Multi-locus Sequence Analysis (MLSA) of Edwardsiella tarda isolates from fish

Veterinary Microbiology

Volumn 158, Issue 3-4, 2012, Pages 367-375

  Abayneh, T ^a,c   Colquhoun, D J ^b   Sorum H ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b NORWEGIAN VETERINARY INSTITUTE   (Norway)

^c ADDIS ABABA UNIVERSITY   (Ethiopia)

Author keywords

Edwardsiella tarda; Fish; Multi locus Sequence Analysis

Indexed keywords

ADENOSINE KINASE; AROE2 PROTEIN; BACTERIAL DNA; BACTERIAL PROTEIN; DNA TOPOISOMERASE (ATP HYDROLYSING) B; GENOMIC DNA; MALATE DEHYDROGENASE; METG PROTEIN; PHOR PROTEIN; PROTEIN DNAK; PYRG PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIUM ISOLATE; CONTROLLED STUDY; EDWARDSIELLA TARDA; GENE CLUSTER; GENE LOCUS; GENETIC VARIABILITY; MOLECULAR PHYLOGENY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; SEQUENCE ANALYSIS;

ANIMALS; DNA GYRASE; EDWARDSIELLA TARDA; ENTEROBACTERIACEAE INFECTIONS; FISH DISEASES; FISHES; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS;

ANIMALIA; BACTERIA (MICROORGANISMS); EDWARDSIELLA TARDA;

EID: 84862576263     PISSN: 03781135     EISSN: 18732542     Source Type: Journal    
DOI: 10.1016/j.vetmic.2012.03.006     Document Type: Article

References (39)

1. Acharya M., Maiti N.K., Mohanty S., Mishra P., Samanta M. Genotyping of Edwardsiella tarda isolated from freshwater fish culture system. Comp. Immunol. Microbiol. Infect. Dis. 2007, 30:33-40.
2. Boni M.F., Posada D., Feldman M.W. An exact non-parametric method for inferring mosaic structure in sequence triplets. Genetics 2007, 176:1035-1047.
3. Castro N., Toranzo A., Barja J.L., Nunez S., Magarinos B. Characterization of E. tarda strains isolated from turbot, Psetta maxima (L.). J. Fish Dis. 2006, 29(9):541-547.
4. Dauga C. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol 2002, 52:531-547.
5. Deleótoile A., Decreó D., Courant S., Passet V., Audo J., Grimont P., Arlet G., Brisse S. Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing. J. Clin. Microbiol. 2009, 47(2):300-310.
6. Etherington G.J., Dicks J., Roberts I.N. Recombination analysis tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics 2005, 21(3):278-281.
7. Gibbs M.J., Armstrong J.S., Gibbs A.J. Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 2000, 16:573-582.
8. Gillings M., Holley M. Repetitive element PCR fingerprinting (REP-PCR) using Enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements. Lett. Appl. Microbiol. 1997, 25:17-21.
9. He Y., Xu T., Han Y., Shi X., Zhang X.H. Phenotypic diversity of Edwardsiella tarda isolated from different origins. Lett. Appl. Microbiol. 2011, 10.1111/j.1472-765X.2011.03103.x.
10. Janda J.M., Abbott S.L., Kroske-Bystrom S., Cheung W.K.W., Powers C., Kokka R.P., Tamura K. Pathogenic properties of Edwardsiella species. J. Clin. Microbiol. 1991, 29:1997-2001.
11. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
12. Lan J., Zhang X.H., Wang X.H., Chen Y.J., Han Y.Y. Isolation of an unusual strain of Edwardsiella tarda from turbot establish a PCR detection technique with the gyrB gene. J. Appl. Microbiol. 2008, 105:644-651. 10.1111/j.1365-2672.2008.03779.x.
13. Li W., Raoult D., Fournier P-E. Bacterial strain typing in the genomic era, a review. FEMS Microbiol. Rev. 2009, 33:892-916.
14. Maiti N.K., Arunika M., Mohanty S., Mandal R.N. Phenotypic genetic characterization of Edwardsiella tarda isolated from pond sediments. Comp. Immunol. Microbiol. Infect. Dis 2009, 32:1-8.
15. Martin D.P., Posada D., Crandall K.A., Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retrovi. 2005, 21:98-102.
16. Martin D., Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics 2000, 16:562-563.
17. Maynard Smith J.M. Analyzing the mosaic structure of genes. J. Mol. Evol. 1992, 34:126-129.
18. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3(5):418-426.
19. Nucci C., Silveria W.D., Correa S.S., Nakazato G., Bando S.Y., Ribeiro M.A., Castro A.F.P. Microbiological comparative study of isolates of Edwardsiella tarda isolated in different countries from fish and humans. Vet. Microbiol. 2002, 89:29-39.
20. Paauw A., Caspers M.P.M., Schuren F.H.J., Hall M.A.L., Delétoile A., Montijn R.C., Verhoef J., Fluit A.C. Genomic diversity within the Enterobacter cloacae complex. PLoS One 2008, 3(8):e3018. 10.1371/journal.pone.0003018.
21. Padidam M., Sawyer S., Fauquet C.M. Possible emergence of new geminiviruses by frequent recombination. Virology. 1999, 265:218-225.
22. Panangala V.S., Shoemaker C.A., McNulty S.T., Arias C.R., Klesius P.H. Intra- inter-specific phenotypic characteristics of fish-pathogenic Edwardsiella ictaluri and E. tarda. Aquacult. Res. 2006, 37:49-60.
23. Papke R.T., Koenig J.E., Rodriguez-Valera F., Doolittle W.F. Frequent recombination in a salter population of Halorubrum. Science 2004, 306:1928-1929.
24. Papke R.T., White E., Reddy P., Weigel G., Kamekura M., Minegishi H., Usami R., Ventosa A. A Multilocus Sequence Analysis (MLSA) approach to Halobacteriales Phylogeny and Taxonomy. Int. J. Syst. Evol. Microbiol 2011, 10.1099/ijs.0.029298-0.
25. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:13757-13762.
26. Renders N., Romling U., Verbrugh H., van Belkum A. Comparative typing of Pseudomonas aeruginosa by random amplification of polymorphic DNA or pulse-field gel electrophoresis of DNA macrorestriction fragments. J. Clin. Microbiol. 1996, 34:3190-3195.
27. Rzhetsky A., Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 1993, 10:1073-1095.
28. Saitou N., Nei M. The neighbor-joining method. A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
29. Salerno A., Delétoile A., Lefevre M., Ciznar I., Krovacek K., Grimont P., Brisse S. Recombining population structure of the Enterobacteriaceae Plesiomonas shigelloides revealed by multilocus sequence typing. J. Bacteriol. 2007, 10.1128/JB.00796-07.
30. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10:512-526.
31. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 10.1093/molbev/msr121.
32. Tan Y.P., Lin Q., Wang X.H., Joshi S., Hew C.L., Leung K.Y. Comparative proteomic analysis of extracellular proteins of Edwardsiella tarda. Infect. Immun. 2002, 70:6475-6480.
33. Thune R.L., Stanley L.A., Cooper R.K. Pathogenesis of Gram-negative bacterial infections in warm water fish. Annu. Rev. Fish Dis. 1993, 3:37-68.
34. Vinuesa P. Multi-locus sequence analysis and bacterial species phylogeny estimation. Molecular Phylogeny of Microorganisms 2010, 41-64. Caister Academic Press. A. Oren, R.T. Papke (Eds.).
35. Wang Q., Yang M., Xiao J., Wu H., Wang X., Lv Y., Xu L., Zheng H., Wang S., Zhao G., Liu Q., Zhang Y. Genome sequence of the versatile fish pathogen, Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PLoS One 2009, 4(10):e7646. 10.1371/journal.pone.0007646.
36. Wang Y., Zhang X., Austin H.B. Comparative analysis of the phenotypic characteristics of high- and low-virulent strains of Edwardsiella tarda. J. Fish Dis. 2010, 33:985-994.
37. Wei L.S., Musa N. Phenotyping, genotyping and whole cell protein profiling of E. tarda isolated from cultured and natural habitat freshwater fish. American-Eurasian J. Agric. Environ. Sci. 2008, 3(5):681-691.
38. Williams M.L., Gillaspy A.F., Dyer D.W., Thune R.L., Waldbieser G.C., Schuster S.C., Gipson J., Zaitshik J., Landry C., Banes M.M., Lawrence M.L. Genome sequence of Edwardsiella ictaluri 93-146, a strain associated with a natural channel catfish outbreak of Enteric Septicemia of Catfish. J. Bacteriol. 2012, 194(3):740-741. 10.1128/JB.06522-11.
39. Zadoks R.N., Schukken Y.H., Wiedmann M. Multi-locus sequence typing of Streptococcus uberis provides sensitive and epidemiologically relevant subtype information and reveals positive selection in the virulence gene pauA. J. Clin. Microbiol. 2005, 43(5):2407-2417.