Edwardsiella comparative phylogenomics reveal the new intra/inter-species taxonomic relationships, virulence evolution and niche adaptation mechanisms

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Yang, Minjun ^a   Lv, Yuanzhi ^a   Xiao, Jingfan ^a   Wu, Haizhen ^a   Zheng, Huajun ^b   Liu, Qin ^a   Zhang, Yuanxing ^a   Wang, Qiyao ^a  

^a EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; CONTROLLED STUDY; EDWARDSIELLA ICTALURI; EDWARDSIELLA TARDA; ENTEROBACTERIACEAE INFECTION; EVOLUTIONARY ADAPTATION; GENE CLUSTER; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; GENOTYPE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENOMICS; SPECIES DIFFERENTIATION; TAXONOMY; TYPE III SECRETION SYSTEM; TYPE IV SECRETION SYSTEM; UNINDEXED SEQUENCE; ANIMAL; ANIMAL DISEASE; CATFISH; COMPARATIVE STUDY; FISH DISEASE; GENETICS; GENOMICS; MICROBIOLOGY; MOLECULAR EVOLUTION; PATHOGENICITY; PHYLOGENY;

ANIMALIA; EDWARDSIELLA ICTALURI; EDWARDSIELLA TARDA; ICTALURUS PUNCTATUS;

ANIMALS; CATFISHES; EDWARDSIELLA ICTALURI; EDWARDSIELLA TARDA; ENTEROBACTERIACEAE INFECTIONS; EVOLUTION, MOLECULAR; FISH DISEASES; GENOME, BACTERIAL; GENOMICS; GENOTYPE; PHYLOGENY;

EID: 84860999721     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036987     Document Type: Article

References (66)

1. Abbott SL, Janda JM, (2006) The genus Edwardsiella. Prokaryotes 6: 72-89.
2. Morrison EE, Plumb JA, (1994) Olfactory organ of channel catfish as a site of experimental Edwardsiella ictaluri infection. J Aquat Anim Health 6: 101-109.
3. Panangala VS, Shoemaker CA, McNulty ST, Arias CR, Klesius PH, (2006) Intra and interspecific phenotypic characteristics of fish pathogenic Edwardsiella ictaluri and E. tarda. Aquac Res 37: 49-60.
4. Mohanty BR, Sahoo PK, (2007) Edwardsiellosis in fish: a brief review. J Biosci 32: 1331-1344.
5. Bockemühl J, Pan-Urai R, Burkhardt F, (1971) Edwardsiella tarda associated with human disease. Pathobiology 37: 393-401.
6. Kawai T, Kusakabe H, Seki A, Kobayashi S, Onodera M, (2011) Osteomyelitis due to trimethoprim/sulfamethoxazole-resistant Edwardsiella tarda infection in a patient with X-linked chronic granulomatous disease. Infection 39: 171-173.
7. Golub V, Kim AC, Krol V, (2010) Surgical wound infection, tuboovarian abscess, and sepsis caused by Edwardsiella tarda: case reports and literature review. Infection 38: 487-489.
8. Castro N, Toranzo AE, Barja JL, Nunez S, Magarinos B, (2006) Characterization of Edwardsiella tarda strains isolated from turbot, Psetta maxima (L.). J Fish Dis 29: 541-547.
9. Kumar G, Rathore G, Sengupta U, Singh V, Kapoor D, et al. (2007) Isolation and characterization of outer membrane proteins of Edwardsiella tarda and its application in immunoassays. Aquaculture 272: 98-104.
10. Acharya M, Maiti NK, Mohanty S, Mishra P, Samanta M, (2007) Genotyping of Edwardsiella tarda isolated from freshwater fish culture system. Comp Immunol Microbiol Infect Dis 30: 33-40.
11. Lan J, Zhang XH, Wang Y, Chen J, Han Y, (2008) Isolation of an unusual strain of Edwardsiella tarda from turbot and establish a PCR detection technique with the gyrB gene. J Appl Microbiol 105: 644-651.
12. Wang YM, Wang QY, Xiao JF, Liu Q, Wu HZ, et al. (2011) Genetic relationships of Edwardsiella strains isolated in China aquaculture revealed by rep-PCR genomic fingerprinting and investigation of Edwardsiella virulence genes. J Appl Microbiol 111: 1337-1348.
13. Castro N, Toranzo AE, Bastardo A, Barja JL, Magariños B, (2011) Intraspecific genetic variability of Edwardsiella tarda strains from cultured turbot. Dis Aquat Org 95: 253-258.
14. Maiti NK, Mandal A, Mohanty S, Samanta M, (2008) Comparative analysis of genome of Edwardsiella tarda by BOX-PCR and PCR-ribotyping. Aquaculture 280: 60-63.
15. Panangala VS, Santen VL, Shoemaker CA, Klesius PH, (2005) Analysis of 16S-23S intergenic spacer regions of the rRNA operons in Edwardsiella ictaluri and Edwardsiella tarda isolates from fish. J Appl Microbiol 99: 657-669.
16. Wang QY, Yang MJ, Xiao JF, Wu HZ, Wang X, et al. (2009) Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PLoS ONE 4: 1331-1344.
17. Soest JJ, (2011) Infectious disease studies in zebrafish: the fish pathogen Edwardsiella tarda as a model system: Department of Molecular Microbiology and Department of Molecular Cell Biology, Institute of Biology Leiden, Faculty of Science, Leiden University.
18. Dumpala PR, Lawrence ML, Karsi A, (2009) Proteome analysis of Edwardsiella ictaluri. Proteomics 9: 1353-1363.
19. Ewing WH, McWhorter AC, Escobar MR, Lubin AH, (1965) Edwardsiella, a new genus of Enterobacteriaceae based on a new species, E. tarda. Int J Syst Evol Microbiol 15: 33-38.
20. Hawke JP, McWhorter A, Steigerwalt AG, Brenner NJ, (1981) Edwardsiella ictaluri sp. nov., the causative agent of enteric septicemia of catfish. Int J Syst Evol Microbiol 31: 396-400.
21. Amandi A, Hiu SF, Rohovec JS, Fryer JL, (1982) Isolation and characterization of Edwardsiella tarda from fall chinook salmon (Oncorhynchus tshawytscha). Appl Environ Microbiol 43: 1380-1384.
22. Baya AM, Romalde JL, Green DE, Navarro RB, Evans J, et al. (1997) Edwardsiellosis in wild striped bass from the Chesapeake Bay. J Wildl Dis 33: 517-525.
23. Thune RL, Stanley LA, Cooper RK, (1993) Pathogenesis of gram-negative bacterial infections in warmwater fish. Annu Rev Fish Dis 3: 37-68.
24. Thune RL, Fernandez DH, Battista JR, (1999) An aroA mutant of Edwardsiella ictaluri is safe and efficacious as a live, attenuated vaccine. J Aquat Anim Health 11: 358-372.
25. Xiao JF, Wang QY, Liu Q, Wang X, Liu H, et al. (2008) Isolation and identification of fish pathogen Edwardsiella tarda from mariculture in China. Aquac Res 40: 13-17.
26. Partridge SR, Hall RM, (2003) The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons. J Bacteriol 185: 6371-6384.
27. Konstantinidis KT, Tiedje JM, (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102: 2567-2572.
28. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, et al. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57: 81-91.
29. Yamamoto S, Okujo N, Yoshida T, Matsuura S, Shinoda S, (1994) Structure and iron transport activity of vibrioferrin, a new siderophore of Vibrio parahaemolyticus. J Biochem 115: 868-874.
30. Wang QY, Liu Q, Ma Y, Zhou LY, Zhang YX, (2007) Isolation, sequencing and characterization of cluster genes involved in the biosynthesis and utilization of the siderophore of marine fish pathogen Vibrio alginolyticus. Arch Microbiol 188: 433-439.
31. Hirakawa H, Nishino K, Hirata T, Yamaguchi A, (2003) Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli. J Bacteriol 185: 1851-1856.
32. Lai TH, Kumagai Y, Hyodo M, Hayakawa Y, Rikihisa Y, (2009) The Anaplasma phagocytophilum PleC histidine kinase and PleD diguanylate cyclase two-component system and role of cyclic Di-GMP in host cell infection. J Bacteriol 191: 693-700.
33. Wipat A, Carter N, Brignell SC, Guy BJ, Piper K, et al. (1996) The dnaB-pheA (256°-240°) region of the Bacillus subtilis chromosome containing genes responsible for stress responses, the utilization of plant cell walls and primary metabolism. Microbiology 142: 3067-3078.
34. Tan YP, Zheng J, Tung SL, Rosenshine I, Leung KY, (2005) Role of type III secretion in Edwardsiella tarda virulence. Microbiology 151: 2301-2313.
35. Zheng J, Leung KY, (2007) Dissection of a type VI secretion system in Edwardsiella tarda. Mol Microbiol 66: 1192-1206.
36. Wang X, Wang QY, Xiao JF, Liu Q, Wu HZ, et al. (2009) Edwardsiella tarda T6SS component evpP is regulated by esrB and iron, and plays essential roles in the invasion of fish. Fish Shellfish Immun 27: 469-477.
37. Wang X, Wang QY, Xiao JF, Liu Q, Wu HZ, et al. (2010) Hemolysin EthA in Edwardsiella tarda is essential for fish invasion in vivo and in vitro and regulated by two-component system EsrA-EsrB and nucleoid protein HhaEt. Fish Shellfish Immun 29: 1082-1091.
38. Tamura K, Sakazaki R, McWhorter AC, Kosako Y, (1988) Edwardsiella tarda serotyping scheme for international use. J Clin Microbiol 26: 2343-2346.
39. Lobb CJ, Ghaffari SH, Hayman JR, Thompson DT, (1993) Plasmid and serological differences between Edwardsiella ictaluri strains. Appl Environ Microbiol 59: 2830-2836.
40. Wang X, Quinn PJ, (2010) Lipopolysaccharide: biosynthetic pathway and structure modification. Prog Lipid Res 49: 97-107.
41. Xu LL, Wang QY, Xiao JF, Liu Q, Wang X, et al. (2010) Characterization of Edwardsiella tarda waaL: roles in lipopolysaccharide biosynthesis, stress adaptation, and virulence toward fish. Arch Microbiol 192: 1039-1047.
42. Nei M, Li WH, (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76: 5269-5273.
43. Nei M, Gojobori T, (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions Mol Biol Evol. 3: 418-426.
44. Yang Z, (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24: 1586-1591.
45. Stojiljkovic I, Hantke K, (1994) Transport of haemin across the cytoplasmic membrane through a haemin specific periplasmic binding protein dependent transport system in Yersinia enterocolitica. Mol Microbiol 13: 719-732.
46. Chamnongpol S, Dodson W, Cromie MJ, Harris ZL, Groisman EA, (2002) Fe (III) mediated cellular toxicity. Mol Microbiol 45: 711-719.
47. Baek JH, Kang YJ, Lee SY, (2007) Transcript and protein level analyses of the interactions among PhoB, PhoR, PhoU and CreC in response to phosphate starvation in Escherichia coli. FEMS Microbiol Lett 277: 254-259.
48. Loprasert S, Whangsuk W, Sallabhan R, Mongkolsuk S, (2005) The unique glutathione reductase from Xanthomonas campestris: gene expression and enzyme characterization. Biochem Biophys Res Commun 331: 1324-1330.
49. Forst S, Delgado J, Inouye M, (1989) Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli. Proc Natl Acad Sci U S A 86: 6052-6056.
50. Jovanovic G, Weiner L, Model P, (1996) Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J Bacteriol 178: 1936-1945.
51. Bernadac A, Gavioli M, Lazzaroni JC, Raina S, Lloubes R, (1998) Escherichia coli tol-pal mutants form outer membrane vesicles. J Bacteriol 180: 4872-4878.
52. Xu C, Lin X, Ren H, Zhang Y, Wang S, et al. (2006) Analysis of outer membrane proteome of Escherichia coli related to resistance to ampicillin and tetracycline. Proteomics 6: 462-473.
53. Rogge ML, Thune RL, (2011) Regulation of the Edwardsiella ictaluri Type III Secretion System by pH and Phosphate Concentration through EsrA, EsrB, and EsrC. Appl Environ Microbiol 77: 4293-4302.
54. Lan MZ, Peng X, Xiang MY, Xia ZY, Bo W, et al. (2007) Construction and characterization of a live, attenuated esrB mutant of Edwardsiella tarda and its potential as a vaccine against the haemorrhagic septicaemia in turbot, Scophthamus maximus (L.). Fish Shellfish Immun 23: 521-530.
55. Cheng S, Hu Y, Zhang M, Sun L, (2010) Analysis of the vaccine potential of a natural avirulent Edwardsiella tarda isolate. Vaccine 28: 2716-2721.
56. Milton DL, Norqvist A, Wolf-Watz H, (1992) Cloning of a metalloprotease gene involved in the virulence mechanism of Vibrio anguillarum. J Bacteriol 174: 7235-7244.
57. Zerbino DR, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
58. Gordon D, Desmarais C, Green P, (2001) Automated finishing with Autofinish. Genome Res 11: 614-625.
59. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
60. Langille MGI, Brinkman FSL, (2009) IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25: 664-665.
61. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M, (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34: D32-D36.
62. Ghai R, Hain T, Chakraborty T, (2004) GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5: 198.
63. Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
64. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
65. Chappey C, (2007) Computational analysis of HIV molecular sequences. Computational Genomics: Current Methods 109.
66. Vilella AJ, Blanco-Garcia A, Hutter S, Rozas J, (2005) VariScan: analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21: 2791-2793.