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Chapter 8 : Selfish Elements and Self-Defense in the Enterococci

Authors: Kelli L. Palmer1, Michael S. Gilmore2
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Affiliations: 1: Schepens Eye Research Institute, 20 Staniford St., Boston, MA 02144; 2: Schepens Eye Research Institute, 20 Staniford St., Boston, MA 02144
Content Type: Monograph
Publication Year: 2012

Category: Microbial Genetics and Molecular Biology; Genomics and Bioinformatics

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Abstract:

This chapter reviews the genome plasticity that has led to distinct subpopulations of enterococci, as well as the evidence for loss of genome defenses as precipitating events in their emergence. It presents evidence as it currently exists describing the role of genome plasticity in the virulence and persistence of hospital-adapted, multidrug-resistant enterococcal lineages. It also highlights the mechanistic and comparatively unappreciated role that loss of endogenous genome defenses, such as restriction modification and clustered, regularly interspaced, short palindromic repeats (CRISPR) systems, may have played in the emergence of these lineages. To the authors knowledge, the extent to which insertion sequence (IS) element inactivation of chromosomal genes contributes to the success of enterococci as pathogens has not been explored. However, there is evidence that intragenomic recombination at IS elements has contributed substantially to genome plasticity of the enterococci. The chapter focuses on genome defense mechanisms in the enterococci, including restriction-modification and CRISPR. Much work remains to be done before understanding whether and how genome defense mechanisms influence enterococcal ecology and evolution.

Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8

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Mobile Genetic Elements
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Genetic Elements
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Urinary Tract Infections
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Multilocus Sequence Typing
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Comparative Genomic Hybridization
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Urinary Tract Infections
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Multilocus Sequence Typing
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Comparative Genomic Hybridization
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Selfish Elements and Self-Defense in the Enterococci
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Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8
/content/10.1128/9781555817213.chap8.fig8-1
FIGURE 1

Phylogenetic relatedness and variable trait profile of diverse isolates. Shown is the MLST dendrogram for 106 strains, aligned with their capsule type (CPS), date of isolation, isolation source, PAI fragment content, antibiotic resistance profile, and phenotypic auxiliary traits. PAI fragments are designated A through F, and a red letter B indicates that the strain can conjugatively transfer cytolysin to other strains. Antibiotic resistance shown includes tetracycline (TL, ; TM, ), erythromycin (E, ), gentamicin (G), chloramphenicol (C, ), ampicillin (A, ), and vancomycin (VA, ; VB, ) resistance. Auxiliary traits are cytolysin production (CYL), conjugated bile salt hydrolase production (CBH), and gelatinase production (GEL). Reprinted from ( ).

10.1128/9781555817213/fig8-1_thmb.gif
10.1128/9781555817213/fig8-1.gif
Image of FIGURE 1
FIGURE 1

Phylogenetic relatedness and variable trait profile of diverse isolates. Shown is the MLST dendrogram for 106 strains, aligned with their capsule type (CPS), date of isolation, isolation source, PAI fragment content, antibiotic resistance profile, and phenotypic auxiliary traits. PAI fragments are designated A through F, and a red letter B indicates that the strain can conjugatively transfer cytolysin to other strains. Antibiotic resistance shown includes tetracycline (TL, ; TM, ), erythromycin (E, ), gentamicin (G), chloramphenicol (C, ), ampicillin (A, ), and vancomycin (VA, ; VB, ) resistance. Auxiliary traits are cytolysin production (CYL), conjugated bile salt hydrolase production (CBH), and gelatinase production (GEL). Reprinted from ( ).

Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8
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/content/10.1128/9781555817213.chap8.fig8-2
FIGURE 2

OG1RF CRISPR loci. (A) Diagram of CRISPR loci identified in the OG1RF genome by . Homologues of V583 genes are shown in black with appropriate V583 locus numbers. CRISPR-associated genes () genes are specific to OG1RF and are shown in red. An ORF that lacks homology to known genes and is also specific to OG1RF was predicted to occur downstream of the CRISPR1 repeat-spacer array ( ). Vertical black lines represent 36-bp repeat sequences of CRISPR repeat-spacer arrays. (B) An OG1RF CRISPR spacer is homologous to a mobile element present in the V583 genome. Shown is the 30-bp OG1RF CRISPR1 spacer 3 sequence aligned with a homologous sequence in V583. Homologous nucleotides are in bold and underlined. The V583 sequence is located in an intergenic region between the ORFs EF2528 and EF2529; this region is found within a predicted integrated plasmid on the V583 genome (EF2512 to EF2545 [ ]). Components of the figure are not drawn to scale.

10.1128/9781555817213/fig8-2_thmb.gif
10.1128/9781555817213/fig8-2.gif
Image of FIGURE 2
FIGURE 2

OG1RF CRISPR loci. (A) Diagram of CRISPR loci identified in the OG1RF genome by . Homologues of V583 genes are shown in black with appropriate V583 locus numbers. CRISPR-associated genes () genes are specific to OG1RF and are shown in red. An ORF that lacks homology to known genes and is also specific to OG1RF was predicted to occur downstream of the CRISPR1 repeat-spacer array ( ). Vertical black lines represent 36-bp repeat sequences of CRISPR repeat-spacer arrays. (B) An OG1RF CRISPR spacer is homologous to a mobile element present in the V583 genome. Shown is the 30-bp OG1RF CRISPR1 spacer 3 sequence aligned with a homologous sequence in V583. Homologous nucleotides are in bold and underlined. The V583 sequence is located in an intergenic region between the ORFs EF2528 and EF2529; this region is found within a predicted integrated plasmid on the V583 genome (EF2512 to EF2545 [ ]). Components of the figure are not drawn to scale.

Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8
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References

/content/book/10.1128/9781555817213.chap8
1. Aarestrup, F. M.,, P. Butaye,, and W. Witte,. 2002. Nonhuman reservoirs of enterococci, p. 55– 99. In M. S. Gilmore (ed.), The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance. ASM Press, Washington, DC.
2. Bachrach, G.,, M. Leizerovici-Zigmond,, A. Zlotkin,, R. Naor,, and D. Steinberg. 2003. Bacteriophage isolation from human saliva. Lett. Appl. Microbiol. 36: 50– 53.
3. Barrangou, R.,, C. Fremaux,, H. Deveau,, M. Richards,, P. Boyaval,, S. Moineau,, D. A. Romero,, and P. Horvath. 2007. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709– 1712.
4. Bertani, G.,, and J. J. Weigle. 1953. Host controlled variation in bacterial viruses. J. Bacteriol. 65: 113– 121.
5. Bolotin, A.,, B. Quinquis,, A. Sorokin,, and S. D. Ehrlich. 2005. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151: 2551– 2561.
6. Bourgogne, A.,, D. A. Garsin,, X. Qin,, K. V. Singh,, J. Sillanpaa,, S. Yerrapragada,, Y. Ding,, S. Dugan-Rocha,, C. Buhay,, H. Shen,, G. Chen,, G. Williams,, D. Muzny,, A. Maadani,, K. A. Fox,, J. Gioia,, L. Chen,, Y. Shang,, C. A. Arias,, S. R. Nallapareddy,, M. Zhao,, V. P. Prakash,, S. Chowdhury,, H. Jiang,, R. A. Gibbs,, B. E. Murray,, S. K. Highlander,, and G. M. Weinstock. 2008. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol. 9: R110.
7. Brock, T. D. 1964. Host range of certain virulent and temperate bacteriophages attacking group D streptococci. J. Bacteriol. 88: 165– 171.
8. Brouns, S. J.,, M. M. Jore,, M. Lundgren,, E. R. Westra,, R. J. Slijkhuis,, A. P. Snijders,, M. J. Dickman,, K. S. Makarova,, E. V. Koonin,, and J. van der Oost. 2008. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321: 960– 964.
9. Callegan, M. C.,, M. Engelbert,, D. W. Parke II,, B. D. Jett,, and M. S. Gilmore. 2002. Bacterial endophthalmitis: epidemiology, therapeutics, and bacterium-host interactions. Clin. Microbiol. Rev. 15: 111– 124.
10. Caprioli, T.,, F. Zaccour,, and S. S. Kasatiya. 1975. Phage typing scheme for group D streptococci isolated from human urogenital tract. J. Clin. Microbiol. 2: 311– 317.
11. Chow, J. W.,, L. A. Thal,, M. B. Perri,, J. A. Vazquez,, S. M. Donabedian,, D. B. Clewell,, and M. J. Zervos. 1993. Plasmid-associated hemolysin and aggregation substance production contribute to virulence in experimental enterococcal endocarditis. Antimicrob. Agents Chemother. 37: 2474– 2477.
12. Chuang, O. N.,, P. M. Schlievert,, C. L. Wells,, D. A. Manias,, T. J. Tripp,, and G. M. Dunny. 2009. Multiple functional domains of Enterococcus faecalis aggregation substance Asc10 contribute to endocarditis virulence. Infect. Immun. 77: 539– 548.
13. Clewell, D. B. 2007. Properties of Enterococcus faecalis plasmid pAD1, a member of a widely disseminated family of pheromone-responding, conjugative, virulence elements encoding cytolysin. Plasmid 58: 205– 227.
14. Clewell, D. B.,, and G. Dunny,. 2002. Conjugation and genetic exchange in enterococci, p. 265– 300. In M. S. Gilmore (ed.), The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance. ASM Press, Washington, DC.
15. Contreras, G. A.,, C. A. DiazGranados,, L. Cortes,, J. Reyes,, S. Vanegas,, D. Panesso,, S. Rincon,, L. Diaz,, G. Prada,, B. E. Murray,, and C. A. Arias. 2008. Nosocomial outbreak of Enterococcus gallinarum: untaming of rare species of enterococci. J. Hosp. Infect. 70: 346– 352.
16. DeVriese, L.,, M. Baele,, and P. Butaye,. 2006. The genus Enterococcus: taxonomy, p. 163– 174. In M. Dworkin,, S. Falkow,, E. Rosenberg,, K.-H. Schleifer,, and E. Stackebrandt (ed.), The Prokaryotes, 3rd ed., vol. 4. Springer, New York, NY.
17. Domann, E.,, T. Hain,, R. Ghai,, A. Billion,, C. Kuenne,, K. Zimmermann,, and T. Chakraborty. 2007. Comparative genomic analysis for the presence of potential enterococcal virulence factors in the probiotic Enterococcus faecalis strain Symbioflor 1. Int. J. Med. Microbiol. 297: 533– 539.
18. Dunny, G. M. 2007. The peptide pheromone-inducible conjugation system of Enterococcus faecalis plasmid pCF10: cell-cell signaling, gene transfer, complexity and evolution. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362: 1185– 1193.
19. Engelbert, M.,, E. Mylonakis,, F. M. Ausubel,, S. B. Calderwood,, and M. S. Gilmore. 2004. Contribution of gelatinase, serine protease, and fsr to the pathogenesis of Enterococcus faecalis endophthalmitis. Infect. Immun. 72: 3628– 3633.
20. Flannagan, S. E.,, J. W. Chow,, S. M. Donabedian,, W. J. Brown,, M. B. Perri,, M. J. Zervos,, Y. Ozawa,, and D. B. Clewell. 2003. Plasmid content of a vancomycin-resistant Enterococcus faecalis isolate from a patient also colonized by Staphylococcus aureus with a VanA phenotype. Antimicrob. Agents Chemother. 47: 3954– 3959.
21. Foulquie Moreno, M. R.,, P. Sarantinopoulos,, E. Tsakalidou,, and L. De Vuyst. 2006. The role and application of enterococci in food and health. Int. J. Food. Microbiol. 106: 1– 24.
22. Freitas, A. R.,, C. Novais,, P. Ruiz-Garbajosa,, T. M. Coque,, and L. Peixe. 2009a. Clonal expansion within clonal complex 2 and spread of vancomycin-resistant plasmids among different genetic lineages of Enterococcus faecalis from Portugal. J. Antimicrob. Chemother. 63: 1104– 1111.
23. Freitas, A. R.,, C. Novais,, P. Ruiz-Garbajosa,, T. M. Coque,, and L. Peixe. 2009b. Dispersion of multidrug-resistant Enterococcus faecium isolates belonging to major clonal complexes in different Portuguese settings. Appl. Environ. Microbiol. 75: 4904– 4908.
24. Garsin, D. A.,, C. D. Sifri,, E. Mylonakis,, X. Qin,, K. V. Singh,, B. E. Murray,, S. B. Calderwood,, and F. M. Ausubel. 2001. A simple model host for identifying Gram-positive virulence factors . Proc. Natl. Acad. Sci. USA 98: 10892– 10897.
25. Gilmore, M. S.,, and J. J. Ferretti. 2003. Microbiology. The thin line between gut commensal and pathogen. Science 299: 1999– 2002.
26. Gold, O. G.,, H. V. Jordan,, and J. van Houte. 1975. The prevalence of enterococci in the human mouth and their pathogenicity in animal models. Arch. Oral Biol. 20: 473– 477.
27. Gorski, A.,, and B. Weber-Dabrowska. 2005. The potential role of endogenous bacteriophages in controlling invading pathogens. Cell. Mol. Life Sci. 62: 511– 519.
28. Grissa, I.,, G. Vergnaud,, and C. Pourcel. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8: 172.
29. Haft, D. H.,, J. Selengut,, E. F. Mongodin,, and K. E. Nelson. 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1: e60.
30. Hale, C. R.,, P. Zhao,, S. Olson,, M. O. Duff,, B. R. Graveley,, L. Wells,, R. M. Terns,, and M. P. Terns. 2009. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139: 945– 956.
31. Hancock, L. E.,, and M. S. Gilmore. 2002. The capsular polysaccharide of Enterococcus faecalis and its relationship to other polysaccharides in the cell wall. Proc. Natl. Acad. Sci. USA 99: 1574– 1579.
32. Hancock, L. E.,, B. D. Shepard,, and M. S. Gilmore. 2003. Molecular analysis of the Enterococcus faecalis serotype 2 polysaccharide determinant. J. Bacteriol. 185: 4393– 4401.
33. Handwerger, S.,, B. Raucher,, D. Altarac,, J. Monka,, S. Marchione,, K. V. Singh,, B. E. Murray,, J. Wolff,, and B. Walters. 1993. Nosocomial outbreak due to Enterococcus faecium highly resistant to vancomycin, penicillin, and gentamicin. Clin. Infect. Dis. 16: 750– 755.
34. Heikens, E.,, W. van Schaik,, H. L. Leavis,, M. J. Bonten,, and R. J. Willems. 2008. Identification of a novel genomic island specific to hospital-acquired clonal complex 17 Enterococcus faecium isolates. Appl. Environ. Microbiol. 74: 7094– 7097.
35. Hidron, A. I.,, J. R. Edwards,, J. Patel,, T. C. Horan,, D. M. Sievert,, D. A. Pollock,, and S. K. Fridkin. 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.>
36. Hirt, H.,, P. M. Schlievert,, and G. M. Dunny. 2002. In vivo induction of virulence and antibiotic resistance transfer in Enterococcus faecalis mediated by the sex pheromone-sensing system of pCF10. Infect. Immun. 70: 716– 723.
37. Horvath, P.,, and R. Barrangou. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327: 167– 170.
38. Huycke, M. M.,, M. S. Gilmore,, B. D. Jett,, and J. L. Booth. 1992. Transfer of pheromone-inducible plasmids between Enterococcus faecalis in the Syrian hamster gastrointestinal tract. J. Infect. Dis. 166: 1188– 1191.
39. Huycke, M. M.,, C. A. Spiegel,, and M. S. Gilmore. 1991. Bacteremia caused by hemolytic, high-level gentamicin-resistant Enterococcus faecalis. Antimicrob. Agents Chemother. 35: 1626– 1634.
40. Ike, Y.,, H. Hashimoto,, and D. B. Clewell. 1984. Hemolysin of Streptococcus faecalis subspecies zymogenes contributes to virulence in mice. Infect. Immun. 45: 528– 530.
41. Ike, Y.,, K. Tanimoto,, H. Tomita,, K. Takeuchi,, and S. Fujimoto. 1998. Efficient transfer of the pheromone-independent Enterococcus faecium plasmid pMG1 (Gm r) (65.1 kilobases) to Enterococcus strains during broth mating. J. Bacteriol. 180: 4886– 4892.
42. Jakubauskas, A.,, E. Kriukiene,, L. Trinkunaite,, R. Sapranauskas,, S. Jurenaite-Urbanaviciene,, and A. Lubys. 2009. Bioinformatic and partial functional analysis of pEspA and pEspB, two plasmids from Exiguobacterium arabatum sp. nov. RFL1109. Plasmid 61: 52– 64.
43. Jansen, R.,, J. D. Embden,, W. Gaastra,, and L. M. Schouls. 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43: 1565– 1575.
44. Jett, B. D.,, and M. S. Gilmore. 1990. The growth-inhibitory effect of the Enterococcus faecalis bacteriocin encoded by pAD1 extends to the oral streptococci. J. Dent. Res. 69: 1640– 1645.
45. Jett, B. D.,, H. G. Jensen,, R. E. Nordquist,, and M. S. Gilmore. 1992. Contribution of the pAD1-encoded cytolysin to the severity of experimental Enterococcus faecalis endophthalmitis. Infect. Immun. 60: 2445– 2452.
46. Kawalec, M.,, M. Gniadkowski,, and W. Hryniewicz. 2000. Outbreak of vancomycin-resistant enterococci in a hospital in Gdask, Poland, due to horizontal transfer of different Tn 1546-like transposon variants and clonal spread of several strains. J. Clin. Microbiol. 38: 3317– 3322.
47. Kawalec, M.,, Z. Pietras,, E. Danilowicz,, A. Jakubczak,, M. Gniadkowski,, W. Hryniewicz,, and R. J. Willems. 2007. Clonal structure of Enterococcus faecalis isolated from Polish hospitals: characterization of epidemic clones. J. Clin. Microbiol. 45: 147– 153.
48. Kirkpatrick, B. D.,, S. M. Harrington,, D. Smith,, D. Marcellus,, C. Miller,, J. Dick,, L. Karanfil,, and T. M. Perl. 1999. An outbreak of vancomycin-dependent Enterococcus faecium in a bone marrow transplant unit. Clin. Infect. Dis. 29: 1268– 1273.
49. Leavis, H.,, J. Top,, N. Shankar,, K. Borgen,, M. Bonten,, J. van Embden,, and R. J. Willems. 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.
50. Leavis, H. L.,, R. J. Willems,, J. Top,, and M. J. Bonten. 2006. High-level ciprofloxacin resistance from point mutations in gyrA and parC confined to global hospital-adapted clonal lineage CC17 of Enterococcus faecium. J. Clin. Microbiol. 44: 1059– 1064.
51. Leavis, H. L.,, R. J. Willems,, W. J. van Wamel,, F. H. Schuren,, M. P. Caspers,, and M. J. Bonten. 2007. Insertion sequence-driven diversification creates a globally dispersed emerging multiresistant subspecies of E. faecium. PLoS Pathog. 3: e7.
52. Lebreton, F.,, E. Riboulet-Bisson,, P. Serror,, M. Sanguinetti,, B. Posteraro,, R. Torelli,, A. Hartke,, Y. Auffray,, and J. C. Giard. 2009. ace, which encodes an adhesin in Enterococcus faecalis, is regulated by Ers and is involved in virulence. Infect. Immun. 77: 2832– 2839.
53. Leendertse, M.,, E. Heikens,, L. M. Wijnands,, M. van Luit-Asbroek,, G. J. Teske,, J. J. Roelofs,, M. J. Bonten,, T. van der Poll,, and R. J. Willems. 2009. Enterococcal surface protein transiently aggravates Enterococcus faecium-induced urinary tract infection in mice. J. Infect. Dis. 200: 1162– 1165.
54. Lepage, E.,, S. Brinster,, C. Caron,, C. Ducroix-Crepy,, L. Rigottier-Gois,, G. Dunny,, C. Hennequet-Antier,, and P. Serror. 2006. Comparative genomic hybridization analysis of Enterococcus faecalis: identification of genes absent from food strains. J. Bacteriol. 188: 6858– 6868.
55. Libisch, B.,, Z. Lepsanovic,, J. Top,, M. Muzslay,, M. Konkoly-Thege,, M. Gacs,, B. Balogh,, M. Fuzi,, and R. J. Willems. 2008. Molecular characterization of vancomycin-resistant Enterococcus spp. clinical isolates from Hungary and Serbia. Scand. J. Infect. Dis. 40: 778– 784.
56. Licht, T. R.,, D. Laugesen,, L. B. Jensen,, and B. L. Jacobsen. 2002. Transfer of the pheromone-inducible plasmid pCF10 among Enterococcus faecalis microorganisms colonizing the intestine of mini-pigs. Appl. Environ. Microbiol. 68: 187– 193.
57. Luria, S. E.,, and M. L. Human. 1952. A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol. 64: 557– 569.
58. Makarova, K. S.,, N. V. Grishin,, S. A. Shabalina,, Y. I. Wolf,, and E. V. Koonin. 2006. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1: 7.
59. Manson, J. M.,, L. Hancock,, and M. S. Gilmore. 2010. Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance and other traits. Proc. Natl. Acad. Sci. USA. 107: 12269– 12274.
60. Marraffini, L. A.,, and E. J. Sontheimer. 2008. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322: 1843– 1845.
61. Mazaheri Nezhad Fard, R.,, M. D. Barton,, and M. W. Heuzenroeder. 2010. Novel Bacteriophages in Enterococcus spp. Curr. Microbiol. 60: 400– 406.
62. McBride, S. M.,, V. A. Fischetti,, D. J. Leblanc,, R. C. Moellering, Jr.,, and M. S. Gilmore. 2007. Genetic diversity among Enterococcus faecalis. PLoS One 2: e582.
63. Mojica, F. J.,, C. Diez-Villasenor,, J. Garcia-Martinez,, and E. Soria. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60: 174– 182.
64. Mojica, F. J.,, C. Diez-Villasenor,, E. Soria,, and G. Juez. 2000. Biological significance of a family of regularly spaced repeats in the genomes of archaea, bacteria and mitochondria. Mol. Microbiol. 36: 244– 246.
65. Murray, B. E. 1990. The life and times of the Enterococcus. Clin. Microbiol. Rev. 3: 46– 65.
66. Murray, N. E. 2002. Immigration control of DNA in bacteria: self versus non-self. Microbiology 148: 3– 20.
67. Nallapareddy, S. R.,, K. V. Singh,, R. W. Duh,, G. M. Weinstock,, and B. E. Murray. 2000. Diversity of ace, a gene encoding a microbial surface component recognizing adhesive matrix molecules, from different strains of Enterococcus faecalis and evidence for production of ace during human infections. Infect. Immun. 68: 5210– 5217.
68. Nallapareddy, S. R.,, H. Wenxiang,, G. M. Weinstock,, and B. E. Murray. 2005. Molecular characterization of a widespread, pathogenic, and antibiotic resistance-receptive Enterococcus faecalis lineage and dissemination of its putative pathogenicity island. J. Bacteriol. 187: 5709– 5718.
69. O’Driscoll, J.,, D. F. Heiter,, G. G. Wilson,, G. F. Fitzgerald,, R. Roberts,, and D. van Sinderen. 2006. A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system. BMC Microbiol. 6: 40.
70. Palmer, K. L.,, K. Carniol,, J. M. Manson,, D. Heiman,, T. Shea,, S. Young,, Q. Zeng,, D. Gevers,, M. Feldgarden,, B. Birren,, and M. S. Gilmore. 2010. High-quality draft genome sequences of 28 Enterococcus sp. isolates. J Bacteriol. 192: 2469– 2470.
71. Paulsen, I. T.,, L. Banerjei,, G. S. Myers,, K. E. Nelson,, R. Seshadri,, T. D. Read,, D. E. Fouts,, J. A. Eisen,, S. R. Gill,, J. F. Heidelberg,, H. Tettelin,, R. J. Dodson,, L. Umayam,, L. Brinkac,, M. Beanan,, S. Daugherty,, R. T. DeBoy,, S. Durkin,, J. Kolonay,, R. Madupu,, W. Nelson,, J. Vamathevan,, B. Tran,, J. Upton,, T. Hansen,, J. Shetty,, H. Khouri,, T. Utterback,, D. Radune,, K. A. Ketchum,, B. A. Dougherty,, and C. M. Fraser. 2003. Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299: 2071– 2074.>
72. Pillar, C. M.,, and M. S. Gilmore. 2004. Enterococcal virulence—pathogenicity island of E. faecalis. Front. Biosci. 9: 2335– 2346.
73. Pourcel, C.,, G. Salvignol,, and G. Vergnaud. 2005. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151: 653– 663.
74. Pournaras, S.,, A. Tsakris,, M. E. Kaufmann,, J. Douboyas,, and A. Antoniadis. 2000. Outbreak of infections in a Greek university hospital involving a single clone of high-level aminoglycoside-resistant Enterococcus faecalis. Infect. Control Hosp. Epidemiol. 21: 786– 789.
75. Roberts, R. J. 1982. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res. 10: r117– r144.
76. Roberts, R. J.,, T. Vincze,, J. Posfai,, and D. Macelis. 2010. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 38: D234– D236.
77. Roberts, R. J.,, T. Vincze,, J. Posfai,, and D. Macelis. 2007. REBASE—enzymes and genes for DNA restriction and modification. Nucleic Acids Res. 35: D269– D270.
78. Rogers, C. G.,, and W. B. Sarles. 1963. Characterization of Enterococcus bacteriophages from the small intestine of the rat. J. Bacteriol. 85: 1378– 1385.
79. Ruiz-Garbajosa, P.,, M. J. Bonten,, D. A. Robinson,, J. Top,, S. R. Nallapareddy,, C. Torres,, T. M. Coque,, R. Canton,, F. Baquero,, B. E. Murray,, R. del Campo,, and R. J. Willems. 2006. Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination. J. Clin. Microbiol. 44: 2220– 2228.
80. Sahm, D. F.,, J. Kissinger,, M. S. Gilmore,, P. R. Murray,, R. Mulder,, J. Solliday,, and B. Clarke. 1989. In vitro susceptibility studies of vancomycin-resistant Enterococcus faecalis. Antimicrob. Agents Chemother. 33: 1588– 1591.
81. Samuel, J.,, H. Coutinho,, A. Galloway,, C. Rennison,, M. E. Kaufmann,, and N. Woodford. 2008. Glycopeptide-resistant Enterococcus raffinosus in a haematology unit: an unusual cause of a nosocomial outbreak. J. Hosp. Infect. 70: 294– 296.
82. Scott, I. U.,, R. H. Loo,, H. W. Flynn, Jr.,, and D. Miller. 2003. Endophthalmitis caused by Enterococcus faecalis: antibiotic selection and treatment outcomes. Ophthalmology 110: 1573– 1577.
83. Serfiotis-Mitsa, D.,, G. A. Roberts,, L. P. Cooper,, J. H. White,, M. Nutley,, A. Cooper,, G. W. Blakely,, and D. T. Dryden. 2008. The Orf18 gene product from conjugative transposon Tn 916 is an ArdA antirestriction protein that inhibits type I DNA restriction-modification systems. J. Mol. Biol. 383: 970– 981.
84. Shankar, N.,, A. S. Baghdayan,, and M. S. Gilmore. 2002. Modulation of virulence within a pathogenicity island in vancomycin-resistant Enterococcus faecalis. Nature 417: 746– 750.
85. Shankar, N.,, C. V. Lockatell,, A. S. Baghdayan,, C. Drachenberg,, M. S. Gilmore,, and D. E. Johnson. 2001. Role of Enterococcus faecalis surface protein Esp in the pathogenesis of ascending urinary tract infection. Infect. Immun. 69: 4366– 4372.
86. Shankar, V.,, A. S. Baghdayan,, M. M. Huycke,, G. Lindahl,, and M. S. Gilmore. 1999. Infection-derived Enterococcus faecalis strains are enriched in esp, a gene encoding a novel surface protein. Infect. Immun. 67: 193– 200.
87. Sifri, C. D.,, E. Mylonakis,, K. V. Singh,, X. Qin,, D. A. Garsin,, B. E. Murray,, F. M. Ausubel,, and S. B. Calderwood. 2002. Virulence effect of Enterococcus faecalis protease genes and the quorum-sensing locus fsr in Caenorhabditis elegans and mice. Infect. Immun. 70: 5647– 5650.
88. Singh, K. V.,, S. R. Nallapareddy,, J. Sillanpaa,, and B. E. Murray. 2010>. Importance of the collagen adhesin Ace in pathogenesis and protection against Enterococcus faecalis experimental endocarditis. PLoS Pathog. 6: e1000716.
89. Singh, K. V.,, X. Qin,, G. M. Weinstock,, and B. E. Murray. 1998. Generation and testing of mutants of Enterococcus faecalis in a mouse peritonitis model. J. Infect. Dis. 178: 1416– 1420.
90. Solheim, M.,, A. Aakra,, L. G. Snipen,, D. A. Brede,, and I. F. Nes. 2009. Comparative genomics of Enterococcus faecalis from healthy Norwegian infants. BMC Genomics 10: 194.
91. Stein, D. C.,, J. S. Gunn,, M. Radlinska,, and A. Piekarowicz. 1995. Restriction and modification systems of Neisseria gonorrhoeae. Gene 157: 19– 22.
92. Stevens, R. H.,, O. D. Porras,, and A. L. Delisle. 2009. Bacteriophages induced from lysogenic root canal isolates of Enterococcus faecalis. Oral Microbiol. Immunol. 24: 278– 284.
93. Suzuki, T.,, T. Wada,, S. Kozai,, Y. Ike,, M. S. Gilmore,, and Y. Ohashi. 2008. Contribution of secreted proteases to the pathogenesis of postoperative Enterococcus faecalis endophthalmitis. J. Cataract Refract. Surg. 34: 1776– 1784.
94. Tanimoto, K.,, and Y. Ike. 2008. Complete nucleotide sequencing and analysis of the 65-kb highly conjugative Enterococcus faecium plasmid pMG1: identification of the transfer-related region and the minimum region required for replication. FEMS Microbiol. Lett. 288: 186– 195.
95. Tannock, G. W.,, and G. Cook,. 2002. Enterococci as members of the intestinal microflora of humans, p. 101– 132. In M. S. Gilmore (ed.), The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance. ASM Press, Washington, DC.>
96. Tendolkar, P. M.,, A. S. Baghdayan,, M. S. Gilmore,, and N. Shankar. 2004. Enterococcal surface protein, Esp, enhances biofilm formation by Enterococcus faecalis. Infect. Immun. 72: 6032– 6039.
97. Tock, M. R.,, and D. T. Dryden. 2005. The biology of restriction and anti-restriction. Curr. Opin. Microbiol. 8: 466– 472.
98. Top, J.,, R. Willems,, and M. Bonten. 2008. Emergence of CC17 Enterococcus faecium: from commensal to hospital-adapted pathogen. FEMS Immunol. Med. Microbiol. 52: 297– 308.
99. Uchiyama, J.,, M. Rashel,, Y. Maeda,, I. Takemura,, S. Sugihara,, K. Akechi,, A. Muraoka,, H. Wakiguchi,, and S. Matsuzaki. 2008. Isolation and characterization of a novel Enterococcus faecalis bacteriophage ϕEF24C as a therapeutic candidate. FEMS Microbiol. Lett. 278: 200– 206.
100. Urwin, R.,, and M. C. Maiden. 2003. Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol. 11: 479– 487.
101. Valdezate, S.,, C. Labayru,, A. Navarro,, M. A. Mantecon,, M. Ortega,, T. M. Coque,, M. Garcia,, and J. A. Saez-Nieto. 2009. Large clonal outbreak of multidrug-resistant CC17 ST17 Enterococcus faecium containing Tn 5382 in a Spanish hospital. J. Antimicrob. Chemother. 63: 17– 20.
102. Weaver, K. E.,, L. B. Rice,, and G. Churchward,. 2002. Plasmids and transposons, p. 219– 263. In M. S. Gilmore (ed.), The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance. ASM Press, Washington, DC.
103. Weigel, L. M.,, D. B. Clewell,, S. R. Gill,, N. C. Clark,, L. K. McDougal,, S. E. Flannagan,, J. F. Kolonay,, J. Shetty,, G. E. Killgore,, and F. C. Tenover. 2003. Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science 302: 1569– 1571.
104. Willems, R. J.,, W. Homan,, J. Top,, M. van Santen-Verheuvel,, D. Tribe,, X. Manzioros,, C. Gaillard,, C. M. Vandenbroucke-Grauls,, E. M. Mascini,, E. van Kregten,, J. D. van Embden,, and M. J. Bonten. 2001. Variant esp gene as a marker of a distinct genetic lineage of vancomycin-resistant Enterococcus faecium spreading in hospitals. Lancet 357: 853– 855.
105. Willems, R. J.,, J. Top,, D. J. Smith,, D. I. Roper,, S. E. North,, and N. Woodford. 2003. Mutations in the DNA mismatch repair proteins MutS and MutL of oxazolidinone-resistant or -susceptible Enterococcus faecium. Antimicrob. Agents Chemother. 47: 3061– 3066.
106. Wu, R.,, C. T. King,, and E. Jay. 1978. A new sequence-specific endonuclease from Streptococcus faecalis subsp. zymogenes. Gene 4: 329– 336.
107. Xu, Q.,, R. D. Morgan,, R. J. Roberts,, and M. J. Blaser. 2000. Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. Proc. Natl. Acad. Sci. USA 97: 9671– 9676.
108. Yasmin, A.,, J. G. Kenny,, J. Shankar,, A. C. Darby,, N. Hall,, C. Edwards,, and M. J. Horsburgh. 2010. Comparative genomics and transduction potential of Enterococcus faecalis temperate bacteriophages. J. Bacteriol. 192: 1122– 1130.
109. Zheng, B.,, H. Tomita,, T. Inoue,, and Y. Ike. 2009. Isolation of VanB-type Enterococcus faecalis strains from nosocomial infections: first report of the isolation and identification of the pheromone-responsive plasmids pMG2200, encoding VanB-type vancomycin resistance and a Bac41-type bacteriocin, and pMG2201, encoding erythromycin resistance and cytolysin (Hly/Bac). Antimicrob. Agents Chemother. 53: 735– 747.
110. Zhu, X.,, B. Zheng,, S. Wang,, R. J. Willems,, F. Xue,, X. Cao,, Y. Li,, S. Bo,, and J. Liu. 2009. Molecular characterisation of outbreak-related strains of vancomycin-resistant Enterococcus faecium from an intensive care unit in Beijing, China. J. Hosp. Infect. 72: 147– 154.

Tables

Selfish Elements and Self-Defense in the Enterococci
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Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8
/content/10.1128/9781555817213.chap8.tab8-1
TABLE 1

Examples of enterococcal plasmids that have served as models for understanding their contribution to virulence and antibiotic resistance transmission

10.1128/9781555817213/tab8-1_thmb.gif
10.1128/9781555817213/tab8-1.gif
Generic image for table
TABLE 1

Examples of enterococcal plasmids that have served as models for understanding their contribution to virulence and antibiotic resistance transmission

Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8
/content/10.1128/9781555817213.chap8.tab8-2
TABLE 2

Putative restriction-modification systems in complete genomes

10.1128/9781555817213/tab8-2_thmb.gif
10.1128/9781555817213/tab8-2.gif
Generic image for table
TABLE 2

Putative restriction-modification systems in complete genomes

Citation: Palmer K, Gilmore M. 2012. Selfish Elements and Self-Defense in the Enterococci, p 125-140. In Hacker J, Dobrindt U, Kurth R (ed), Genome Plasticity and Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/9781555817213.ch8

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