Advertisement

Archives of Virology

, Volume 165, Issue 1, pp 219–222 | Cite as

Genomic characterization of bacteriophage pEt-SU, a novel phiKZ-related virus infecting Edwardsiella tarda

  • Sang Guen Kim
  • Sib Sankar Giri
  • Saekil Yun
  • Hyoun Joong Kim
  • Sang Wha Kim
  • Jung Woo Kang
  • Se Jin Han
  • Jun Kwon
  • Jin Woo Jun
  • Woo Taek Oh
  • Se Chang ParkEmail author
Annotated Sequence Record

Abstract

A bacteriophage infecting Edwardsiella tarda (named pEt-SU) was isolated from freshwater collected in Chung-ju, South Korea. The whole genome of pEt-SU was 276,734 bp in length, representing the first giant phage infecting Edwardsiella reported to date. A total of 284 putative open reading frames were predicted and annotated. Morphology and genome analyses verified that pEt-SU may be distantly related to the phiKZ-like phages, a well-known giant myovirus. The findings in this study provide new insights into the phages infecting E. tarda ads well as fundamental data for the study of giant phages.

Notes

Acknowledgements

This research was supported by the Cooperative Research Program of the Center for Companion Animal Research (PJ0139852019) of the Rural Development Administration, Republic of Korea, and the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2017R1C1B2004616).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain studies with human participants or animals performed by any of the authors.

Supplementary material

705_2019_4432_MOESM1_ESM.docx (71 kb)
Supplementary material 1 (DOCX 70 kb)

References

  1. 1.
    Xu T, Zhang XH (2014) Edwardsiella tarda: an intriguing problem in aquaculture. Aquaculture 431:129–135CrossRefGoogle Scholar
  2. 2.
    Hirai Y, Asahata-Tago S, Ainoda Y, Fujita T, Kikuchi K (2015) Edwardsiella tarda bacteremia. A rare but fatal water-and foodborne infection: review of the literature and clinical cases from a single centre. Can J Infect Dis Med Microbiol 26:313–318CrossRefGoogle Scholar
  3. 3.
    Lee K, Kim HK, Park SK, Sohn H, Cho Y, Choi YM, Jeong DG, Kim JH (2018) First report of the occurrence and whole-genome characterization of Edwardsiella tarda in the false killer whale (Pseudorca crassidens). J Vet Med Sci 80:1041–1046CrossRefGoogle Scholar
  4. 4.
    Shin DM, Hossain S, Wimalasena S, Heo GJ (2016) Antimicrobial resistance and virulence factors of Edwardsiella tarda isolated from pet turtles. Pak Vet J 37:85–89Google Scholar
  5. 5.
    Miniero Davies Y, Xavier de Oliveira MG, Paulo Vieira Cunha M, Soares Franco L, Pulecio Santos SL, Zanolli Moreno L, Tulio de Moura Gomes V, Zanolli Sato MI, Schiavo Nardi M, Micke Moreno A, Becker Saidenberg A, de Sa RM (2018) Edwardsiella tarda outbreak affecting fishes and aquatic birds in Brazil. Vet Q 38:99–105CrossRefGoogle Scholar
  6. 6.
    Park SB, Aoki T, Jung TS (2012) Pathogenesis of and strategies for preventing Edwardsiella tarda infection in fish. Vet Res 43:67CrossRefGoogle Scholar
  7. 7.
    Nakai T (2010) Application of bacteriophages for control of infectious diseases in aquaculture. In: Sabour PM, Griffiths MW (eds) Bacteriophages in the control of food- and waterborne pathogens. ASM Press, Washington, DC, pp 257–272CrossRefGoogle Scholar
  8. 8.
    Wu JL (1982) Isolation and application of a new bacteriophage, ET-1, which infect Edwardsiella tarda, the pathogen of edwardsiellosis. Rep Fish Dis Res 4:8–17Google Scholar
  9. 9.
    Yasuike M, Sugaya E, Nakamura Y, Shigenobu Y, Kawato Y, Kai W, Nagai S, Fujiwara A, Sano M, Kobayashi T, Nakai T (2013) Complete genome sequence of a novel myovirus which infects atypical strains of Edwardsiella tarda. Genome Announc 1:e00248-12CrossRefGoogle Scholar
  10. 10.
    Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Sugaya E, Kawato Y, Nagai S, Kobayashi T, Ototake M, Nakai T (2015) Full-genome sequence of a novel myovirus, GF-2, infecting Edwardsiella tarda: comparison with other Edwardsiella myoviral genomes. Arch Virol 160:2129–2133CrossRefGoogle Scholar
  11. 11.
    Kim SG, Jun JW, Giri SS, Yun S, Kim HJ, Kim SW, Kang JW, Han SJ, Jeong D, Park SC (2019) Isolation and characterisation of pVa-21, a giant bacteriophage with anti-biofilm potential against Vibrio alginolyticus. Sci Rep 9:6284CrossRefGoogle Scholar
  12. 12.
    Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618CrossRefGoogle Scholar
  13. 13.
    Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
  14. 14.
    Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefGoogle Scholar
  15. 15.
    Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25:119–120CrossRefGoogle Scholar
  16. 16.
    Rice P, Longden I, Bleasby A (2000) EMBOSS: the european molecular biology open software suite. Trends Genet 16:276–277CrossRefGoogle Scholar
  17. 17.
    Cornelissen A, Hardies SC, Shaburova OV, Krylov VN, Mattheus W, Kropinski AM, Lavigne R (2012) Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse ϕKZ-related phages. J Virol 86:1844–1852CrossRefGoogle Scholar
  18. 18.
    Shaburova OV, Hertveldt K, de la Cruz DMA, Krylov SV, Pleteneva EA, Bourkaltseva MV, Lavigne R, Volckaert G, Krylov VN (2006) Comparison of new giant bacteriophages OBP and Lu11 of soil pseudomonads with bacteriophages of the ϕKZ-supergroup of Pseudomonas aeruginosa. Russ J Genet 42:877–885CrossRefGoogle Scholar
  19. 19.
    Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W (2003) Bacteriophage T4 genome. Microbiol Mol Biol Rev 67:86–156CrossRefGoogle Scholar
  20. 20.
    Carrias A, Welch TJ, Waldbieser GC, Mead DA, Terhune JS, Liles MR (2011) Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri. Virol J 8:6CrossRefGoogle Scholar
  21. 21.
    Katharios P, Kalatzis PG, Kokkari C, Pavlidis M, Wang Q (2019) Characterization of a highly virulent Edwardsiella anguillarum strain isolated from Greek aquaculture, and a spontaneously induced prophage therein. Front Microbiol 10:141CrossRefGoogle Scholar
  22. 22.
    Kawato Y, Nakai T (2012) Infiltration of bacteriophages from intestinal tract to circulatory system in goldfish. Fish Pathol 47:1–6CrossRefGoogle Scholar
  23. 23.
    Yasuike M, Kai W, Nakamura Y, Fujiwara A, Kawato Y, Hassan ES, Mahmoud MM, Nagai S, Kobayashi T, Ototake M, Nakai T (2014) Complete genome sequence of the Edwardsiella ictaluri-specific bacteriophage PEi21, isolated from river water in Japan. Genome Announc 2:e00228-14CrossRefGoogle Scholar
  24. 24.
    Leblanc C, Caumont-Sarcos A, Comeau AM, Krisch HM (2009) Isolation and genomic characterization of the first phage infecting Iodobacteria: ϕPLPE, a myovirus having a novel set of features. Environ Microbiol Rep 1:499–509CrossRefGoogle Scholar
  25. 25.
    Yasuike M, Sugaya E, Nakamura Y, Shigenobu Y, Kawato Y, Kai W, Fujiwara A, Sano M, Kobayashi T, Nakai T (2013) Complete genome sequences of Edwardsiella tarda-lytic bacteriophages KF-1 and IW-1. Genome Announc 1:e00089-12CrossRefGoogle Scholar
  26. 26.
    Krumsiek J, Arnold R, Rattei T (2007) Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23:1026–1028CrossRefGoogle Scholar
  27. 27.
    Meier-Kolthoff JP, Göker M (2017) VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 33:3396–3404CrossRefGoogle Scholar
  28. 28.
    Turner D, Reynolds D, Seto D, Mahadevan P (2013) CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Res Notes 6:140CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Sang Guen Kim
    • 1
  • Sib Sankar Giri
    • 1
  • Saekil Yun
    • 1
  • Hyoun Joong Kim
    • 1
  • Sang Wha Kim
    • 1
  • Jung Woo Kang
    • 1
  • Se Jin Han
    • 1
  • Jun Kwon
    • 1
  • Jin Woo Jun
    • 2
  • Woo Taek Oh
    • 1
  • Se Chang Park
    • 1
    Email author
  1. 1.Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary ScienceSeoul National UniversitySeoulRepublic of Korea
  2. 2.Department of AquacultureKorea National College of Agriculture and FisheriesJeonju-siRepublic of Korea

Personalised recommendations