Comparative analysis of the first complete Enterococcus faecium genome

Journal of Bacteriology

Volumn 194, Issue 9, 2012, Pages 2334-2341

  Lam, Margaret M C ^a,e   Seemann, Torsten ^b   Bulach, Dieter M ^b   Gladman, Simon L ^c   Chen, Honglei ^c   Haring, Volker ^c   Moore, Robert J ^c,d   Ballard, Susan ^e   Grayson, M Lindsay ^a,e   Johnson, Paul D R ^a,e   Howden, Benjamin P ^a,b,e   Stineara, Timothy P ^a,b  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b MONASH UNIVERSITY   (Australia)

^c CSIRO   (Australia)

^d Australian Government Australian Research Council   (Australia)

^e AUSTIN HEALTH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ADHESIN; HEMOLYSIN; VIRULENCE FACTOR;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM ISOLATION; BLOODSTREAM INFECTION; COMPARATIVE STUDY; ENTEROCOCCUS; GENE INSERTION SEQUENCE; GENOME ANALYSIS; HOSPITAL INFECTION; HUMAN; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROPHAGE; VANCOMYCIN RESISTANT ENTEROCOCCUS FAECIUM;

CHROMOSOMES, BACTERIAL; ENTEROCOCCUS FAECIUM; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMIDS; PROPHAGES; VANCOMYCIN; VANCOMYCIN RESISTANCE; VIRULENCE;

ENTEROCOCCUS FAECIUM;

EID: 84861203966     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00259-12     Document Type: Article

References (59)

1. Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. 2011. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402.
2. Arduino RC, Murray BE, Rakita RM. 1994. Roles of antibodies and complement in phagocytic killing of enterococci. Infect. Immun. 62:987-993.
3. Arias CA, Panesso D, Singh KV, Rice LB, Murray BE. 2009. Cotransfer of antibiotic resistance genes and a hylEfm-containing virulence plasmid in Enterococcus faecium. Antimicrob. Agents Chemother. 53:4240-4246.
4. Arias CA, et al. 2007. Failure of daptomycin monotherapy for endocarditis caused by an Enterococcus faecium strain with vancomycin-resistant and vancomycin-susceptible subpopulations and evidence of in vivo loss of the vanA gene cluster. Clin. Infect. Dis. 45:1343-1346.
5. Arthur M, Reynolds P, Courvalin P. 1996. Glycopeptide resistance in enterococci. Trends Microbiol. 4:401-407.
6. Baldassarri L, Bertuccini L, Ammendolia MG, Gherardi G, Creti R. 2001. Variant esp gene in vancomycin-sensitive Enterococcus faecium. Lancet 357:1802.
7. Barrangou R, et al. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709-1712.
8. Bell JM, Paton JC, Turnidge J. 1998. Emergence of vancomycin-resistant enterococci in Australia: phenotypic and genotypic characteristics of isolates. J. Clin. Microbiol. 36:2187-2190.
9. Billstrom H, Lund B, Sullivan A, Nord CE. 2008. Virulence and antimicrobial resistance in clinical Enterococcus faecium. Int. J. Antimicrob. Agents 32:374-377.
10. Bonfield JK, Smith K, Staden R. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:4992-4999.
11. Bonten MJ, Willems R, Weinstein RA. 2001. Vancomycin-resistant enterococci: why are they here, and where do they come from? Lancet Infect. Dis. 1:314-325.
12. Carias LL, Rudin SD, Donskey CJ, Rice LB. 1998. Genetic linkage and cotransfer of a novel, vanB-containing transposon (Tn5382) and a lowaffinity penicillin-binding protein 5 gene in a clinical vancomycinresistant Enterococcus faecium isolate. J. Bacteriol. 180:4426-4434.
13. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. 2012. Artemis: an integrated platform for visualization and analysis of highthroughput sequence-based experimental data. Bioinformatics 28:464-469.
14. Chua KY, et al. 2011. The dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct. PLoS One 6:e25887.
15. Cox CR, Coburn PS, Gilmore MS. 2005. Enterococcal cytolysin: a novel two component peptide system that serves as a bacterial defense against eukaryotic and prokaryotic cells. Curr. Protein Pept. Sci. 6:77-84.
16. Elsner HA, et al. 2000. Virulence factors of Enterococcus faecalis and Enterococcus faecium blood culture isolates. Eur. J. Clin. Microbiol. Infect. Dis. 19:39-42.
17. Endtz HP, van den Braak N, Verbrugh HA, van Belkum A. 1999. Vancomycin resistance: status quo and quo vadis. Eur. J. Clin. Microbiol. Infect. Dis. 18:683-690.
18. Fisher K, Phillips C. 2009. The ecology, epidemiology and virulence of Enterococcus. Microbiology 155:1749-1757.
19. Fox J. 2000. DOE Joint Genome Institute feat: one-day sequencing of E. faecium. ASM News 66:388.
20. Galloway-Pena J, Roh JH, Latorre M, Qin X, Murray BE. 2012. Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium. PLoS One 7:e30187.
21. Garcia-Migura L, Hasman H, Jensen LB. 2009. Presence of pRI1: a small cryptic mobilizable plasmid isolated from Enterococcus faecium of human and animal origin. Curr. Microbiol. 58:95-100.
22. Garcia-Migura L, Liebana E, Jensen LB. 2007. Transposon characterization of vancomycin-resistant Enterococcus faecium (VREF) and dissemination of resistance associated with transferable plasmids. J. Antimicrob. Chemother. 60:263-268.
23. Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35:W52-W57.
24. Hasman H, et al. 2006. Copper resistance in Enterococcus faecium, mediated by the tcrB gene, is selected by supplementation of pig feed with copper sulfate. Appl. Environ. Microbiol. 72:5784-5789.
25. Hayes F. 2003. Toxins-antitoxins: plasmid maintenance, programmed cell death, and cell cycle arrest. Science 301:1496-1499.
26. Heikens E, et al. 2009. Enterococcal surface protein Esp is not essential for cell adhesion and intestinal colonization of Enterococcus faecium in mice. BMC Microbiol. 9:19.
27. Hendrickson H, Lawrence JG. 2007. Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. Mol. Microbiol. 64:42-56.
28. Homan WL, et al. 2002. Multilocus sequence typing scheme for Enterococcus faecium. J. Clin. Microbiol. 40:1963-1971.
29. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
30. Iwen PC, et al. 1997. Change in prevalence and antibiotic resistance of Enterococcus species isolated from blood cultures over an 8-year period. Antimicrob. Agents Chemother. 41:494-495.
31. Jensen LB, et al. 2010. A classification system for plasmids from enterococci and other Gram-positive bacteria. J. Microbiol. Methods 80:25-43.
32. Johnson PD, et al. 2010. A sustained hospital outbreak of vancomycinresistant Enterococcus faecium bacteremia due to emergence of vanB E. faecium sequence type 203. J. Infect. Dis. 202:1278-1286.
33. Kamarulzaman A, Tosolini FA, Boquest J, Geddes JE, Richards MJ. 1995. Vancomycin-resistant Enterococcus faecium in a liver transplant recipient. ANZ J. Med. 25:560.
34. Launay A, Ballard SA, Johnson PD, Grayson ML, Lambert T. 2006. Transfer of vancomycin resistance transposon Tn1549 from Clostridium symbiosum to Enterococcus spp. in the gut of gnotobiotic mice. Antimicrob. Agents Chemother. 50:1054-1062.
35. Leavis H, et al. 2004. A novel putative enterococcal pathogenicity island linked to the esp virulence gene of Enterococcus faecium and associated with epidemicity. J. Bacteriol. 186:672-682.
36. Leavis HL, et al. 2007. Insertion sequence-driven diversification creates a globally dispersed emerging multiresistant subspecies of E. faecium. PLoS Pathog. 3:e7.
37. Matthews TD, Maloy S. 2010. Fitness effects of replichore imbalance in Salmonella enterica. J. Bacteriol. 192:6086-6088.
38. McBride SM, Fischetti VA, Leblanc DJ, Moellering RC, Jr, Gilmore MS. 2007. Genetic diversity among Enterococcus faecalis. PLoS One 2:e582.
39. Metan G, Zarakolu P, Unal S. 2005. Rapid detection of antibacterial resistance in emerging Gram-positive cocci. J. Hosp. Infect. 61:93-99.
40. Moritz EM, Hergenrother PJ. 2007. Toxin-antitoxin systems are ubiquitous and plasmid-encoded in vancomycin-resistant enterococci. Proc. Natl. Acad. Sci. U. S. A. 104:311-316.
41. Nallapareddy SR, Singh KV, Murray BE. 2006. Construction of improved temperature-sensitive and mobilizable vectors and their use for constructing mutations in the adhesin-encoding acm gene of poorly transformable clinical Enterococcus faecium strains. Appl. Environ. Microbiol. 72:334-345.
42. Nallapareddy SR, Weinstock GM, Murray BE. 2003. Clinical isolates of Enterococcus faecium exhibit strain-specific collagen binding mediated by Acm, a new member of the MSCRAMM family. Mol. Microbiol. 47:1733-1747.
43. Padiglione AA, et al. 2003. Risk factors for new detection of vancomycinresistant enterococci in acute-care hospitals that employ strict infection control procedures. Antimicrob. Agents Chemother. 47:2492-2498.
44. Palmer KL, et al. 2010. High-quality draft genome sequences of 28 Enterococcus sp. isolates. J. Bacteriol. 192:2469-2470.
45. Pultz NJ, Shankar N, Baghdayan AS, Donskey CJ. 2005. Enterococcal surface protein Esp does not facilitate intestinal colonization or translocation of Enterococcus faecalis in clindamycin-treated mice. FEMS Microbiol. Lett. 242:217-219.
46. Rambaut A. 2009. FigTree, tree figure drawing tool, v. 1.3.1.
47. Rice LB, et al. 2009. Transferable capacity for gastrointestinal colonization in Enterococcus faecium in a mouse model. J. Infect. Dis. 199:342-349.
48. Rumble SM, et al. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 5:e1000386.
49. Solheim M, Aakra A, Snipen LG, Brede DA, Nes IF. 2009. Comparative genomics of Enterococcus faecalis from healthy Norwegian infants. BMC Genomics 10:194.
50. Sorek R, Kunin V, Hugenholtz P. 2008. CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6:181-186.
51. Stinear TP, et al. 2004. Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc. Natl. Acad. Sci. U. S. A. 101:1345-1349.
52. Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27:1009-1010.
53. Top J, Willems R, Bonten M. 2008. Emergence of CC17 Enterococcus faecium: from commensal to hospital-adapted pathogen. FEMS Immunol. Med. Microbiol. 52:297-308.
54. Top J, Willems R, van der Velden S, Asbroek M, Bonten M. 2008. Emergence of clonal complex 17 Enterococcus faecium in the Netherlands. J. Clin. Microbiol. 46:214-219.
55. van Schaik W, et al. 2010. Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island. BMC Genomics 11:239.
56. van Schaik W, Willems RJL. 2010. Genome-based insights into the evolution of enterococci. Clin. Microbiol. Infect. 16:527-532.
57. Vernikos GS, Parkhill J. 2006. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22:2196-2203.
58. Willems RJ, et al. 2005. Global spread of vancomycin-resistant Enterococcus faecium from distinct nosocomial genetic complex. Emerg. Infect. Dis. 11:821-828.
59. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res. 39:W347-W352.