Watarai,, T. Ikeda,, K. Takeshi, and, C. Sasakawa. 2003. Distribution of the secondary type III secretion system locus found in enterohemorrhagic Escherichia coli O157:H7 isolates among Shiga toxin– producing E. coli strains. J. Clin. Microbiol. 41: 2341– 2347.
74. Maurelli, A. T.,, R. E. Fernandez,, C. A. Bloch,, C. K. Rode, and, A. Fasano. 1998. “Black holes” and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc. Natl. Acad. Sci. USA 95: 3943– 3948.
75. McDaniel, T. K.,, K. G. Jarvis,, M. S. Donnenberg, and, J. B. Kaper. 1995. A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc. Natl. Acad. Sci. USA 92: 1664– 1668.
76. Menard, R.,, P. Sansonetti, and, C. Parsot. 1994. The secretion of the Shigella flexneri Ipa invasins is activated by epithelial cells and controlled by IpaB and IpaD. EMBO J. 13: 5293– 5302.
77. Michino, H.,, K. Araki,, S. Minami,, S. Takaya,, N. Sakai,, M. Miyazaki,, A. Ono, and, H. Yanagawa. 1999. Massive outbreak of Escherichia coli O157:H7 infection in schoolchildren in Sakai City, Japan, associated with consumption of white radish sprouts. Am. J. Epidemiol. 150: 787– 796.
78. Misra, R. V.,, R. S. Horler,, W. Reindl,, I. I. Goryanin, and, G. H. Thomas. 2005. EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 33: D329– D333.
79. Mori, H. 2004. From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli. J. Biochem. Mol. Biol. 37: 83– 92.
80. Moszer, I.,, P. Glaser, and, A. Danchin. 1995. SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141 (Pt. 2): 261– 268.
81. Nakata, N.,, T. Tobe,, I. Fukuda,, T. Suzuki,, K. Komatsu,, M. Yoshikawa, and, C. Sasakawa. 1993. The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci. Mol. Microbiol. 9: 459– 468.
82. Nataro, J. P., and, J. B. Kaper. 1998. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11: 142– 201.
83. Nataro, J. P.,, J. Seriwatana,, A. Fasano,, D. R. Maneval,, L. D. Guers,, F. Noriega,, F. Dubovsky,, M. M. Levine, and, J. G. Morris, Jr. 1995. Identification and cloning of a novel plasmid-encoded enterotoxin of enteroinvasive Escherichia coli and Shigella strains. Infect. Immun. 63: 4721– 4728.
84. Ochman, H.,, J. G. Lawrence, and, E.A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299– 304.
85. Ochman, H., and, R. K. Selander. 1984. Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157: 690– 693.
86. Ohnishi, M.,, K. Kurokawa, and, T. Hayashi. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9: 481– 485.
87. Ohnishi, M.,, J. Terajima,, K. Kurokawa,, K. Nakayama,, T. Murata,, K. Tamura,, Y. Ogura,, H. Watanabe, and, T. Hayashi. 2002. Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc. Natl. Acad. Sci. USA 99: 17043– 17048.
88. Okeke, I. N.,, A. Lamikanra,, J. Czeczulin,, F. Dubovsky,, J. B. Kaper, and, J. P. Nataro. 2000. Heterogeneous virulence of enteroaggregative Escherichia coli strains isolated from children in southwest Nigeria. J. Infect. Dis. 181: 252– 260.
89. Olsen, G. J., and, C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. FASEB J. 7: 113– 123.
90. Oshima, T.,, H. Aiba,, T. Baba,, K. Fujita,, K. Hayashi,, A. Honjo,, K. Ikemoto,, T. Inada,, T. Itoh,, M. Kajihara,, K. Kanai,, K. Kashimoto,, S. Kimura,, M. Kitagawa,, K. Makino,, S. Masuda,, T. Miki,, K. Mizobuchi,, H. Mori,, K. Motomura,, Y. Nakamura,, H. Nashimoto,, Y. Nishio,, N. Saito, and, T. Horiuchi. 1996. A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7–28.0 min region on the linkage map (supplement). DNA Res. 3: 211– 223.
91. Parham, N. J.,, U. Srinivasan,, M. Desvaux,, B. Foxman,, C. F. Marrs, and, I. R. Henderson. 2004. PicU, a second serine protease autotrans-porter of uropathogenic Escherichia coli. FEMS Microbiol. Lett. 230: 73– 83.
92. 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.
93. Pennisi, E. 1997. Laboratory workhorse decoded. Science 277: 1432– 1434.
94. Perna, N. T.,, G. Plunkett III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grotbeck,, N. W. Davis,, A. Lim,, E.T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch, and, F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529– 533.
95. Picard, B.,, J. S. Garcia,, S. Gouriou,, P. Duriez,, N. Brahimi,, E. Bingen,, J. Elion, and, E. Denamur. 1999. The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect. Immun. 67: 546– 553.
96. Plunkett, G.,, III, V. Burland,, D. L. Daniels, and, F. R. Blattner. 1993. Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res. 21: 3391– 3398.
97. Plunkett, G., III,, D. J. Rose,, T. J. Durfee, and, F. R. Blattner. 1999. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J. Bacteriol. 181: 1767– 1778.
98. Pruitt, K. D.,, T. Tatusova, and, D. R. Maglott. 2005. NCBI Reference Sequence (Ref-Seq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 33: D501– D504.
99. Pupo, G. M.,, D. K. Karaolis,, R. Lan, and, P. R. Reeves. 1997. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65: 2685– 2692.
100. Pupo, G. M.,, R. Lan, and, P. R. Reeves. 2000. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc. Natl. Acad. Sci. USA 97: 10567– 10572.
101. Reid, S. D.,, C. J. Herbelin,, A. C. Bumbaugh,, R. K. Selander, and, T. S. Whittam. 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406: 64– 67.
102. Ren, C. P.,, S. A. Beatson,, J. Parkhill, and, M. J. Pallen. 2005. The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli. J. Bacteriol. 187: 1430– 1440.
103. Ren, C. P.,, R. R. Chaudhuri,, A. Fivian,, C. M. Bailey,, M. Antonio,, W. M. Barnes, and, M. J. Pallen. 2004. The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J. Bacteriol. 186: 3547– 3560.
104. Riley, L. W.,, R. S. Remis,, S. D. Helgerson,, H. B. McGee,, J. G. Wells,, B. R. Davis,, R. J. Hebert,, E. S. Olcott,, L. M. Johnson,, N. T. Hargrett,, P. A. Blake, and, M. L. Cohen. 1983. Hemorrhagic colitis associated with a rare Escherichia coli serotype. N. Engl. J. Med. 308: 681– 685.
105. Riley, M.,, T. Abe,, M. B. Arnaud,, M. K. B. Berlyn,, F. R. Blattner,, R. R. Chaudhuri,, J. D. Glasner,, T. Horiuchi,, I. M. Keseler,, T. Kosuge,, H. Mori,, N. T. Perna,, G. Plunkett III,, K. E. Rudd,, M. H. Serres,, G. H. Thomas,, N. R. Thomson,, D. Wishart, and, B. L. Wanner. 2006. Escherichia coli K-12: a cooperatively developed annotation snapshot— 2005. Nucleic Acids Res. 34: 1– 9.
106. Rudd, K. E. 2000. EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res. 28: 60– 64.
107. Russo, T. A., and, J. R. Johnson. 2000. Proposal for a new inclusive designation for extraintestinal pathogenic isolates of Escherichia coli: ExPEC. J. Infect. Dis. 181: 1753– 1754.
108. Salgado, H.,, S. Gama-Castro,, M. Peralta-Gil,, E. Diaz-Peredo,, F. Sanchez-Solano,, A. Santos-Zavaleta,, I. Martinez-Flores,, V. Jimenez-Jacinto,, C. Bonavides-Martinez,, J. Segura-Salazar,, A. Martinez-Antonio, and, J. Collado-Vides. 2006. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34: D394– D397.
109. Schneider, D.,, E. Duperchy,, E. Coursange,, R. E. Lenski, and, M. Blot. 2000. Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence–mediated mutations and rearrangements. Genetics 156: 477– 488.
110. Schwartz, S.,, W. J. Kent,, A. Smit,, Z. Zhang,, R. Baertsch,, R. C. Hardison,, D. Haussler, and, W. Miller. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103– 107.
111. Schwartz, S.,, Z. Zhang,, K. A. Frazer,, A. Smit,, C. Riemer,, J. Bouck,, R. Gibbs,, R. Hardison, and, W. Miller. 2000. PipMaker—a web server for aligning two genomic DNA sequences. Genome Res. 10: 577– 586.
112. Serres, M. H.,, S. Gopal,, L. A. Nahum,, P. Liang,, T. Gaasterland, and, M. Riley. 2001. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2: RESEARCH0035.
113. Serres, M. H.,, S. Goswami, and, M. Riley. 2004. GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res. 32: D300– D302.
114. Sofia, H. J.,, V. Burland,, D. L. Daniels,, G. Plunkett III, and, F. R. Blattner. 1994. Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res. 22: 2576– 2586.
115. Sun, J.,, F. Gunzer,, A. M. Westendorf,, J. Buer,, M. Scharfe,, M. Jarek,, F. Gossling,, H. Blocker, and, A. P. Zeng. 2005. Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. J. Biotechnol. 117: 147– 161.
116. Tettelin, H.,, V. Masignani,, M. J. Cieslewicz,, C. Donati,, D. Medini,, N. L. Ward,, S. V. Angiuoli,, J. Crabtree,, A. L. Jones,, A. S. Durkin,, R. T. Deboy,, T. M. Davidsen,, M. Mora,, M. Scarselli,, I. Margarit y Ros,, J. D. Peterson,, C. R. Hauser,, J. P. Sundaram,, W. C. Nelson,, R. Madupu,, L. M. Brinkac,, R. J. Dodson,, M. J. Rosovitz,, S. A. Sullivan,, S. C. Daugherty,, D. H. Haft,, J. Selengut,, M. L. Gwinn,, L. Zhou,, N. Zafar,, H. Khouri,, D. Radune,, G. Dimitrov,, K. Watkins,, K. J. O’Connor,, S. Smith,, T. R. Utterback,, O. White,, C. E. Rubens,, G. Grandi,, L. C. Madoff,, D. L. Kasper,, J. L. Telford,, M. R. Wessels,, R. Rappuoli, and, C. M. Fraser. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.” Proc. Natl. Acad. Sci. USA 102: 13950– 13955.
117. Thomas, G. H. 1999. Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence. Bioinformatics 15: 860– 861.
118. Thomas, G. H., and, K. A. Bettelheim. 1998. Escherichia coli on the WWW. Lett. Appl. Microbiol. 27: 122– 123.
119. Turner, S. M.,, R. R. Chaudhuri,, Z. D. Jiang,, H. Dupont,, C. Gyles,, C. W. Penn,, M. J. Pallen, and, I. R. Henderson. 2006. Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages. J. Clin. Microbiol. 44: 4528– 4536.
120. Vandemaele, F.,, D. Vandekerchove,, M. Vereecken,, J. Derijcke,, M. DhoMoulin, and, B. M. Goddeeris. 2003. Sequence analysis demonstrates the conservation of fimH and variability of fimA throughout avian pathogenic Escherichia coli (APEC). Vet. Res. 34: 153– 163.
121. Wahl, R., and, M. Kroger. 1995. ECDC—a totally integrated and interactively usable genetic map of Escherichia coli K12. Microbiol. Res. 150: 7– 61.
122. Wang, H. C.,, J. Badger,, P. Kearney, and, M. Li. 2001. Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Mol. Biol. Evol. 18: 792– 800.
123. Wei, J.,, M. B. Goldberg,, V. Burland,, M. M. Venkatesan,, W. Deng,, G. Fournier,, G. F. Mayhew,, G. Plunkett III,, D. J. Rose,, A. Darling,, B. Mau,, N. T. Perna,, S. M. Payne,, L. J. Runyen-Janecky,, S. Zhou,, D. C. Schwartz, and, F. R. Blattner. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71: 2775– 2786.
124. Welch, R. A.,, V. Burland,, G. Plunkett III,, P. Redford,, P. Roesch,, D. Rasko,, E. L. Buckles,, S. R. Liou,, A. Boutin,, J. Hackett,, D. Stroud,, G. F. Mayhew,, D. J. Rose,, S. Zhou,, D. C. Schwartz,, N. T. Perna,, H. L. Mobley,, M. S. Donnenberg, and, F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99: 17020– 17024.
125. Whittam, T. S.,, H. Ochman, and, R. K. Selander. 1983. Multilocus genetic structure in natural populations of Escherichia coli. Proc. Natl. Acad. Sci. USA 80: 1751– 1755.
126. Whittam, T. S.,, M. L. Wolfe,, I. K. Wachsmuth,, F. Orskov,, I. Orskov, and, R. A. Wilson. 1993. Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect. Immun. 61: 1619– 1629.
127. Wirth, T.,, D. Falush,, R. Lan,, F. Colles,, P. Mensa,, L. H. Wieler,, H. Karch,, P. R. Reeves,, M. C. J. Maiden,, H. Ochman, and, M. Achtman. 2006. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60: 1136– 1151.
128. Yamamoto, Y.,, H. Aiba,, T. Baba,, K. Hayashi,, T. Inada,, K. Isono,, T. Itoh,, S. Kimura,, M. Kitagawa,, K. Makino,, T. Miki,, N. Mitsuhashi,, K. Mizobuchi,, H. Mori,, S. Nakade,, Y. Nakamura,, H. Nashimoto,, T. Oshima,, S. Oyama,, N. Saito,, G. Sampei,, Y. Satoh,, S. Sivasundaram,, H. Tagami, and, T. Horiuchi. 1997. Construction of a contiguous 874-kb sequence of the Escherichia coli—K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. DNA Res. 4: 91– 113.
129. Yang, F.,, J. Yang,, X. Zhang,, L. Chen,, Y. Jiang,, Y. Yan,, X. Tang,, J. Wang,, Z. Xiong,, J. Dong,, Y. Xue,, Y. Zhu,, X. Xu,, L. Sun,, S. Chen,, H. Nie,, J. Peng,, J. Xu,, Y. Wang,, Z. Yuan,, Y. Wen,, Z. Yao,, Y. Shen,, B. Qiang,, Y. Hou,, J. Yu, and, Q. Jin. 2005. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33: 6445– 6458.
130. Yang, J.,, L. Chen,, J. Yu,, L. Sun, and, Q. Jin. 2006. ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res. 34: D398– D401.
131. Yang, J.,, J. Wang,, Z. J. Yao,, Q. Jin,, Y. Shen, and, R. Chen. 2003. GenomeComp: a visualization tool for microbial genome comparison. J. Microbiol. Methods 54: 423– 426.
132. Yang, Z., and, R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19: 908– 917.
133. Yura, T.,, H. Mori,, H. Nagai,, T. Nagata,, A. Ishihama,, N. Fujita,, K. Isono,, K. Mizobuchi, and, A. Nakata. 1992. Systematic sequencing of the Escherichia coli genome: analysis of the 0–2.4 min region. Nucleic Acids Res. 20: 3305– 3308.

Tables

Understanding the Model and the Menace: a Postgenomic View of Escherichia coli
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Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
/content/10.1128/9781555815530.ch02.ch02tab01
TABLE 1
genome projects completed and underway as of April 2006
Generic image for table
TABLE 1

genome projects completed and underway as of April 2006

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2
/content/10.1128/9781555815530.ch02.ch02tab02
TABLE 2
Selected online resources for genomics
Generic image for table
TABLE 2

Selected online resources for genomics

Citation: Chaudhuri R, Thomas G. 2007. Understanding the Model and the Menace: a Postgenomic View of , p 21-48. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch2

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