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Complete genome sequence analysis of a novel Staphylococcus phage StAP1 and proposal of a new species in the genus Silviavirus

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Abstract

Bacteriophage StAP1 was isolated from a soil sample infecting Staphylococcus aureus and S. xylosus. Its genome was found to be 135,502 base pairs (bp) long with 30.00 mol% G+C content and 192 open reading frames. While no tRNA encoding genes were identified, 7 mobile elements were found to interrupt five StAP1 open reading frames. Comparative genomic and proteomic analysis consistently supports the establishment of a new species in the genus Silviavirus.

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References

  1. Virus Taxonomy: 2015 Release. International Committee on Taxonomy of Viruses. http://www.ictvonline.org/virusTaxonomy.asp. Accessed on 25th August 2016

  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:1

    Article  Google Scholar 

  4. Bean NH, Griffin PM, Goulding JS, Ivey CB (1990) Foodborne disease outbreaks, 5-year summary, 1983–1987. J Food Prot 53:711–728

    Article  Google Scholar 

  5. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147

    Article  PubMed  PubMed Central  Google Scholar 

  6. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard J-F, Guindon S, Lefort V, Lescot M (2008) Phylogeny. fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36:W465–W469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Dias R, Eller M, Duarte V, Pereira Â, Silva C, Mantovani H, Oliveira L, de Silva AM, De Paula S (2013) Use of phages against antibiotic-resistant isolated from bovine mastitis. J Anim Sci 91:3930–3939

    Article  CAS  PubMed  Google Scholar 

  9. Emori TG, Gaynes RP (1993) An overview of nosocomial infections, including the role of the microbiology laboratory. Clin Microbiol Rev 6:428–442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Enright MC, Day NP, Davies CE, Peacock SJ, Spratt BG (2000) Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 38:1008–1015

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Hagens S, Loessner MJ (2007) Application of bacteriophages for detection and control of foodborne pathogens. Appl Microbiol Biotechnol 76:513–519

    Article  CAS  PubMed  Google Scholar 

  12. Kwan T, Liu J, DuBow M, Gros P, Pelletier J (2005) The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci USA 102:5174–5179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Mann NH (2008) The potential of phages to prevent MRSA infections. Res Microbiol 159:400–405

    Article  CAS  PubMed  Google Scholar 

  16. Murray R (2005) Recognition and management of Staphylococcus aureus toxin-mediated disease. Intern Med J 35:S106–S119

    Article  PubMed  Google Scholar 

  17. O’Flaherty S, Coffey A, Edwards R, Meaney W, Fitzgerald G, Ross R (2004) Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G+ C content. J Bacteriol 186:2862–2871

    Article  PubMed  PubMed Central  Google Scholar 

  18. Rombel IT, Sykes KF, Rayner S, Johnston SA (2002) ORF-FINDER: a vector for high-throughput gene identification. Gene 282:33–41

    Article  CAS  PubMed  Google Scholar 

  19. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson M-A, Roy SL, Jones JL, Griffin PM (2011) Foodborne illness acquired in the United States—major pathogens. Emerg Infect Dis 17:7–15

    Article  PubMed  PubMed Central  Google Scholar 

  20. Shin H, Bandara N, Shin E, Ryu S, Kim K-P (2011) Prevalence of Bacillus cereus bacteriophages in fermented foods and characterization of phage JBP901. Res Microbiol 162:791–797

    Article  CAS  PubMed  Google Scholar 

  21. Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244–W248

    Article  PubMed  PubMed Central  Google Scholar 

  22. Steinberg JP, Clark CC, Hackman BO (1996) Nosocomial and community-acquired Staphylococcus aureus bacteremias from 1980 to 1993: impact of intravascular devices and methicillin resistance. Clin Infect Dis 23:255–259

    Article  CAS  PubMed  Google Scholar 

  23. Vandersteegen K, Kropinski AM, Nash JH, Noben J-P, Hermans K, Lavigne R (2013) Romulus and Remus, two phage isolates representing a distinct clade within the Twortlikevirus genus, display suitable properties for phage therapy applications. J Virol 87:3237–3247

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Wilcox M (2011) MRSA new treatments on the horizon: current status. Injury 42:S42–S44

    Article  PubMed  Google Scholar 

  25. Zafar N, Mazumder R, Seto D (2002) CoreGenes: a computational tool for identifying and cataloging “core” genes in a set of small genomes. BMC Bioinform 3:1

    Article  Google Scholar 

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Acknowledgements

This work was supported by the High Value-added Food Technology Development Program, Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET), and the Ministry for Food, Agriculture, Forestry, and Fisheries of the Republic of Korea (IPET) (Project No. 313037-3).

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Authors and Affiliations

  1. Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Republic of Korea

    Amal Senevirathne, Kuntal Ghosh & Kwang-Pyo Kim

  2. Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 55365, Republic of Korea

    Eunjung Roh

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  1. Amal Senevirathne
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  2. Kuntal Ghosh
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  3. Eunjung Roh
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Correspondence to Kwang-Pyo Kim.

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Author Amal Senevirathne declares that he has no conflict of interest; Author Kuntal Ghosh declares that he has no conflict of interest; Author Eunjung Roh declares that she has no conflict of interest, and Author Kwang-Pyo Kim declares that he has no conflict of interest.

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

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Senevirathne, A., Ghosh, K., Roh, E. et al. Complete genome sequence analysis of a novel Staphylococcus phage StAP1 and proposal of a new species in the genus Silviavirus . Arch Virol 162, 2145–2148 (2017). https://doi.org/10.1007/s00705-017-3316-2

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  • DOI: https://doi.org/10.1007/s00705-017-3316-2

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