AsaGEI2b: A new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland

FEMS Microbiology Letters

Volumn 362, Issue 13, 2015, Pages

  Emond Rheault, Jean Guillaume ^a,b   Vincent, Antony T ^a,b   Trudel, Mélanie V ^a,b   Frey, Joachim ^c   Frenette, Michel ^a   Charette, Steve J ^a,b  

^a UNIVERSITÉ LAVAL   (Canada)

^b LAVAL UNIVERSITY   (Canada)

^c UNIVERSITY OF BERN   (Switzerland)

Author keywords

Aeromonas salmonicida subsp. salmonicida; AsaGEI2b; Genomic island; Type three secretion system

Indexed keywords

INTEGRASE; TRANSPOSON; TYPE III SECRETION SYSTEM; VIRULENCE FACTOR;

AEROMONAS SALMONICIDA; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; CONTROLLED STUDY; GENE LOCUS; GENE REARRANGEMENT; GENOME ANALYSIS; GENOMIC ISLAND; GENOTYPE; GEOGRAPHIC ORIGIN; INTEGRASE GENE; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SWITZERLAND; ANIMAL; BACTERIAL GENOME; CLASSIFICATION; DNA SEQUENCE; FURUNCULOSIS; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; MICROBIOLOGY; SALMONINE; SEQUENCE ALIGNMENT; TRANSPOSON; TYPE III SECRETION SYSTEM; WILD ANIMAL;

AEROMONAS SALMONICIDA; ANIMALS; ANIMALS, WILD; DNA TRANSPOSABLE ELEMENTS; FURUNCULOSIS; GENOME, BACTERIAL; GENOMIC ISLANDS; GENOTYPE; INTEGRASES; PLASMIDS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SWITZERLAND; TROUT; TYPE III SECRETION SYSTEMS; VIRULENCE FACTORS;

EID: 84949008538     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1093/femsle/fnv093     Document Type: Article

References (28)

1. Altschul S, Madden T, Schaffer A, et al. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
2. Bellanger X, Payot S, Leblond-Bourget N, et al. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 2013;38:1-42.
3. Bernoth E-M, Ellis AE, Midtlyng PJ, et al. Furunculosis: Multidisciplinary Fish Disease Research. New York: Academic Press, 1997.
4. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a selftraining method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001;29:2607-18.
5. Boyd J, Williams J, Curtis B, et al. Three small, cryptic plasmids from Aeromonas salmonicida subsp. salmonicida A449. Plasmid 2003;50:131-44.
6. Burr SE, Pugovkin D, Wahli T, et al. Attenuated virulence of an Aeromonas salmonicida subsp. salmonicida type III secretion mutant in a rainbow trout model. Microbiology 2005;151: 2111-8.
7. Carver T, Harris SR, Berriman M, et al. Artemis: an integrated platform for visualization and analysis of highthroughput sequence-based experimental data. Bioinformatics 2012;28:464-9.
8. Carver TJ, Rutherford KM, Berriman M, et al. ACT: the Artemis Comparison Tool. Bioinformatics 2005;21:3422-3.
9. Charette SJ, Brochu F, Boyle B, et al. Draft genome sequence of the virulent strain 01-B526 of the fish pathogen Aeromonas salmonicida. J Bacteriol 2012;194:722-3.
10. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015;31:587-9.
11. Daher RK, Filion G, Tan SGE, et al. Alteration of virulence factors and rearrangement of pAsa5 plasmid caused by the growth of Aeromonas salmonicida in stressful conditions. Vet Microbiol 2011;152:353-60.
12. Darmon E, Leach DRF. Bacterial genome instability. Microbiol Mol Biol Rev 2014;78:1-39.
13. Emond-Rheault J-G, Vincent AT, Trudel MV, et al. Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins. Vet Microbiol 2015;175:68-76.
14. Fehr D, Casanova C, Liverman A, et al. AopP, a type III effector protein of Aeromonas salmonicida, inhibits the NF-kappaB signalling pathway. Microbiology 2006;152:2809-18.
15. GalardiniM, Biondi EG, Bazzicalupo M, et al. CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes. Source Code Biol Med 2011;6:1-5.
16. Hanninen M, Hirveri-koski V. Microbiology molecular and phenotypic methods for the characterization of atypical Aeromonas salmonicida. Vet Microbiol 1997;56:147-58.
17. Hedrick RP. Movements of pathogens with the international trade of live fish: problems and solutions. Rev Sci Tech 1996;15:523-31.
18. Hyatt D, Chen G-L, Locascio PF, et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119.
19. Janda JM, Abbott SL. The genus Aeromonas: taxonomy, pathogenicity, and infection. Clin Microbiol Rev 2010;23:35-73.
20. JuhasM, van derMeer JR, Gaillard M, et al. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 2009;33:376-93.
21. Reith ME, Singh RK, Curtis B, et al. The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen. BMC Genomics 2008;9:427.
22. Stuber K, Burr SE, Braun M, et al. Type III secretion genes in Aeromonas salmonicida subsp. salmonicida are located on a large thermolabile virulence plasmid. J Clin Microbiol 2003;41:3854-6.
23. Studer N, Frey J, Vanden Bergh P. Clustering subspecies of Aeromonas salmonicida using IS630 typing. BMC Microbiol 2013;13:13-36.
24. SullivanMJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011;27:1009-10.
25. Tanaka KH, Dallaire-Dufresne S, Daher RK, et al. An insertion sequence-dependent plasmid rearrangement in Aeromonas salmonicida causes the loss of the type three secretion system. PLoS One 2012;7:e33725.
26. Trudel M V, Tanaka KH, Filion G, et al. Insertion sequence AS5 (ISAS5) is involved in the genomic plasticity of Aeromonas salmonicida. Mob Genet Elements 2013;5:1-7.
27. Vincent AT, Boyle B, Derome N, et al. Improvement in the DNA sequencing of genomes bearing long repeated elements.JMicrobiol Meth 2014;107:186-8.
28. Vincent AT, Tanaka KH, Trudel MV, et al. Draft genome sequences of two Aeromonas salmonicida subsp. salmonicida isolates harboring plasmids conferring antibiotic resistance. FEMS Microbiol Lett 2015;1:3-4.