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Volume 95, Issue 11

Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Free

Abstract

We isolated and characterized a novel virulent bacteriophage, IME-EFm1, specifically infecting multidrug-resistant . IME-EFm1 is morphologically similar to members of the family . It was found capable of lysing a wide range of our collections, including two strains resistant to vancomycin. One-step growth tests revealed the host lysis activity of phage IME-EFm1, with a latent time of 30 min and a large burst size of 116 p.f.u. per cell. These biological characteristics suggested that IME-EFm1 has the potential to be used as a therapeutic agent. The complete genome of IME-EFm1 was 42 597 bp, and was linear, with terminally non-redundant dsDNA and a G+C content of 35.2 mol%. The termini of the phage genome were determined with next-generation sequencing and were further confirmed by nuclease digestion analysis. To our knowledge, this is the first report of a complete genome sequence of a bacteriophage infecting . IME-EFm1 exhibited a low similarity to other phages in terms of genome organization and structural protein amino acid sequences. The coding region corresponded to 90.7 % of the genome; 70 putative ORFs were deduced and, of these, 29 could be functionally identified based on their homology to previously characterized proteins. A predicted metallo-β-lactamase gene was detected in the genome sequence. The identification of an antibiotic resistance gene emphasizes the necessity for complete genome sequencing of a phage to ensure it is free of any undesirable genes before use as a therapeutic agent against bacterial pathogens.

  • Received:
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© 2014 The Authors
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2014-11-01
2024-04-23
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References

  1. Abedon S.(editor) ( 2008 Bacteriophage Ecology: Population Growth, Evolution and Impact of Bacterial Viruses. Advances in Molecular and Cellular Microbiology Cambridge: Cambridge University Press; [View Article]
     [Google Scholar]
  2. Abedon S. 2011; Phage therapy pharmacology: calculating phage dosing. Adv Appl Microbiol 77:1–40 [View Article][PubMed]
     [Google Scholar]
  3. Adams M. H. 1959; Methods of study of bacterial viruses. In Bacteriophages pp. 445–447 Edited by Adams M. H. New York: Interscience;
     [Google Scholar]
  4. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [View Article][PubMed]
     [Google Scholar]
  5. Anisimov A. P., Amoako K. K. 2006; Treatment of plague: promising alternatives to antibiotics. J Med Microbiol 55:1461–1475 [View Article][PubMed]
     [Google Scholar]
  6. Arias C. A., Murray B. E. 2012; The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol 10:266–278 [View Article][PubMed]
     [Google Scholar]
  7. Aziz R. K., Bartels D., Best A. A., DeJongh M., Disz T., Edwards R. A., Formsma K., Gerdes S., Glass E. M.other authors 2008; The rast Server: rapid annotations using subsystems technology. BMC Genomics 9:75 [View Article][PubMed]
     [Google Scholar]
  8. Bateman A., Coin L., Durbin R., Finn R. D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S.other authors 2004; The Pfam protein families database. Nucleic Acids Res 32:suppl 1D138–D141 [View Article][PubMed]
     [Google Scholar]
  9. Biswas B., Adhya S., Washart P., Paul B., Trostel A. N., Powell B., Carlton R., Merril C. R. 2002; Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun 70:204–210 [View Article][PubMed]
     [Google Scholar]
  10. Brabban A. D., Hite E., Callaway T. R. 2005; Evolution of foodborne pathogens via temperate bacteriophage-mediated gene transfer. Foodborne Pathog Dis 2:287–303 [View Article][PubMed]
     [Google Scholar]
  11. Brueggemann A. B., Pai R., Crook D. W., Beall B. 2007; Vaccine escape recombinants emerge after pneumococcal vaccination in the United States. PLoS Pathog 3:e168 [View Article][PubMed]
     [Google Scholar]
  12. Carlson K. 2005; Appendix: working with bacteriophages: common techniques and methodological approaches. In Bacteriophages: Biology and Applications pp. 437–494 Edited by Kutter E., Sulakvelidze A. Boca Raton, FL: CRC Press;
     [Google Scholar]
  13. CLSI 2012 Performance Standards for Antimicrobial Disk Susceptibility Tests; Approved standard, 11th edn, M02-A11. Wayne, PA: Clinical and Laboratory Standards Institute
     [Google Scholar]
  14. Courchesne N. M., Parisien A., Lan C. Q. 2009; Production and application of bacteriophage and bacteriophage-encoded lysins. Recent Pat Biotechnol 3:37–45 [View Article][PubMed]
     [Google Scholar]
  15. de Been M., van Schaik W., Cheng L., Corander J., Willems R. J. 2013; Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium. Genome Biol Evol 5:1524–1535 [View Article][PubMed]
     [Google Scholar]
  16. Debarbieux L. 2008; [Experimental phage therapy in the beginning of the 21st century]. Med Mal Infect 38:421–425 (in French) [View Article][PubMed]
     [Google Scholar]
  17. Desiere F., Lucchini S., Canchaya C., Ventura M., Brüssow H. 2002; Comparative genomics of phages and prophages in lactic acid bacteria. Antonie van Leeuwenhoek 82:73–91 [View Article][PubMed]
     [Google Scholar]
  18. Ellis E. L., Delbrück M. 1939; The growth of bacteriophage. J Gen Physiol 22:365–384 [View Article][PubMed]
     [Google Scholar]
  19. Fard R. M. N., Barton M. D., Arthur J. L., Heuzenroeder M. W. 2010; Whole-genome sequencing and gene mapping of a newly isolated lytic enterococcal bacteriophage EFRM31. Arch Virol 155:1887–1891 [View Article][PubMed]
     [Google Scholar]
  20. Gallet R., Shao Y., Wang I. N. 2009; High adsorption rate is detrimental to bacteriophage fitness in a biofilm-like environment. BMC Evol Biol 9:241 [View Article][PubMed]
     [Google Scholar]
  21. Hemminga M. A., Vos W. L., Nazarov P. V., Koehorst R. B., Wolfs C. J., Spruijt R. B., Stopar D. 2010; Viruses: incredible nanomachines. New advances with filamentous phages. Eur Biophys J 39:541–550 [View Article][PubMed]
     [Google Scholar]
  22. ICTV 2005 Virus Taxonomy: Classification and Nomenclature of Viruses: Eighth Report of the International Committee on Taxonomy of Viruses Edited by Fauquet C. M. , Mayo M. A., Maniloff J., Desselberger U., Ball L. A. London: Elsevier;
     [Google Scholar]
  23. Krogh S., Jørgensen S. T., Devine K. M. 1998; Lysis genes of the Bacillus subtilis defective prophage PBSX. J Bacteriol 180:2110–2117[PubMed]
     [Google Scholar]
  24. Kutter E. 2009; Phage host range and efficiency of plating. Methods Mol Biol 501:141–149 [View Article][PubMed]
     [Google Scholar]
  25. Li S., Fan H., An X., Fan H., Jiang H., Chen Y., Tong Y. 2014; Scrutinizing virus genome termini by high-throughput sequencing. PLoS ONE 9:e85806 [View Article][PubMed]
     [Google Scholar]
  26. Lima-Mendez G., Toussaint A., Leplae R. 2007; Analysis of the phage sequence space: the benefit of structured information. Virology 365:241–249 [View Article][PubMed]
     [Google Scholar]
  27. Lowe T. M., Eddy S. R. 1997; tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964 [View Article][PubMed]
     [Google Scholar]
  28. Lu S., Le S., Tan Y., Zhu J., Li M., Rao X., Zou L., Li S., Wang J.other authors 2013; Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages. PLoS ONE 8:e62933 [View Article][PubMed]
     [Google Scholar]
  29. Marchler-Bauer A., Anderson J. B., Cherukuri P. F., DeWeese-Scott C., Geer L. Y., Gwadz M., He S., Hurwitz D. I., Jackson J. D.other authors 2005; CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res 33:Suppl. 1D192–D196 [View Article][PubMed]
     [Google Scholar]
  30. Marchler-Bauer A., Anderson J. B., Chitsaz F., Derbyshire M. K., DeWeese-Scott C., Fong J. H., Geer L. Y., Geer R. C., Gonzales N. R.other authors 2009; CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37:suppl 1D205–D210 [View Article][PubMed]
     [Google Scholar]
  31. Marti E., Variatza E., Balcázar J. L. 2013; Bacteriophages as a reservoir of extended. Clin Microbiol Infect 20:O456–O459 [View Article][PubMed]
     [Google Scholar]
  32. Matsuzaki S., Rashel M., Uchiyama J., Sakurai S., Ujihara T., Kuroda M., Imai S., Ikeuchi M., Tani T.other authors 2005; Bacteriophage therapy: a revitalized therapy against bacterial infectious diseases. J Infect Chemother 11:211–219 [View Article][PubMed]
     [Google Scholar]
  33. Muniesa M., García A., Miró E., Mirelis B., Prats G., Jofre J., Navarro F. 2004; Bacteriophages and diffusion of β-lactamase genes. Emerg Infect Dis 10:1134–1137 [View Article][PubMed]
     [Google Scholar]
  34. Pajunen M., Kiljunen S., Skurnik M. 2000; Bacteriophage φYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. J Bacteriol 182:5114–5120 [View Article][PubMed]
     [Google Scholar]
  35. Parsley L. C., Consuegra E. J., Kakirde K. S., Land A. M., Harper W. F. Jr, Liles M. R. 2010; Identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage. Appl Environ Microbiol 76:3753–3757 [View Article][PubMed]
     [Google Scholar]
  36. Pastagia M., Schuch R., Fischetti V. A., Huang D. B. 2013; Lysins: the arrival of pathogen-directed anti-infectives. J Med Microbiol 62:1506–1516 [View Article][PubMed]
     [Google Scholar]
  37. Petrovski S., Seviour R. J., Tillett D. 2011; Genome sequence and characterization of the Tsukamurella bacteriophage TPA2. Appl Environ Microbiol 77:1389–1398 [View Article][PubMed]
     [Google Scholar]
  38. Raytcheva D. A., Haase-Pettingell C., Piret J. M., King J. A. 2011; Intracellular assembly of cyanophage Syn5 proceeds through a scaffold-containing procapsid. J Virol 85:2406–2415 [View Article][PubMed]
     [Google Scholar]
  39. Reese M. G. 2001; Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26:51–56 [View Article][PubMed]
     [Google Scholar]
  40. Rosseel T., Scheuch M., Höper D., De Regge N., Caij A. B., Vandenbussche F., Van Borm S. 2012; DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS ONE 7:e41967 [View Article][PubMed]
     [Google Scholar]
  41. Salifu S. P., Valero-Rello A., Campbell S. A., Inglis N. F., Scortti M., Foley S., Vázquez-Boland J. A. 2013; Genome and proteome analysis of phage E3 infecting the soil-borne actinomycete Rhodococcus equi. Environ Microbiol Rep 5:170–178 [View Article][PubMed]
     [Google Scholar]
  42. Sambrook J., Russell D. 2001 Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  43. Solovyev V., Salamov A. 2011; Automatic annotation of microbial genomes and metagenomic sequences. In Metagenomics and its Applications in Agriculture, Biomedicine and Environmental Studies pp. 61–78 Edited by Li R. W. . Hauppauge, NY: Nova Science Publishers;
     [Google Scholar]
  44. Sullivan M. J., Petty N. K., Beatson S. A. 2011; Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010 [View Article][PubMed]
     [Google Scholar]
  45. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  46. Tatusov R. L., Galperin M. Y., Natale D. A., Koonin E. V. 2000; The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36 [View Article][PubMed]
     [Google Scholar]
  47. Wang I.-N., Smith D. L., Young R. 2000; Holins: the protein clocks of bacteriophage infections. Annu Rev Microbiol 54:799–825 [View Article][PubMed]
     [Google Scholar]
  48. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703[PubMed]
     [Google Scholar]
  49. Wilcox S. A., Toder R., Foster J. W. 1996; Rapid isolation of recombinant lambda phage DNA for use in fluorescence in situ hybridization. Chromosome Res 4:397–404 [View Article][PubMed]
     [Google Scholar]
  50. Witte W. 2004; International dissemination of antibiotic resistant strains of bacterial pathogens. Infect Genet Evol 4:187–191 [View Article][PubMed]
     [Google Scholar]
  51. Yele A. B., Thawal N. D., Sahu P. K., Chopade B. A. 2012; Novel lytic bacteriophage AB7-IBB1 of Acinetobacter baumannii: isolation, characterization and its effect on biofilm. Arch Virol 157:1441–1450 [View Article][PubMed]
     [Google Scholar]
  52. Zhu J., Rao X., Tan Y., Xiong K., Hu Z., Chen Z., Jin X., Li S., Chen Y., Hu F. 2010; Identification of lytic bacteriophage MmP1, assigned to a new member of T7-like phages infecting Morganella morganii. Genomics 96:167–172 [View Article][PubMed]
     [Google Scholar]
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Characterization and complete genome sequence analysis of novel bacteriophage IME-EFm1 infecting Enterococcus faecium
J. Gen. Virol. 95, 2565 (2014); https://doi.org/10.1099/vir.0.067553-0
/content/journal/jgv/10.1099/vir.0.067553-0
/content/journal/jgv/10.1099/vir.0.067553-0
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