Chapter 7 : How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic

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The main symptom of cholera, profuse rice water stool, is primarily caused by the action of cholera toxin (CT), a very potent AB-type enterotoxin that consists of five binding B subunits and one active A subunit. Many bacterial pathogens attain or increase their virulence potential through HGT of genetic material carried on mobile and integrative genetic elements (MIGEs) such as plasmids, bacteriophages, pathogenicity islands (PAIs), integrons, and integrative conjugative elements (ICEs). The impact of horizontal gene transfer (HGT) on bacterial evolution--particularly its role in the emergence of many human gastrointestinal pathogens--is unquestionable. This chapter gives a brief overview of the features that differentiate integrative genetic elements such as integrases, transposases, phage structural genes, or plasmid conjugal transfer genes, from one another. In evolutionary terms, while phylogenetic analysis of housekeeping gene groups and strains separately, both species group together based on the gene, which indicates recent HGT between the species. The authors identified 24 regions, gaps in the genome atlas, of greater than 10 kb that were unique to RIMD2210633. 22 members of the family in the genome database were examined, and only 5 species encode neuraminidase: pathogenic isolates, , strain 16, V. shilonii AK1 and sp. strain MED222. The last two are the only strains to encode sialic acid scavenging, synthesis, and catabolism genes.

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7

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Mobile Genetic Elements
Bacterial Pathogenesis
Type VI Secretion System
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1. Alam, M.,, N. A. Hasan,, A. Sadique,, N. A. Bhuiyan,, K. U. Ahmed,, S. Nusrin,, G. B. Nair,, A. K. Siddique,, R. B. Sack,, D. A. Sack,, A. Huq, and, R. R. Colwell. 2006. Seasonal cholera caused by Vibrio cholerae serogroups O1 and 0139 in the coastal aquatic environment of Bangladesh. Appl. Environ. Microbiol. 72:40964104.
2. Albert, J., and, J. G. Morris. 2000. Cholera and other vibrioses, p. 323-334. In G. T. Strickland (ed.), Hunter’s Tropical Medicine and Emerging and Infectious Diseases, 8th ed. W. B. Saunders, Philadelphia, PA.
3. Almagro-Moreno, S., and, E. F. Boyd. 2010. Bacteriol catabolism of nonulosonic (sialic) acid and fitness in the gut. Gut Microbes 1:16.
4. Almagro-Moreno, S., and, E. F. Boyd. 2009. Insights into the evolution of sialic acid catabolism among bacteria. BMC Evol. Biol. 9:118.
5. Almagro-Moreno, S., and, E. F. Boyd. 2009. Sialic acid catabolism confers a competitive advantage to pathogenic Vibrio cholerae in the mouse intestine. Infect. Immun. 77:38073816.
6. Austin, B., and, X. H. Zhang. 2006. Vibrio harveyi: a significant pathogen of marine vertebrates and invertebrates. Lett. Appl. Microbiol. 43:119124.
7. Bhattacharya, S.,, R. Black,, L. Bourgeois,, J. Clemens,, A. Cravioto,, J. L. Deen,, G. Dougan,, R. Glass,, R. F. Grais,, M. Greco,, I. Gust,, J. Holmgren,, S. Kariuki,, P. H. Lambert,, M. A. Liu,, I. Longini,, G. B. Nair,, R. Norrby,, G. J. Nossal,, P. Ogra,, P. Sansonetti,, L. von Seidlein,, F. Songane,, A. M. Svennerholm,, D. Steele, and, R. Walker. 2009. Public health. The cholera crisis in Africa. Science 324:885.
8. Bik, E. M.,, A. E. Bunschoten,, R. D. Gouw, and, F. R. Mooi. 1995. Genesis of the novel epidemic Vibrio cholerae 0139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis. EMBO J. 14:209216.
9. Boyd, E. F. 2004. Bacteriophages and bacterial virulence, p. 223-266. In E. Kutter and, A. Sulakvelidze (ed.), Bacteriophages: Molecular Biology and Applications. CRC Press LLC, Boca Raton, FL.
10. Boyd, E. F. 2010. Efficiency and specificity of CTXphi chromosomal integration: dif makes all the difference. Proc. Natl. Acad. Sci. USA 107:39513952.
11. Boyd, E. F. 2008. Filamentous bacteriophages in Vibrio cholerae genetics and evolution, p. 49-66. In S. M. Faruque and, G. B. Nair (ed.), Vibrio cholerae: Molecular Biology and Genomics. Caister Academic Press, Norfolk, UK.
12. Boyd, E. F.,, A.L. Cohen,, L. M. Naughton,, T. T. Binnewies,, D. W. Ussery,, O. C. Stine, and, M. A. Parent. 2008. Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus. BMC Microbiology 8:110.
13. Boyd, E. F.,, S. Almagro-Moreno, and, M. A. Parent. 2009. Genomic islands are dynamic, ancient integrative elements in bacterial evolution. Trends Microbiol. 17:4753.
14. Boyd, E. F.,, B.M. Davis, and, B. Hochhut. 2001. Contribution of bacteriophage-bacteriophage interactions to the evolution of bacterial pathogens. Trends Microbiol. 9:137144.
15. Boyd, E. F., and, H. Brussow. 2002. Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 10:521529.
16. Boyd, E. F.,, A. J. Heilpern, and, M. K. Waldor. 2000. Molecular analyses of a putative CTXϕ precursor and evidence for independent acquisition of distinct CTXϕs by toxigenic Vibrio cholerae. J. Bacteriol. 182:55305538.
17. Boyd, E. F., and, M. K. Waldor. 1999. Alternative mechanism of cholera toxin acquisition by Vibrio cholerae: generalized transduction of CTXPhi by bacteriophage CP-T1. Infect. Immun. 67:58985905.
18. Broza, M., and, M. Halpern. 2001. Pathogen reservoirs. Chi-ronomid egg masses and Vibrio cholerae. Nature 412:40.
19. Brussow, H.,, C. Canchaya, and, W. D. Hardt. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68:560602.
20. Burrus, V.,, J. Marrero, and, M. K. Waldor. 2006. The current ICE age: biology and evolution of SXT-related integrating conjugative elements. Plasmid 55:173183.
21. Burrus, V.,, G. Pavlovic,, B. Decaris, and, G. Guedon. 2002. Con-jugative transposons: the tip of the iceberg. Mol. Microbiol. 46:601610.
22. Burrus, V., and, M. K. Waldor. 2003. Control of SXT integration and excision. J. Bacteriol. 185:50455054.
23. Chen, C. Y.,, K. M. Wu,, Y. C. Chang,, C. H. Chang,, H. C. Tsai,, T. L. Liao,, Y. M. Liu,, H. J. Chen,, A. B. Shen,, J. C. Li,, T. L. Su,, C. P. Shao,, C. T. Lee,, L. I. Hor, and, S. F. Tsai. 2003. Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13:25772587.
24. Chen, Y.,, J. A. Johnson,, G. D. Pusch,, J. G. Morris, Jr., and, O. C. Stine. 2007. The genome of non-O1 Vibrio cholerae NRT36S demonstrates the presence of pathogenic mechanisms that are distinct from those of O1 Vibrio cholerae. Infect. Immun. 75:26452647.
25. Cholera Working Group. 1993. Large epidemic of choleralike disease in Bangladesh caused by Vibrio Cholerae 0139 Synonym Bengal. Lancet 342:387390.
26. Cohen, A. L.,, J.D. Oliver,, A. DePaola,, E. Feil, and, E. F. Boyd. 2007. Molecular phylogeny of Vibrio vulnificus based on multilocus sequence analysis and a 33 kb genomic island correlates with pathogenic potential. Appl. Environ. Microbiol. 73:55535565.
27. Colwell, R. R. 1996. Global climate and infectious disease: the cholera paradigm. Science 274:20252031.
28. Colwell, R. R. 2000. Viable but nonculturable bacteria: a survival strategy. J. Infect. Chemother. 6:121125.
29. Colwell, R. R.,, J. Kaper, and, S. W. Joseph. 1977. Vibrio cholerae, Vibrio parahaemolyticus, and other vibrios: occurrence and distribution in Chesapeake Bay. Science 198:394396.
30. Comstock, L. E.,, D. Maneval, Jr.,, P. Panigrahi,, A. Joseph,, M. M. Levine,, J. B. Kaper,, J. G. Morris, Jr., and, J. A. Johnson. 1995. The capsule and O antigen in Vibrio cholerae 0139 Bengal are associated with a genetic region not present in Vibrio cholerae Ol. Infect. Immun. 63:317323.
31. Dalsgaard, A.,, A. Forslund,, D. Sandvang,, L. Arntzen, and, K. Keddy. 2001. Vibrio cholerae O1 outbreak isolates in Mozambique and South Africa in 1998 are multiple-drug resistant, contain the SXT element and the aadA2 gene located on class 1 integrons. J. Antimicrob. Chemother. 48:827838.
32. Das, B.,, J. Bischerour,, M. Val, and, F.-X. Barre. 2010. Molecular keys of the tropism of integration of the Cholera Toxin phage. Proc. Natl. Acad. Sci. USA 107:43774382.
33. Davis, B. M.,, H. H. Kimsey,, W. Chang, and, M. K. Waldor. 1999. The Vibrio cholerae 0139 Calcutta bacteriophage CTXϕ is infectious and encodes a novel repressor. J. Bacteriol. 181:67796787.
34. Davis, B. M.,, H. H. Kimsey,, A. V. Kane, and, M. K. Waldor. 2002. A satellite phage-encoded antirepressor induces repressor aggregation and cholera toxin gene transfer. EMBO J. 21:42404249.
35. Davis, B. M.,, K. E. Moyer,, E. F. Boyd, and, M. K. Waldor. 2000. CTX prophages in classical biotype Vibrio cholerae: functional phage genes but dysfunctional phage genomes. J. Bacteriol. 182:69926998.
36. De, S. N. 1959. Enterotoxicity of bacteria-free culture-filtrate of Vibrio cholerae. Nature 183:15331534.
37. Duigou, S.,, K. G. Knudsen,, O. Skovgaard,, E. S. Egan,, A. Lobner-Olesen, and, M. K. Waldor. 2006. Independent control of replication initiation of the two Vibrio cholerae chromosomes by DnaA and RctB. J. Bacteriol. 188:64196424.
38. Dziejman, M.,, E. Balon,, D. Boyd,, C. M. Fraser,, J. F. Heidelberg, and, J. J. Mekalanos. 2002. Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc. Natl. Acad. Sci. USA 99:15561561.
39. Egan, E. S.,, S. Duigou, and, M. K. Waldor. 2006. Autorepression of RctB, an initiator of Vibrio cholerae chromosome II replication. J. Bacteriol. 188:789793.
40. Faruque, S. M.,, M. J. Albert, and, J. J. Mekalanos. 1998. Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae. Microbiol. Mol. Biol. Rev. 62:13011314.
41. Faruque, S. M.,, Asadulghani, M. M. Rahman,, M. K. Waldor, and, D. A. Sack. 2000. Sunlight-induced propagation of the lysogenic phage encoding cholera toxin. Infect. Immun. 68:47954801.
42. Faruque, S. M.,, M. J. Islam,, Q. S. Ahmad,, A. S. Faruque,, D. A. Sack,, G. B. Nair, and, J. J. Mekalanos. 2005. Self-limiting nature of seasonal cholera epidemics: role of host-mediated amplification of phage. Proc. Natl. Acad. Sci. USA 102:61196124.
43. Faruque, S. M., and, J. J. Mekalanos. 2003. Pathogenic-ity islands and phages in Vibrio cholerae evolution. Trends Microbiol. 11:505510.
44. Faruque, S. M.,, V. C. Tam,, N. Chowdhury,, P. Diraphat,, M. Dziejman,, J. F. Heidelberg,, J. D. Clemens,, J. J. Mekalanos, and, G. B. Nair. 2007. Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the origin of El Tor strains carrying classical CTX prophage. Proc. Natl. Acad. Sci. USA 104:51515156.
45. Field, M.,, D. Fromm,, Q. al-Awqati, and, W. B. Greenough III. 1972. Effect of cholera enterotoxin on ion transport across isolated ileal mucosa. J. Clin. Invest. 51:796804.
46. Fogel, M. A., and, M. K. Waldor. 2005. Distinct segregation dynamics of the two Vibrio cholerae chromosomes. Mol. Microbiol. 55:125136.
47. Frost, L. S.,, R. Leplae,, A. O. Summers, and, A. Toussaint. 2005. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3:722732.
48. Galen, J. E.,, J. M. Ketley,, A. Fasano,, S. H. Richardson,, S. S. Wasserman, and, J. B. Kaper. 1992. Role of Vibrio cholerae neuraminidase in the function of cholera toxin. Infect. Immun. 60:406415.
49. Gill, D. M. 1976. The arrangement of subunits in cholera toxin. Biochemistry 15:12421248.
50. Reference deleted.
51. Hacker, J.,, G. Blum-Oehler,, I. Muhldorfer, and, H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:10891097.
52. Hacker, J., and, J. B. Kaper. 2000. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54:641679.
53. Haniford, D. B. 2006. Transpososome dynamics and regulation in Tn10 transposition. Crit. Rev. Biochem. Mol. Biol. 41:407424.
54. Hatfull, G. F. 2008. Bacteriophage genomics. Curr. Opin. Microbiol. 11:447453.
55. Heidelberg, J. F.,, J. A. Eisen,, W. C. Nelson,, R. A. Clayton,, M. L. Gwinn,, R. J. Dodson,, D. H. Haft,, E. K. Hickey,, J. D. Peterson,, L. Umayam,, S. R. Gill,, K. E. Nelson,, T. D. Read,, H. Tettelin,, D. Richardson,, M. D. Ermolaeva,, J. Vamathevan,, S. Bass,, H. Qin,, I. Dragoi,, P. Sellers,, L. McDonald,, T. Utterback,, R. D. Fleishmann,, W. C. Nierman,, O. White,, S. L. Salzberg,, H. O. Smith,, R. R. Colwell,, J. J. Mekalanos,, J. C. Venter, and, C. M. Fraser. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477483.
56. Hjerde, E.,, M. S. Lorentzen,, M. T. Holden,, K. Seeger,, S. Paulsen,, N. Bason,, C. Churcher,, D. Harris,, H. Norbertczak,, M. A. Quail,, S. Sanders,, S. Thurston,, J. Parkhill,, N. P. Willassen, and, N. R. Thomson. 2008. The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay. BMC Genomics 9:616.
57. Hochhut, B., and, M. K. Waldor. 1999. Site-Specific integration of the conjugal Vibrio cholerae SXT element into prfC. Mol. Microbiol. 32:99110.
58. Holmgren, J.,, I. Lonnroth, and, L. Svennerholm. 1973. Fixation and inactivation of cholera toxin by GM1 ganglioside. Scand. J. Infect. Dis. 5:7778.
59. Huber, K. E., and, M. K. Waldor. 2002. Filamentous phage integration requires the host recombinases XerC and XerD. Nature 417:656659.
60. Huq, A.,, E. B. Small,, P. A. West,, M. I. Huq,, R. Rahman, and, R. R. Colwell. 1983. Ecological relationships between Vibrio cholerae and planktonic crustacean copepods. Appl. Environ. Microbiol. 45:275283.
61. Huq, A.,, P. A. West,, E. B. Small,, M. I. Huq, and, R. R. Colwell. 1984. Influence of water temperature, salinity, and pH on survival and growth of toxigenic Vibrio cholerae serovar 01 associated with live copepods in laboratory microcosms. Appl. Environ. Microbiol. 48:420424.
62. Hurley, C. C.,, A. Quirke,, F. J. Reen, and, E. F. Boyd. 2006. Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates. BMC Genomics 7:104.
63. Islam, M. S.,, B. S. Drasar, and, D. J. Bradley. 1990. Long-term persistence of toxigenic Vibrio cholerae O1 in the mucilaginous sheath of a blue-green alga, Anabaena variabilis. J. Trop. Med. Hyg. 93:133139.
64. Islam, M. S.,, B. S. Drasar, and, R. B. Sack. 1994. Probable role of blue-green algae in maintaining endemicity and seasonality of cholera in Bangladesh: a hypothesis. J. Diarrhoeal Dis. Res. 12:245256.
65. Jensen, M. A.,, S. M. Faruque,, J. J. Mekalanos, and, B. R. Levin. 2006. Modeling the role of bacteriophage in the control of cholera outbreaks. Proc. Natl. Acad. Sci. USA 103:46524657.
66. Jeong, H. G.,, M. H. Oh,, B. S. Kim,, M. Y. Lee,, H. J. Han, and, S. H. Choi. 2009. Capability of catabolic utilization of N-acetylneuraminic acid, a sialic acid, is essential for patho-genesis of Vibrio vulnificus. Infect. Immun. 77:32093217.
67. Jermyn, W. S., and, E. F. Boyd. 2002. Characterization of a novel Vibrio pathogenicity island (VPI-2) encoding neuraminidase (nanH) among toxigenic Vibrio cholerae isolates. Microbiology 148:36813693.
68. Jermyn, W. S., and, E. F. Boyd. 2005. Molecular evolution of Vibrio pathogenicity island-2 (VPI-2): mosaic structure among Vibrio cholerae and Vibrio mimicus natural isolates. Microbiology 151:311322.
69. Jermyn, W. S.,, Y. A. O’Shea,, A. M. Quirke, and, E. F. Boyd. 2006. Genomics and the emergence of pathogenic Vibrio cholerae, p. 227-253. In V. Chan,, P. Sherman, and, B. Bourke (ed.), Bacteriol Genomes and Infectious Diseases, Humana Press, New York, NY.
70. Johnson, J. A.,, C. A. Salles,, P. Panigrahi,, M. J. Albert,, A. C. Wright,, R. J. Johnson, and, J. G. Morris, Jr. 1994. Vibrio cholerae 0139 synonym bengal is closely related to Vibrio cholerae El Tor but has important differences. Infect. Immun. 62:21082110.
71. Jones, M. K., and, J. D. Oliver. 2009. Vibrio vulnificus: disease and pathogenesis. Infect. Immun. 77:17231733.
72. Kaper, J. B.,, J. G. Morris, Jr., and, M. M. Levine. 1995. Cholera. Clin. Microbiol. Rev. 8:4886.
73. Karaolis, D. K.,, J. A. Johnson,, C. C. Bailey,, E. C. Boedeker,, J. B. Kaper, and, P. R. Reeves. 1998. A Vibrio cholerae pathogenicity island associated with epidemic and pandemic strains. Proc. Natl. Acad. Sci. USA 95:31343139.
74. Kimsey, H. H.,, G. B. Nair,, A. Ghosh, and, M. K. Waldor. 1998. Diverse CTXphis and evolution of new pathogenic Vibrio cholerae. Lancet 352:457458.
75. Kovach, M. E.,, M. D. Shaffer, and, K. M. Peterson. 1996. A putative integrase gene defines the distal end of a large cluster of ToxR-regulated colonization genes in Vibrio cholerae. Microbiology 142:21652174.
76. Le Roux, F.,, M. Zouine,, N. Chakroun,, J. Binesse,, D. Saulnier,, C. Bouchier,, N. Zidane,, L. Ma,, C. Rusniok,, A. Lajus,, C. Buchrieser,, C. Medigue,, M. F. Polz, and, D. Mazel. 2009. Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environ. Microbiol.
77. Lipp, E. K.,, A. Huq, and, R. R. Colwell. 2002. Effects of global climate on infectious disease: the cholera model. Clin. Microbiol. Rev. 15:757770.
78. Liu, P. C., and, K. K. Lee. 1999. Cysteine protease is a major exotoxin of pathogenic luminous Vibrio harveyi in the tiger prawn, Penaeus monodon. Lett. Appl. Microbiol. 28:428430.
79. Liu, P. C.,, K. K. Lee,, K. C. Yii,, G. H. Kou, and, S. N. Chen. 1996. Isolation of Vibrio harveyi from diseased kuruma prawns Penaeus japonicus. Curr. Microbiol. 33:129132.
80. Lobitz, B.,, L. Beck,, A. Huq,, B. Wood,, G. Fuchs,, A. S. Faruque, and, R. Colwell. 2000. Climate and infectious disease: use of remote sensing for detection of Vibrio cholerae by indirect measurement. Proc. Natl. Acad. Sci. USA 97:14381443.
81. Lonnroth, I., and, J. Holmgren. 1973. Subunit structure of cholera toxin. J. Gen. Microbiol. 76:417427.
82. Mahillon, J., and, M. Chandler. 1998. Insertion sequences. Microbiol. Mol. Biol. Rev. 62:725774.
83. Makino, K.,, K. Oshima,, K. Kurokawa,, K. Yokoyama,, T. Uda,, K. Tagomori,, Y. Iijima,, M. Najima,, M. Nakano,, A. Yamashita,, Y. Kubota,, S. Kimura,, T. Yasunaga,, T. Honda,, H. Shinagawa,, M. Hattori, and, T. Iida. 2003. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet 361:743749.
84. Matz, C.,, D. McDougald,, A. M. Moreno,, P. Y. Yung,, F. H. Yildiz, and, S. Kjelleberg. 2005. Biofilm formation and phenotypic variation enhance predation-driven persistence of Vibrio cholerae. Proc. Natl. Acad. Sci. USA 102:168191624.
85. Mazel, D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4:608620.
86. Mazel, D.,, B. Dychinco,, V. A. Webb, and, J. Davies. 1998. A distinctive class of integron in the Vibrio cholerae genome. Science 280:605608.
87. McCarthy, S. A., and, F. M. Khambaty. 1994. International dissemination of epidemic Vibrio cholerae by cargo ship ballast and other nonpotable waters. Appl. Environ. Microbiol. 60:25972601.
88. McLeod, S. M., and, M. K. Waldor. 2004. Characterization of XerC- and XerD-dependent CTX phage integration in Vibrio cholerae. Mol. Microbiol. 54:935947.
89. Meibom, K.,, M. Blokesch,, N. Dolganov,, C. Wu, and, G. Schoolnik. 2005. Chitin induces natural competence in Vibrio cholerae. Science 310:18241827.
90. Mekalanos, J. J. 1983. Duplication and amplification of toxin genes in Vibrio cholerae. Cell 35:253263.
91. Mekalanos, J. J.,, D. J. Swartz,, G. D. Pearson,, N. Harford,, F. Groyne, and, M. de Wilde. 1983. Cholera toxin genes: nucleotide sequence, deletion analysis and vaccine development. Nature 306:551557.
92. Mintz, E. D., and, R. L. Guerrant. 2009. A lion in our village—the unconscionable tragedy of cholera in Africa. N. Engl. J. Med. 360:10601063.
93. Mooi, F. R., and, E. M. Bik. 1997. The evolution of epidemic Vibrio cholerae strains. Trends Microbiol. 5:161165.
94. Morris, J. G., Jr. 2003. Cholera and other types of vibriosis: a story of human pandemics and oysters on the half shell. Clin. Infect. Dis. 37:272280.
95. Morris, J. G., Jr. 1990. Non-O group 1 Vibrio cholerae: a look at the epidemiology of an occasional pathogen. Epidemiol. Rev. 12:179191.
96. Murphy, R.A. and, E. F. Boyd. 2008. Three pathogenicity islands of Vibrio cholerae can excise from the chromosome and form circular intermediates. J. Bacteriol. 190:636647.
97. Nair, G. B.,, S. K. Bhattacharya, and, B. C. Deb. 1994. Vibrio cholerae 0139 Bengal: the eighth pandemic strain of cholera. Indian J. Public Health 38:3336.
98. Nair, G. B.,, Y. Oku,, Y. Takeda,, A. Ghosh,, R. K. Ghosh,, S. Chattopadhyay,, S. C. Pal,, J. B. Kaper, and, T. Takeda. 1988. Toxin profiles of Vibrio cholerae non-O1 from environmental sources in Calcutta, India. Appl. Environ. Microbiol. 54:31803182.
99. O’Shea, Y. A., and, E. F. Boyd. 2002. Mobilization of the Vibrio pathogenicity island between Vibrio cholerae isolates mediated by CP-T1 generalized transduction. FEMS Microbiol. Lett. 214:153157.
100. O’Shea, Y. A.,, S. Finnan,, F. J. Reen,, J. P. Morrissey,, F. O’Gara, and, E. F. Boyd. 2004. The Vibrio seventh pandemic island-II is a 26.9 kb genomic island present in Vibrio cholerae El Tor and 0139 serogroup isolates that shows homology to a 43.4 kb genomic island in V vulnificus. Microbiology 150:40534063.
101. O’Shea, Y. A.,, F. J. Reen,, A. M. Quirke, and, E. F. Boyd. 2004. Evolutionary genetic analysis of the emergence of epidemic Vibrio cholerae isolates on the basis of comparative nucleotide sequence analysis and multilocus virulence gene profiles. J. Clin. Microbiol. 42:46574671.
102. Pascual, M.,, X. Rodo,, S. P. Ellner,, R. Colwell, and, M. J. Bouma. 2000. Cholera dynamics and El Nino-Southern Oscillation. Science 289:17661769.
103. Pearson, G. D.,, A. Woods,, S. L. Chiang, and, J. J. Mekalanos. 1993. CTX genetic element encodes a site-specific recombination system and an intestinal colonization factor. Proc. Natl. Acad. Sci. USA 90:37503754.
104. Centers for Disease Control and Prevention. 2009. Preliminary FoodNet data on the incidence of infection with pathogens transmitted commonly through food—10 states, 2008. MMWR Morb. Mortal. Wkly. Rep. 58:333337.
105. Quirke, A. M.,, F. J. Reen,, M. J. Claesson, and, E. F. Boyd. 2006. Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen. Bioinformatics 22:905910.
106. Rajanna, C.,, J. Wang,, D. Zhang,, Z. Xu,, A. Ali,, Y. M. Hou, and, D. K. Karaolis. 2003. The vibrio pathogenicity island of epidemic Vibrio cholerae forms precise extrachromosomal circular excision products. J. Bacteriol. 185:68936901.
107. Ramamurthy, T.,, S. Garg,, R. Sharma,, S. K. Bhattacharya,, G. B. Nair,, T. Shimada,, T. Takeda,, T. Karasawa,, H. Kurazano,, A. Pal, and et al. 1993. Emergence of novel strain of Vibrio cholerae with epidemic potential in southern and eastern India. Lancet 341:703704.
108. Reen, F. J.,, S. Almagro-Moreno,, D. Ussery, and, E. F. Boyd. 2006. The genomic code: inferring Vibrionaceae niche specialization. Nat. Rev. Microbiol. 4:697704.
109. Reen, F. J., and, E. F. Boyd. 2005. Adaptation of Vibrio species to the environment and host. In M. Griffiths and, F. Dodds (ed.), Understanding Pathogen Behaviour. Woodhead Publishing, Great Abington, Cambridge, England.
110. Reguera, G., and, R. Kolter. 2005. Virulence and the environment: a novel role for Vibrio cholerae toxin-coregulated pili in biofilm formation on chitin. J. Bacteriol. 187:35513555.
111. Reidl, J., and, K. E. Klose. 2002. Vibrio cholerae and cholera: out of the water and into the host. FEMS Microbiol. Rev. 26:125139.
112. Rowe-Magnus, D. A.,, A. M. Guerout, and, D. Mazel. 2002. Bacteriol resistance evolution by recruitment of super-integron gene cassettes. Mol. Microbiol. 43:16571669.
113. Ruby, E. G. 1996. Lessons from a cooperative, bacterial-animal association: the Vibrio fischeri-Euprymna scolopes light organ symbiosis. Annu. Rev. Microbiol. 50:591624.
114. Ruby, E. G.,, M. Urbanowski,, J. Campbell,, A. Dunn,, M. Faini,, R. Gunsalus,, P. Lostroh,, C. Lupp,, J. McCann,, D. Millikan,, A. Schaefer,, E. Stabb,, A. Stevens,, K. Visick,, C. Whistler, and, E. P. Greenberg. 2005. Complete genome sequence of Vibrio fischeri: a symbiotic bacterium with pathogenic congeners. Proc. Natl. Acad. Sci. USA 102:30043009.
115. Sørum, H.,, A. B. Hvaal,, M. Heum,, F. L. Daae, and, R. Wiik. 1990. Plasmid profiling of Vibrio salmonicida for epidemiological studies of cold-water vibriosis in Atlantic salmon (Salmo salar) and cod (Gadus morhua). Appl. Environ. Microbiol. 56:10331037.
116. Stroeher, U. H., K. E. Jedani, and, P. A. Manning. 1998. Genetic organization of the regions associated with surface poly-saccharide synthesis in Vibrio cholerae O1, 0139 and Vibrio anguillarum O1 and O2: a review. Gene 223:269282.
117. Stroeher, U. H.,, G. Parasivam,, B. K. Dredge, and, P. A. Manning. 1997. Novel Vibrio cholerae 0139 genes involved in lipopolysaccharide biosynthesis. J. Bacteriol. 179:27402747.
118. Taylor, R. K.,, V. L. Miller,, D. B. Furlong, and, J. J. Mekalanos. 1987. Use of phoA gene fusions to identify a pilus colonization factor coordinately regulated with cholera toxin. Proc. Natl. Acad. Sci. USA 84:28332837.
119. Thompson, F. L.,, T. Iida, and, J. Swings. 2004. Biodiversity of vibrios. Microbiol. Mol. Biol. Rev. 68:403431.
120. Trucksis, M.,, J. Michalski,, Y. K. Deng, and, J. B. Kaper. 1998. The Vibrio cholerae genome contains two unique circular chromosomes. Proc. Natl. Acad. Sci. USA 95:1446414469.
121. Udden, S. M.,, M. S. Zahid,, K. Biswas,, Q. S. Ahmad,, A. Cravioto,, G. B. Nair,, J. J. Mekalanos, and, S. M. Faruque. 2008. Acquisition of classical CTX prophage from Vibrio cholerae O141 by El Tor strains aided by lytic phages and chitin-induced competence. Proc. Natl. Acad. Sci. USA 105:1195111956.
122. Val, M. E.,, M. Bouvier,, J. Campos,, D. Sherratt,, F. Cornet,, D. Mazel, and, F. X. Barre. 2005. The single-Stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae. Mol. Cell 19:559566.
123. Van Heyningen, W. E.,, C. C. Carpenter,, N. F. Pierce, and, W. B. Greenough, III. 1971. Deactivation of cholera toxin by ganglioside. J. Infect. Dis. 124:415418.
124. Vezzi, A.,, S. Campanaro,, M. D’Angelo, F. Simonato,, N. Vitulo,, F. M. Lauro,, A. Cestaro,, G. Malacrida,, B. Simionati,, N. Cannata,, C. Romualdi,, D. H. Bartlett, and, G. Valle. 2005. Life at depth: Photobacterium profundum genome sequence and expression analysis. Science 307:14591461.
125. Wachsmuth, I. K.,, G. M. Evins,, P. I. Fields,, O. Olsvik,, T. Popovic,, C. A. Bopp,, J. G. Wells,, C. Carrillo, and, P. A. Blake. 1993. The molecular epidemiology of cholera in Latin America. J. Infect. Dis. 167:621626.
126. Waldor, M. K., and, J. J. Mekalanos. 1996. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272:19101914.
127. Waldor, M. K., and, J. J. Mekalanos. 1994. Vibrio cholerae 0139 specific gene sequences. Lancet 343:1366.
128. Waldor, M. K.,, E. J. Rubin,, G. D. Pearson,, H. Kimsey, and, J. J. Mekalanos. 1997. Regulation, replication, and integration functions of the Vibrio cholerae CTXphi are encoded by region RS2. Mol. Microbiol. 24:917926.
129. Waldor, M. K.,, H. Tschape, and, J. J. Mekalanos. 1996. A new type of conjugative transposon encodes resistance to sulfamethoxazole, trimethoprim, and streptomycin in Vibrio cholerae 0139. J. Bacteriol. 178:41574165.
130. Watnick, P. I.,, C. M. Lauriano,, K. E. Klose,, L. Croal, and, R. Kolter. 2001. The absence of a flagellum leads to altered colony morphology, biofilm development and virulence in Vibrio cholerae 0139. Mol. Microbiol. 39:223235.
131. Williams, K. P. 2002. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res. 30:866875.
132. Williams, K. P. 2003. Traffic at the tmRNA gene. J. Bacteriol. 185:10591070.
133. Yamaichi, Y.,, T. Iida,, K. S. Park,, K. Yamamoto, and, T. Honda. 1999. Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species. Mol. Microbiol. 31:15131521.
134. Yamasaki, S.,, T. Shimizu,, K. Hoshino,, S. T. Ho,, T. Shi-mada,, G. B. Nair, and, Y. Takeda. 1999. The genes responsible for O-antigen synthesis of Vibrio cholerae 0139 are closely related to those of Vibrio cholerae O22. Gene 237:321332.
135. Zhang, X. H.,, P. G. Meaden, and, B. Austin. 2001. Duplication of hemolysin genes in a virulent isolate of Vibrio harveyi. Appl. Environ. Microbiol. 67:31613167.
136. Zuckerman, J. N.,, L. Rombo, and, A. Fisch. 2007. The true burden and risk of cholera: implications for prevention and control. Lancet Infect Dis. 7:521530.


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Table 1

General characteristics of 27 sequenced genomes

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7
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Table 2

In silico and in vitro methods for detection of horizontal gene transfer

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7
Generic image for table
Table 3

General characteristics of mobile and integrative genetic elements

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7
Generic image for table
Table 4

Mobile and integrative genetic elements identified in

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7
Generic image for table
Table 5

Distribution of mobile and integrative genetic elements among different isolates

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7
Generic image for table
Table 6

Genomic analysis of sialic acid metabolism genes among the

Citation: Almagro-Moreno S, Murphy R, Boyd E. 2011. How Genomics Has Shaped Our Understanding of the Evolution and Emergence of Pathogenic , p 85-99. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch7

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