Characterization of Enterococcus faecalis phage IME-EF1 and its endolysin

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Zhang, Wenhui ^a   Mi, Zhiqiang ^a   Yin, Xiuyun ^a   Fan, Hang ^a   An, Xiaoping ^a   Zhang, Zhiyi ^a   Chen, Jiankui ^a   Tong, Yigang ^a  

^a BEIJING INSTITUTE OF MICROBIOLOGY AND EPIDEMIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; ENDOLYSIN; GENOMIC DNA; UNCLASSIFIED DRUG; VANCOMYCIN; VIRUS PROTEIN;

AMINO TERMINAL SEQUENCE; ANIMAL EXPERIMENT; ANIMAL MODEL; ANTIBACTERIAL ACTIVITY; ARTICLE; BACTERIAL STRAIN; BACTERIOPHAGE; BACTERIOPHAGE IME EF1; CONTROLLED STUDY; DNA BASE COMPOSITION; ENTEROCOCCAL INFECTION; ENTEROCOCCUS FAECALIS; FEMALE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; SEQUENCE ANALYSIS; SURVIVAL RATE; TADPOLE; TREATMENT OUTCOME; VIRUS EXAMINATION;

ANIMALS; BACTERIOLYSIS; BACTERIOPHAGES; ENDOPEPTIDASES; ENTEROCOCCUS FAECALIS; FEMALE; GENE ORDER; GENOME, VIRAL; GRAM-POSITIVE BACTERIAL INFECTIONS; MICE; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84893419706     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080435     Document Type: Article

References (48)

1. Jett BD, Huycke MM, Gilmore MS (1994) Virulence of enterococci. Clin Microbiol Rev 7: 462-478. PubMed: 7834601.
2. Johnson AP (1994) The pathogenicity of enterococci. J Antimicrob Chemother 33: 1083-1089. doi:10.1093/jac/33.6.1083. PubMed: 7928803.
3. Murray BE (1990) The life and times of the Enterococcus. Clin Microbiol Rev 3: 46-65. PubMed: 2404568.
4. Giraffa G (2003) Functionality of enterococci in dairy products. Int J Food Microbiol 88: 215-222. doi:10.1016/S0168-1605(03)00183-1. PubMed: 14596993.
5. Rao N, Lipsky BA (2007) Optimising antimicrobial therapy in diabetic foot infections. Drugs 67: 195-214. doi: 10.2165/00003495-200767020-00003. PubMed: 17284084.
6. Vinodkumar CS, Srinivasa H, Basavarajappa KG, Geethalakshmi S, Bandekar N (2011) Isolation of bacteriophages to multi-drug resistant Enterococci obtained from diabetic foot: a novel antimicrobial agent waiting in the shelf? Indian J Pathol Microbiol 54: 90-95. doi: 10.4103/0377-4929.77333. PubMed: 21393885.
7. Stuart CH, Schwartz SA, Beeson TJ, Owatz CB (2006) Enterococcus faecalis: its role in root canal treatment failure and current concepts in retreatment. J Endod 32: 93-98. doi:10.1016/j.joen.2005.10.049. PubMed: 16427453. (Pubitemid 43309634)
8. Hidron AI, Edwards JR, Patel J, Horan TC, Sievert DM et al. (2008) NHSN annual update: antimicrobial-resistant pathogens associated with healthcare-associated infections: annual summary of data reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006-2007. Infect Control Hosp Epidemiol 29: 996-1011. doi:10.1086/591861. PubMed: 18947320.
9. Huycke MM, Spiegel CA, Gilmore MS (1991) Bacteremia caused by hemolytic, high-level gentamicin-resistant Enterococcus faecalis. Antimicrob Agents Chemother 35: 1626-1634. doi:10.1128/AAC.35.8.1626. PubMed: 1929336.
10. Chow JW, Thal LA, Perri MB, Vazquez JA, Donabedian SM et al. (1993) Plasmid-associated hemolysin and aggregation substance production contribute to virulence in experimental enterococcal endocarditis. Antimicrob Agents Chemother 37: 2474-2477. doi: 10.1128/AAC.37.11.2474. PubMed: 8285637. (Pubitemid 23324477)
11. Ike Y, Hashimoto H, Clewell DB (1984) Hemolysin of Streptococcus faecalis subspecies zymogenes contributes to virulence in mice. Infect Immun 45: 528-530. PubMed: 6086531. (Pubitemid 14092635)
12. Courvalin P (2006) Vancomycin resistance in gram-positive cocci. Clin Infect Dis 42 Suppl 1: S25-S34. doi:10.1086/491711. PubMed: 16323116.
13. Amyes SG (2007) Enterococci and streptococci. Int J Antimicrob Agents 29 Suppl 3: S43-S52. doi:10.1016/S0924-8579(07)70137-1. PubMed: 17659211.
14. Arias CA, Contreras GA, Murray BE (2010) Management of multidrug-resistant enterococcal infections. Clin Microbiol Infect 16: 555-562. doi: 10.1111/j.1469-0691.2010.03214.x. PubMed: 20569266.
15. Harper DR, Anderson J, Enright MC (2011) Phage therapy: delivering on the promise. Ther Deliv 2: 935-947. doi:10.4155/tde.11.64. PubMed: 22833904.
16. Carlton RM (1999) Phage therapy: past history and future prospects. Arch Immunol Ther Exp (Warsz) 47: 267-274. PubMed: 10604231.
17. Son JS, Jun SY, Kim EB, Park JE, Paik HR et al. (2010) Complete genome sequence of a newly isolated lytic bacteriophage, EFAP-1 of Enterococcus faecalis, and antibacterial activity of its endolysin EFAL-1. J Appl Microbiol 108: 1769-1779. doi:10.1111/j.1365-2672.2009.04576.x. PubMed: 19863688.
18. Yasmin A, Kenny JG, Shankar J, Darby AC, Hall N et al. (2010) Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages. J Bacteriol 192: 1122-1130. doi: 10.1128/JB.01293-09. PubMed: 20008075.
19. Fard RM, Barton MD, Arthur JL, Heuzenroeder MW (2010) Whole-genome sequencing and gene mapping of a newly isolated lytic enterococcal bacteriophage EFRM31. Arch Virol 155: 1887-1891. doi: 10.1007/s00705-010-0800-3. PubMed: 20844906.
20. Uchiyama J, Rashel M, Maeda Y, Takemura I, Sugihara S et al. (2008) Isolation and characterization of a novel Enterococcus faecalis bacteriophage phiEF24C as a therapeutic candidate. FEMS Microbiol Lett 278: 200-206. doi:10.1111/j.1574-6968.2007.00996.x. PubMed: 18096017. (Pubitemid 350264582)
21. Stevens RH, Ektefaie MR, Fouts DE (2011) The annotated complete DNA sequence of Enterococcus faecalis bacteriophage phiEf11 and its comparison with all available phage and predicted prophage genomes. FEMS Microbiol Lett 317: 9-26. doi:10.1111/j.1574-6968.2010.02203.x. PubMed: 21204936.
22. Lee YD, Park JH (2012) Complete genome sequence of enterococcal bacteriophage SAP6. J Virol 86: 5402-5403. doi:10.1128/JVI.00321-12. PubMed: 22492926.
23. Horiuchi T, Sakka M, Hayashi A, Shimada T, Kimura T et al. (2012) Complete genome sequence of bacteriophage BC-611 specifically infecting Enterococcus faecalis strain NP-10011. J Virol 86: 9538-9539. doi:10.1128/JVI.01424-12. PubMed: 22879611.
24. Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33: W686-W689. doi:10.1093/nar/gki366. PubMed: 15980563. (Pubitemid 44530010)
25. 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. doi:10.1093/nar/25.5.955. PubMed: 9023104. (Pubitemid 27298263)
26. Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8: 317-327. doi:10.1038/nrmicro2315. PubMed: 20348932.
27. Loessner MJ (2005) Bacteriophage endolysins - current state of research and applications. Curr Opin Microbiol 8: 480-487. doi:10.1016/j.mib.2005.06.002. PubMed: 15979390.
28. Fischetti VA (2008) Bacteriophage lysins as effective antibacterials. Curr Opin Microbiol 11: 393-400. doi:10.1016/j.mib.2008.09.012. PubMed: 18824123.
29. Loeffler JM, Nelson D, Fischetti VA (2001) Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase. Science 294: 2170-2172. doi:10.1126/science.1066869. PubMed: 11739958. (Pubitemid 33150674)
30. Schuch R, Nelson D, Fischetti VA (2002) A bacteriolytic agent that detects and kills Bacillus anthracis. Nature 418: 884-889. doi:10.1038/ nature01026. PubMed: 12192412. (Pubitemid 34966308)
31. Díaz E, López R, García JL (1990) Chimeric phage-bacterial enzymes: a clue to the modular evolution of genes. Proc Natl Acad Sci U S A 87: 8125-8129. doi:10.1073/pnas.87.20.8125. PubMed: 1978320.
32. García P, García JL, García E, Sánchez- Puelles JM, López R (1990) Modular organization of the lytic enzymes of Streptococcus pneumoniae and its bacteriophages. Gene 86: 81-88. doi: 10.1016/0378-1119(90)90116-9. PubMed: 2311937.
33. López R, García E (2004) Recent trends on the molecular biology of pneumococcal capsules, lytic enzymes, and bacteriophage. FEMS Microbiol Rev 28: 553-580. doi:10.1016/j.femsre.2004.05.002. PubMed: 15539074.
34. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-D229. doi: 10.1093/nar/gkq1189. PubMed: 21109532.
35. Bateman A, Rawlings ND (2003) The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases. Trends Biochem Sci 28: 234-237. doi:10.1016/S0968-0004(03)00061-6. PubMed: 12765834. (Pubitemid 36588664)
36. Yoong P, Schuch R, Nelson D, Fischetti VA (2004) Identification of a broadly active phage lytic enzyme with lethal activity against antibiotic-resistant Enterococcus faecalis and Enterococcus faecium. J Bacteriol 186: 4808-4812. doi:10.1128/JB.186.14.4808-4812.2004. PubMed: 15231813. (Pubitemid 38891043)
37. Uchiyama J, Takemura I, Hayashi I, Matsuzaki S, Satoh M et al. (2011) Characterization of lytic enzyme open reading frame 9 (ORF9) derived from Enterococcus faecalis bacteriophage phiEF24C. Appl Environ Microbiol 77: 580-585. doi:10.1128/AEM.01540-10. PubMed: 21097580.
38. Pérez-Dorado I, Campillo NE, Monterroso B, Hesek D, Lee M et al. (2007) Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1. J Biol Chem 282: 24990-24999. doi:10.1074/jbc.M704317200. PubMed: 17581815. (Pubitemid 47347516)
39. Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF (2011) Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant. J Bacteriol 193: 2377-2378. doi:10.1128/JB.00183-11. PubMed: 21398545.
40. Buist G, Steen A, Kok J, Kuipers OP (2008) LysM, a widely distributed protein motif for binding to (peptido)glycans. Mol Microbiol 68: 838-847. doi:10.1111/j.1365-2958.2008.06211.x. PubMed: 18430080. (Pubitemid 351581067)
41. Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL et al. (1999) Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 112: 531-552. PubMed: 10027275.
42. Eisenberg D, Schwarz E, Komaromy M, Wall R (1984) Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol 179: 125-142. doi: 10.1016/0022-2836(84)90309-7. PubMed: 6502707. (Pubitemid 16223392)
43. Germida JJ, Casida LE Jr (1983) Ensifer adhaerens predatory activity against other bacteria in soil, as monitored by indirect phage analysis. Appl Environ Microbiol 45: 1380-1388. PubMed: 16346275. (Pubitemid 13132972)
44. Adams MH, Comroe JH, Venning E (1950) Methods of study of bacterial viruses: Year Book Publishers.
45. Sambrook J, Fritsch F, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
46. Pajunen M, Kiljunen S, Skurnik M (2000) Bacteriophage phiYeO3-12, specific for Yersinia enterocolitica serotype O:3, is related to coliphages T3 and T7. J Bacteriol 182: 5114-5120. doi:10.1128/JB.182.18.5114-5120.2000. PubMed: 10960095.
47. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829. doi: 10.1101/gr.074492.107. PubMed: 18349386. (Pubitemid 351645072)
48. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75. doi:10.1186/1471-2164-9-75. PubMed: 18261238.