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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials

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  • Authors: Val Fernández Lanza1, Ana P. Tedim4, José Luís Martínez7, Fernando Baquero9, Teresa M. Coque12
  • Editors: Marcelo Tolmasky15, Juan Carlos Alonso16
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 2: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 3: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 4: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 5: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 6: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 7: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 8: Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; 9: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 10: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 11: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 12: Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; 13: Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (HRYC-CSIC), Madrid, Spain; 14: Centro de Investigación en Red en Epidemiología y Salud Pública (CIBER-ESP), Spain; 15: California State University, Fullerton, CA; 16: Centro Nacional de Biotecnología, Cantoblanco, Madrid, Spain
    • Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.PLAS-0039-2014
  • Received 14 January 2015 Accepted 15 January 2015 Published 03 April 2015
  • Teresa M. Coque, [email protected]; [email protected]
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  • Abstract:

    The phylum is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.

    The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among , , and species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a “single centric” perspective (“gene tracking” or “vehicle centric” in “single host-single pathogen” systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.

    This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.

  • Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials. Microbiol Spectrum 3(2):PLAS-0039-2014. doi:10.1128/microbiolspec.PLAS-0039-2014.

References

1. Centers for Disease Control and Prevention. 2013. Threat Report 2013. Antimicrobial Resistance. http://www.cdc.gov/drugresistance/threat-report-2013/
2. Murphree CA, Heist EP, Moe LA. 2014. Antibiotic resistance among cultured bacterial isolates from bioethanol fermentation facilities across the United States. Curr Microbiol 69:277–285. [PubMed][CrossRef]
3. Salyers AA, Gupta A, Wang Y. 2004. Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol 12:412–416. [PubMed][CrossRef]
4. European Food Safety Authority. 2012. Technical specifications on the harmonised monitoring and reporting of antimicrobial resistance in Salmonella, Campylobacter and indicator Escherichia coli and Enterococcus spp. bacteria transmitted through food. EFSA J 10:2742.
5. European Food Safety Authority. 2012. Technical specifications for the analysis and reporting of data on antimicrobial resistance (AMR) in the European Union Summary Report. EFSA J 10:2587.
6. Schwarz S, Shen J, Wendlandt S, Feßler AT, Wang Y, Kadlec K, Wu C. 2015. Plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes. In Tolmasky ME, Alonso JC (ed), Plasmids: Biology and Impact in Biotechnolgy and Discovery. ASM Press, Washington, DC, in press.
7. Clewell DB, Weaver KE, Dunny GM, Coque TM, Francia MV, Hayes F. 2014. Extrachromosomal and mobile elements in enterococci: transmission, maintenance, and epidemiology. In Gilmore MS, Clewell DB, Ike Y, Shankar N (ed), Enterococci: From Commensals to Leading Causes of Drug Resistant Infection. Massachusetts Eye and Ear Infirmary, Boston, MA.
8. DiPersio LP, DiPersio JR, Beach JA, Loudon AM, Fuchs AM. 2011. Identification and characterization of plasmid-borne erm(T) macrolide resistance in group B and group A Streptococcus. Diagn Microbiol Infect Dis 71:217–223. [PubMed][CrossRef]
9. Lindsay JA. 2014. Staphylococcus aureus genomics and the impact of horizontal gene transfer. Int J Med Microbiol 304:103–109. [PubMed][CrossRef]
10. Lebreton F, van Schaik W, McGuire AM, Godfrey P, Griggs A, Mazumdar V, Corander J, Cheng L, Saif S, Young S, Zeng Q, Wortman J, Birren B, Willems RJL, Earl AM, Gilmore MS. 2013. Emergence of epidemic multidrug-resistant Enterococcus faecium from animal and commensal strains. MBio 4(4) :e00534-13. doi:10.1128/mBio.00534-13. [CrossRef]
11. Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102:14332–14337. [PubMed][CrossRef]
12. Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E. 2010. Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci USA 107:127–132. [PubMed][CrossRef]
13. Popa O, Dagan T. 2011. Trends and barriers to lateral gene transfer in prokaryotes. Curr Opin Microbiol 14:615–623. [PubMed][CrossRef]
14. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. 2011. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599–609. [PubMed][CrossRef]
15. Tamminen M, Virta M, Fani R, Fondi M. 2012. Large-scale analysis of plasmid relationships through gene-sharing networks. Mol Biol Evol 29:1225–1240. [PubMed][CrossRef]
16. Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EPC. 2009. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol 19:1683–1691. [PubMed][CrossRef]
17. McGinty SE, Rankin DJ, Brown SP. 2011. Horizontal gene transfer and the evolution of bacterial cooperation. Evolution 65:21–32. [PubMed][CrossRef]
18. Friedman J, Alm EJ, Shapiro BJ. 2013. Sympatric speciation: when is it possible in bacteria? PLoS One 8:e53539. doi:10.1371/journal.pone.0053539. [PubMed]
19. Hobman JL. 2015. Molecular Life Sciences. Springer, New York, NY.
20. Eberhard WG. 1990. Evolution in bacterial plasmids and levels of selection. Q Rev Biol 65:3–22. [PubMed][CrossRef]
21. Kloesges T, Popa O, Martin W, Dagan T. 2011. Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28:1057–1074. [PubMed][CrossRef]
22. Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EPC. 2011. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7:e1002222. doi:10.1371/journal.pgen.1002222. [PubMed][CrossRef]
23. Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ. 2012. Population genomics of early events in the ecological differentiation of bacteria. Science 336:48–51. [PubMed][CrossRef]
24. DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JAE, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R. 2013. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110:16939–16944. [PubMed][CrossRef]
25. Toussaint A, Chandler M. 2012. Prokaryote genome fluidity: toward a system approach of the mobilome. Methods Mol Biol 804:57–80. [PubMed][CrossRef]
26. Shen J, Wang Y, Schwarz S. 2013. Presence and dissemination of the multiresistance gene cfr in Gram-positive and Gram-negative bacteria. J Antimicrob Chemother 68:1697–1706. [PubMed][CrossRef]
27. Bonafede ME, Carias LL, Rice LB. 1997. Enterococcal transposon Tn5384: evolution of a composite transposon through cointegration of enterococcal and staphylococcal plasmids. Antimicrob Agents Chemother 41:1854–1858. [PubMed]
28. Hung W-C, Takano T, Higuchi W, Iwao Y, Khokhlova O, Teng L-J, Yamamoto T. 2012. Comparative genomics of community-acquired ST59 methicillin-resistant Staphylococcus aureus in Taiwan: novel mobile resistance structures with IS1216V. PLoS One 7:e46987. doi:10.1371/journal.pone.0046987. [PubMed][CrossRef]
29. Marraffini LA, Sontheimer EJ. 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11:181–190. [PubMed][CrossRef]
30. Johnston C, Martin B, Polard P, Claverys J-P. 2013. Postreplication targeting of transformants by bacterial immune systems? Trends Microbiol 21:516–521. [PubMed][CrossRef]
31. McCarthy AJ, Lindsay JA. 2012. The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated. BMC Microbiol 12:104. [PubMed][CrossRef]
32. Roberts GA, Houston PJ, White JH, Chen K, Stephanou AS, Cooper LP, Dryden DTF, Lindsay JA. 2013. Impact of target site distribution for type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations. Nucleic Acids Res 41:7472–7484. [PubMed][CrossRef]
33. Attaiech L, Olivier A, Mortier-Barrière I, Soulet A-L, Granadel C, Martin B, Polard P, Claverys J-P. 2011. Role of the single-stranded DNA-binding protein SsbB in pneumococcal transformation: maintenance of a reservoir for genetic plasticity. PLoS Genet 7:e1002156. doi:10.1371/journal.pgen.1002156. [CrossRef]
34. Iacobino A, Scalfaro C, Franciosa G. 2013. Structure and genetic content of the megaplasmids of neurotoxigenic clostridium butyricum type E strains from Italy. PLoS One 8:e71324. doi:10.1371/journal.pone.0071324. [PubMed]
35. Hatoum-Aslan A, Maniv I, Samai P, Marraffini LA. 2014. Genetic characterization of antiplasmid immunity through a type III-A CRISPR-Cas system. J Bacteriol 196:310–317. [PubMed][CrossRef]
36. Palmer KL, Gilmore MS. 2010. Multidrug-resistant enterococci lack CRISPR-cas. MBio 1(4) :e00227-10. doi:10.1128/mBio.00227-10. [PubMed][CrossRef]
37. Serbanescu MA, Cordova M, Krastel K, Flick R, Beloglazova N, Latos A, Yakunin AF, Senadheera DB, Cvitkovitch DG. 2014. Role of the Streptococcus mutans CRISPR/Cas systems in immunity and cell physiology. J Bacteriol. [Epub ahead of print.] doi:10.1128/JB.02333-14. [PubMed][CrossRef]
38. Hermsen R, Deris JB, Hwa T. 2012. On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient. Proc Natl Acad Sci USA 109:10775–10780. [PubMed][CrossRef]
39. Shu C-C, Chatterjee A, Hu W-S, Ramkrishna D. 2013. Role of intracellular stochasticity in biofilm growth. Insights from population balance modeling. PLoS One 8:e79196. doi:10.1371/journal.pone.0079196. [PubMed][CrossRef]
40. Król JE, Wojtowicz AJ, Rogers LM, Heuer H, Smalla K, Krone SM, Top EM. 2013. Invasion of E. coli biofilms by antibiotic resistance plasmids. Plasmid 70:110–119. [PubMed][CrossRef]
41. Hermsen R, Hwa T. 2010. Sources and sinks: a stochastic model of evolution in heterogeneous environments. Phys Rev Lett 105:248104. [PubMed][CrossRef]
42. Nielsen KM, Bøhn T, Townsend JP. 2014. Detecting rare gene transfer events in bacterial populations. Front Microbiol 4:415. [PubMed][CrossRef]
43. McCarthy AJ, Loeffler A, Witney AA, Gould KA, Lloyd DH, Lindsay JA. 2014. Extensive horizontal gene transfer during Staphylococcus aureus co-colonization in vivo. Genome Biol Evol 6:2697–2708. [PubMed][CrossRef]
44. Gullberg E, Albrecht LM, Karlsson C, Sandegren L, Andersson DI. 2014. Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals. MBio 5:e01918-14. doi:10.1128/mBio.01918-14. [PubMed]
45. Baquero F, Coque TM. 2014. Widening the spaces of selection: evolution along sublethal antimicrobial gradients. MBio 5:e02270-14. doi:10.1128/mBio.02270-14 [PubMed][CrossRef]
46. Datta N. 1985. Plasmids in bacteria, p 3–16. In Helinski DR, Cohen SN, Clewell DB, Jackson DA, Hollaender A (ed), Plasmids in Bacteria. Basic Life Sciences, Vol. 30. Springer US, New York, New York. [PubMed][CrossRef]
47. Eberhard WG. 1989. Why do bacterial plasmids carry some genes and not others? Plasmid 21:167–174. [PubMed][CrossRef]
48. Souza V, Eguiarte LE. 1997. Bacteria gone native vs. bacteria gone awry?: plasmidic transfer and bacterial evolution. Proc Natl Acad Sci USA 94:5501–5503. [PubMed][CrossRef]
49. Kozlowicz BK, Dworkin M, Dunny GM. 2009. Pheromone-inducible conjugation in Enterococcus faecalis: a model for the evolution of biological complexity? Int J Med Microbiol 296:141–147. [PubMed][CrossRef]
50. Taylor DE, Gibreel A, Lawley TD, Tracz DM. 2004. Antibiotic resistance plasmids, p 473–491. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. [CrossRef]
51. Shearer JES, Wireman J, Hostetler J, Forberger H, Borman J, Gill J, Sanchez S, Mankin A, Lamarre J, Lindsay JA, Bayles K, Nicholson A, O'Brien F, Jensen SO, Firth N, Skurray RA, Summers AO. 2011. Major families of multiresistant plasmids from geographically and epidemiologically diverse staphylococci. G3 1:581–591. [PubMed][CrossRef]
52. Lacey RW. 1975. Antibiotic resistance plasmids of Staphylococcus aureus and their clinical importance. Bacteriol Rev 39:1–32. [PubMed]
53. Novick RP. 1989. Staphylococcal plasmids and their replication. Annu Rev Microbiol 43:537–565. [PubMed][CrossRef]
54. Mills S, McAuliffe OE, Coffey A, Fitzgerald GF, Ross RP. 2006. Plasmids of lactococci: genetic accessories or genetic necessities? FEMS Microbiol Rev 30:243–273. [PubMed][CrossRef]
55. Wang TT, Lee BH. 1997. Plasmids in Lactobacillus. Crit Rev. Biotechnol 17:227–272. [PubMed][CrossRef]
56. Li J, Adams V, Bannam TL, Miyamoto K, Garcia JP, Uzal FA, Rood JI, McClane BA. 2013. Toxin plasmids of Clostridium perfringens. Microbiol Mol Biol Rev 77:208–233. [PubMed][CrossRef]
57. Dib JR, Liebl W, Wagenknecht M, Farías ME, Meinhardt F. 2013. Extrachromosomal genetic elements in Micrococcus. Appl Microbiol Biotechnol 97:63–75. [PubMed][CrossRef]
58. Guglielmetti S, Mayo B, Álvarez-Martín P. 2013. Mobilome and genetic modification of bifidobacteria. Benef Microbes 4:143–166. [PubMed][CrossRef]
59. Jensen LB, Garcia-Migura L, Valenzuela AJ, Løhr M, Hasman H, Aarestrup FM. 2010. A classification system for plasmids from enterococci and other Gram-positive bacteria. J Microbiol Methods 80:25–43. [PubMed][CrossRef]
60. Iordanescu S, Surdeanu M, Della Latta P, Novick R. 1978. Incompatibility and molecular relationships between small staphylococcal plasmids carrying the same resistance marker. Plasmid 1:468–479. [PubMed][CrossRef]
61. Macrina FL, Archer GL. 1993. Bacterial Conjugation. Plenum, New York, NY.
62. Novick RP. 1987. Plasmid incompatibility. Microbiol Rev 51:381–395. [PubMed]
63. Projan SJ, Novick R. 1988. Comparative analysis of five related staphylococcal plasmids. Plasmid 19:203–221. [PubMed][CrossRef]
64. Brantl S, Behnke D, Alonso JC. 1990. Molecular analysis of the replication region of the conjugative Streptococcus agalactiae plasmid pIP501 in Bacillus subtilis. Comparison with plasmids pAM beta 1 and pSM19035. Nucleic Acids Res 18:4783–4790. [PubMed][CrossRef]
65. Dunny GM. 2013. Enterococcal sex pheromones: signaling, social behavior, and evolution. Annu Rev Genet 47:457–482. [PubMed][CrossRef]
66. Lozano C, García-Migura L, Aspiroz C, Zarazaga M, Torres C, Aarestrup FM. 2012. Expansion of a plasmid classification system for Gram-positive bacteria and determination of the diversity of plasmids in Staphylococcus aureus strains of human, animal, and food origins. Appl Environ Microbiol 78:5948–5955. [PubMed][CrossRef]
67. Sadowy E, Luczkiewicz A. 2014. Drug-resistant and hospital-associated Enterococcus faecium from wastewater, riverine estuary and anthropogenically impacted marine catchment basin. BMC Microbiol 14:66. [PubMed][CrossRef]
68. Wardal E, Gawryszewska I, Hryniewicz W, Sadowy E. 2013. Abundance and diversity of plasmid-associated genes among clinical isolates of Enterococcus faecalis. Plasmid 70:329–342. [PubMed][CrossRef]
69. Wardal E, Markowska K, Zabicka D, Wróblewska M, Giemza M, Mik E, Połowniak-Pracka H, Woźniak A, Hryniewicz W, Sadowy E. 2014. Molecular analysis of vanA outbreak of Enterococcus faecium in two Warsaw hospitals: the importance of mobile genetic elements. Biomed Res Int 2014:575367. [PubMed][CrossRef]
70. Rosvoll TCS, Pedersen T, Sletvold H, Johnsen PJ, Sollid JE, Simonsen GS, Jensen LB, Nielsen KM, Sundsfjord A. 2010. PCR-based plasmid typing in Enterococcus faecium strains reveals widely distributed pRE25-, pRUM-, pIP501- and pHTbeta-related replicons associated with glycopeptide resistance and stabilizing toxin-antitoxin systems. FEMS Immunol Med Microbiol 58:254–268. [PubMed][CrossRef]
71. Freitas AR, Novais C, Tedim AP, Francia MV, Baquero F, Peixe L, Coque TM. 2013. Microevolutionary events involving narrow host plasmids influences local fixation of vancomycin-resistance in Enterococcus populations. PLoS One 8:e60589. doi:10.1371/journal.pone.0060589. [PubMed]
72. Francia MV, Varsaki A, Garcillán-Barcia MP, Latorre A, Drainas C, de la Cruz F. 2004. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev 28:79–100. [PubMed][CrossRef]
73. Garcillan-Barcia MP, Francia MV, de la Cruz F. 2009. The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 33:657–687. [PubMed][CrossRef]
74. Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC, de la Cruz F. 2010. Mobility of plasmids. Microbiol Mol Biol Rev 74:434–452. [PubMed][CrossRef]
75. Lorenzo-Díaz F, Fernández-López C, Garcillán-Barcia MP, Espinosa M. 2014. Bringing them together: plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective. Plasmid 74:15–31. [PubMed][CrossRef]
76. Weaver KE, Kwong SM, Firth N, Francia MV. 2009. The RepA_N replicons of Gram-positive bacteria: a family of broadly distributed but narrow host range plasmids. Plasmid 61:94–109. [PubMed][CrossRef]
77. Gruss A, Ehrlich SD. 1989. The Family of highly interrelated single-stranded deoxyribonucleic acid plasmids. Microbiol Rev 53:231–241. [PubMed]
78. del Solar G, Moscoso M, Espinosa M. 1993. Rolling circle-replicating plasmids from Gram-positive and Gram-negative bacteria: a wall falls. Mol Microbiol 8:789–796. [PubMed][CrossRef]
79. Khan SA. 1997. Rolling-circle replication of bacterial plasmids. Microbiol Mol Biol Rev 61:442–455. [PubMed]
80. Widdowson CA, Adrian PV, Klugman KP. 2000. Acquisition of Chloramphenicol resistance by the linearization and integration of the entire staphylococcal plasmid pC194 into the chromosome of Streptococcus pneumoniae. Antimicrob Agents Chemother 44:393–395. [PubMed][CrossRef]
81. Del Solar G, Moscoso M, Espinosa M. 1993. Rolling circle-replicating plasmids from Gram-positive and Gram-negative bacteria: a wall falls. Mol Microbiol 8:789–796. [PubMed][CrossRef]
82. Heng NCK, Burtenshaw GA, Jack RW, Tagg JR. 2004. Sequence analysis of pDN571, a plasmid encoding novel bacteriocin production in M-type 57 Streptococcus pyogenes. Plasmid 52:225–229. [PubMed][CrossRef]
83. Romero P, Llull D, García E, Mitchell TJ, López R, Moscoso M. 2007. Isolation and characterization of a new plasmid pSpnP1 from a multidrug-resistant clone of Streptococcus pneumoniae. Plasmid 58:51–60. [PubMed][CrossRef]
84. Gillespie MT, May JW, Skurray RA. 1985. Antibiotic resistance in Staphylococcus aureus isolated at an Australian hospital between 1946 and 1981. J Med Microbiol 19:137–147. [PubMed][CrossRef]
85. Schiwon K, Arends K, Rogowski KM, Fürch S, Prescha K, Sakinc T, Van Houdt R, Werner G, Grohmann E. 2013. Comparison of antibiotic resistance, biofilm formation and conjugative transfer of Staphylococcus and Enterococcus isolates from International Space Station and Antarctic Research Station Concordia. Microb Ecol 65:638–651. [PubMed][CrossRef]
86. Shiwa Y, Yanase H, Hirose Y, Satomi S, Araya-Kojima T, Watanabe S, Zendo T, Chibazakura T, Shimizu-Kadota M, Yoshikawa H, Sonomoto K. 2014. Complete genome sequence of Enterococcus mundtii QU 25, an efficient L-(+)-lactic acid-producing bacterium. DNA Res 21:369–377. [PubMed][CrossRef]
87. 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. [PubMed][CrossRef]
88. De Vries LE, Christensen H, Agersø Y. 2012. The diversity of inducible and constitutively expressed erm(C) genes and association to different replicon types in staphylococci plasmids. Mob Genet Elements 2:72–80. [PubMed][CrossRef]
89. Gómez-Sanz E, Kadlec K, Feßler AT, Zarazaga M, Torres C, Schwarz S. 2013. Novel erm(T)-carrying multiresistance plasmids from porcine and human isolates of methicillin-resistant Staphylococcus aureus ST398 that also harbor cadmium and copper resistance determinants. Antimicrob Agents Chemother 57:3275–3282. [PubMed][CrossRef]
90. Firth N, Skurray RA. 1998. Mobile elements in the evolution and spread of multiple-drug resistance in staphylococci. Drug Resist Updat 1:49–58. [PubMed][CrossRef]
91. Charlebois A, Jalbert L-A, Harel J, Masson L, Archambault M. 2012. Characterization of genes encoding for acquired bacitracin resistance in Clostridium perfringens. PLoS One 7:e44449. doi:10.1371/journal.pone.0044449. [PubMed]
92. Palmer KL, Kos VN, Gilmore MS. 2010. Horizontal gene transfer and the genomics of enterococcal antibiotic resistance. Curr Opin Microbiol 13:632–639. [PubMed][CrossRef]
93. Montilla A, Zavala A, Cáceres Cáceres R, Cittadini R, Vay C, Gutkind G, Famiglietti A, Bonofiglio L, Mollerach M. 2014. Genetic environment of the lnu(B) gene in a Streptococcus agalactiae clinical isolate. Antimicrob Agents Chemother 58:5636–5637. [PubMed][CrossRef]
94. Zong Z. 2013. Characterization of a complex context containing mecA but lacking genes encoding cassette chromosome recombinases in Staphylococcus haemolyticus. BMC Microbiol 13:64. [PubMed][CrossRef]
95. Locke JB, Zuill DE, Scharn CR, Deane J, Sahm DF, Denys GA, Goering RV, Shaw KJ. 2014. Linezolid-resistant Staphylococcus aureus strain 1128105, the first known clinical isolate possessing the cfr multidrug resistance gene. Antimicrob Agents Chemother 58:6592–6598. [PubMed][CrossRef]
96. Goessweiner-Mohr N, Arends K, Keller W, Grohmann E. 2013. Conjugative type IV secretion systems in Gram-positive bacteria. Plasmid 70:289–302. [PubMed][CrossRef]
97. Li J, Li B, Wendlandt S, Schwarz S, Wang Y, Wu C, Ma Z, Shen J. 2014. Identification of a novel vga(E) gene variant that confers resistance to pleuromutilins, lincosamides and streptogramin A antibiotics in staphylococci of porcine origin. J Antimicrob Chemother 69:919–923. [PubMed][CrossRef]
98. Lozano C, Aspiroz C, Rezusta A, Gómez-sanz E, Simon C, Gómez P, Ortega C, José M, Zarazaga M, Torres C. 2012. Identification of novel vga(A)-carrying plasmids and a Tn 5406-like transposon in meticillin-resistant Staphylococcus aureus and Staphylococcus epidermidis of human and animal origin. Int J Antimicrob Agents 40:306–312. [PubMed][CrossRef]
99. Brantl S. 2014. Antisense-RNA mediated control of plasmid replication: pIP501 revisited. Plasmid. [Epub ahead of print.] doi:10.1016/j.plasmid.2014.07.004. [PubMed]
100. Grohmann E, Muth G, Espinosa M. 2003. Conjugative plasmid transfer in Gram-positive bacteria. Microbiol Mol Biol Rev 67:277–301. [PubMed][CrossRef]
101. Behnke D, Malke H, Hartmann M, Walter F. 1979. Post-transformational rearrangement of an in vitro reconstructed group-A streptococcal erythromycin resistance plasmid. Plasmid 2:605–616. [CrossRef]
102. Clewell DB, Yagi Y, Dunny GM, Schultz SK. 1974. Characterization of three plasmid deoxyribonucleic acid molecules in a strain of Streptococcus faecalis: identification of a plasmid determining erythromycin resistance. J Bacteriol 117:283–289. [PubMed]
103. Horodniceanu T, Bouanchaud DH, Bieth G, Chabbert YA. 1976. R plasmids in Streptococcus agalactiae (group B). Antimicrob Agents Chemother 10:795–801. [PubMed][CrossRef]
104. Thompson JK, Collins MA. 2003. Completed sequence of plasmid pIP501 and origin of spontaneous deletion derivatives. Plasmid 50:28–35. [PubMed][CrossRef]
105. Horaud T, Le Bouguenec C, Pepper K. 1985. Molecular genetics of resistance to macrolides, lincosamides and streptogramin B (MLS) in streptococci. J Antimicrob Chemother 16:111–135. [PubMed][CrossRef]
106. Derome A, Hoischen C, Bussiek M, Grady R, Adamczyk M, Kedzierska B, Diekmann S, Barillà D, Hayes F. 2008. Centromere anatomy in the multidrug-resistant pathogen Enterococcus faecium. Proc Natl Acad Sci USA 105:2151–2156. [PubMed][CrossRef]
107. Li X, Alvarez V, Harper WJ, Wang HH. 2011. Persistent, toxin-antitoxin system-independent, tetracycline resistance-encoding plasmid from a dairy Enterococcus faecium isolate. Appl Environ Microbiol 77:7096–7103. [PubMed][CrossRef]
108. Abajy MY, Kopeć J, Schiwon K, Burzynski M, Döring M, Bohn C, Grohmann E. 2007. A type IV-secretion-like system is required for conjugative DNA transport of broad-host-range plasmid pIP501 in Gram-positive bacteria. J Bacteriol 189:2487–2496. [PubMed][CrossRef]
109. Krah ER, Macrina FL. 1991. Identification of a region that influences host range of the streptococcal conjugative plasmid pIP501. Plasmid 25:64–69. [PubMed][CrossRef]
110. Schaberg DR, Zervos MJ. 1986. Intergeneric and interspecies gene exchange in Gram-positive cocci. Antimicrob Agents Chemother 30:817–822. [PubMed][CrossRef]
111. Teuber M, Meile L, Schwarz F. 1999. Acquired antibiotic resistance in lactic acid bacteria from food. Antonie Van Leeuwenhoek 76:115–137. [PubMed][CrossRef]
112. El-Solh N, Bouanchaud DH, Horodniceanu T, Roussel A, Chabbert YA. 1978. Molecular studies and possible relatedness between R plasmids from groups B and D streptococci. Antimicrob Agents Chemother 14:19–23. [PubMed][CrossRef]
113. Engel HW, Soedirman N, Rost JA, van Leeuwen WJ, van Embden JD. 1980. Transferability of macrolide, lincomycin, and streptogramin resistances between group A, B, and D streptococci, Streptococcus pneumoniae, and Staphylococcus aureus. J Bacteriol 142:407–413. [PubMed]
114. Clewell DB. 1981. Plasmids, drug resistance, and gene transfer in the genus Streptococcus. Microbiol Rev 45:409–436. [PubMed]
115. Sletvold H, Johnsen PJ, Simonsen GS, Aasnaes B, Sundsfjord A, Nielsen KM. 2007. Comparative DNA analysis of two vanA plasmids from Enterococcus faecium strains isolated from poultry and a poultry farmer in Norway. Antimicrob Agents Chemother 51:736–739. [PubMed][CrossRef]
116. Sletvold H, Johnsen PJ, Wikmark O-G, Simonsen GS, Sundsfjord A, Nielsen KM. 2010. Tn1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages. J Antimicrob Chemother 65:1894–1906. [PubMed][CrossRef]
117. Zhu W, Clark NC, McDougal LK, Hageman J, McDonald LC, Patel JB. 2008. Vancomycin-resistant Staphylococcus aureus isolates associated with Inc18-like vanA plasmids in Michigan. Antimicrob Agents Chemother 52:452–457. [PubMed][CrossRef]
118. Zhu W, Murray PR, Huskins WC, Jernigan JA, McDonald LC, Clark NC, Anderson KF, McDougal LK, Hageman JC, Olsen-Rasmussen M, Frace M, Alangaden GJ, Chenoweth C, Zervos MJ, Robinson-Dunn B, Schreckenberger PC, Reller LB, Rudrik JT, Patel JB. 2010. Dissemination of an Enterococcus Inc18-Like vanA plasmid associated with vancomycin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 54:4314–4320. [PubMed][CrossRef]
119. Teuber M, Schwarz F, Perreten V. 2003. Molecular structure and evolution of the conjugative multiresistance plasmid pRE25 of Enterococcus faecalis isolated from a raw-fermented sausage. Int J Food Microbiol 88:325–329. [PubMed][CrossRef]
120. Maki T, Santos MD, Kondo H, Hirono I, Aoki T. 2009. A transferable 20-kilobase multiple drug resistance-conferring R plasmid (pKL0018) from a fish pathogen ( Lactococcus garvieae) is highly homologous to a conjugative multiple drug resistance-conferring enterococcal plasmid. Appl Environ Microbiol 75:3370–3372. [PubMed][CrossRef]
121. Lim S-K, Tanimoto K, Tomita H, Ike Y. 2006. Pheromone-responsive conjugative vancomycin resistance plasmids in Enterococcus faecalis isolates from humans and chicken feces. Appl Environ Microbiol 72:6544–6553. [PubMed][CrossRef]
122. Tanimoto K, Ike Y. 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. [PubMed][CrossRef]
123. Tomita H, Pierson C, Lim SK, Clewell DB, Ike Y. 2002. Possible connection between a widely disseminated conjugative gentamicin resistance (pMG1-like) plasmid and the emergence of vancomycin resistance in Enterococcus faecium. J Clin Microbiol 40:3326–3333. [PubMed][CrossRef]
124. Tomita H, Tanimoto K, Hayakawa S, Morinaga K, Ezaki K, Oshima H, Ike Y. 2003. Highly conjugative pMG1-like plasmids carrying Tn1546-like transposons that encode vancomycin resistance in Enterococcus faecium. J Bacteriol 185:7024–7028. [PubMed][CrossRef]
125. Manson JM, Hancock LE, Gilmore MS. 2010. Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits. Proc Natl Acad Sci USA 107:12269–12274. [PubMed][CrossRef]
126. 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. [PubMed][CrossRef]
127. Firth N, Apisiridej S, Berg T, Rourke BAO, Curnock S, Dyke KGH, Skurray RA. 2006. Replication of staphylococcal multiresistance plasmids. J Bacteriol 182:2170–2178. [PubMed][CrossRef]
128. Kwong SM, Lim R, Lebard RJ, Skurray RA, Firth N. 2008. Analysis of the pSK1 replicon, a prototype from the staphylococcal multiresistance plasmid family. Microbiology 154:3084–3094. [PubMed][CrossRef]
129. Berg T, Firth N, Apisiridej S, Leelaporn A, Skurray RA, Hettiaratchi A. 2006. Complete nucleotide sequence of pSK41: evolution of staphylococcal conjugative multiresistance plasmids. J Bacteriol 180:4350–4359. [PubMed]
130. Littlejohn TG, DiBerardino D, Messerotti LJ, Spiers SJ, Skurray RA. 1991. Structure and evolution of a family of genes encoding antiseptic and disinfectant resistance in Staphylococcus aureus. Gene 101:59–66. [PubMed][CrossRef]
131. Pérez-Roth E, Kwong SM, Alcoba-Florez J, Firth N, Méndez-Alvarez S. 2010. Complete nucleotide sequence and comparative analysis of pPR9, a 41.7-kilobase conjugative staphylococcal multiresistance plasmid conferring high-level mupirocin resistance. Antimicrob Agents Chemother 54:2252–2257. [PubMed][CrossRef]
132. Pérez-Roth E, Potel-Alvarellos C, Espartero X, Constela-Caramés L, Méndez-Álvarez S, Alvarez-Fernández M. 2013. Molecular epidemiology of plasmid-mediated high-level mupirocin resistance in methicillin-resistant Staphylococcus aureus in four Spanish health care settings. Int J Med Microbiol 303:201–204. [PubMed][CrossRef]
133. Udo EE, Jacob LE. 1998. Conjugative transfer of high-level mupirocin resistance and the mobilization of non-conjugative plasmids in Staphylococcus. Microb Drug Resist 4:185–193. [PubMed][CrossRef]
134. Weigel LM, Clewell DB, Gill SR, Clark NC, McDougal LK, Flannagan SE, Kolonay JF, Shetty J, Killgore GE, Tenover FC. 2003. Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science 302:1569–1571. [PubMed][CrossRef]
135. Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, Sensabaugh GF, Perdreau-Remington F. 2006. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet 367:731–739. [PubMed][CrossRef]
136. Thomas WD, Archer GL. 1992. Mobilization of recombinant plasmids from Staphylococcus aureus into coagulase negative Staphylococcus species. Plasmid 27:164–168. [PubMed][CrossRef]
137. Projan SJ, Archer GL. 1989. Mobilization of the relaxable Staphylococcus aureus plasmid pC221 by the conjugative plasmid pGO1 involves three pC221 loci. J Bacteriol 171:1841–1845. [PubMed]
138. Wardal E, Sadowy E, Hryniewicz W. 2010. Complex nature of enterococcal pheromone-responsive plasmids. Pol J Microbiol 59:79–87. [PubMed]
139. Clewell DB, Francia MV. 2004. Conjugation in Gram-positive bacteria. In Funnell B, Phillips JG (ed), Plasmid Biology. ASM Press, Washington, DC. [CrossRef]
140. Clewell DB, Francia MV, Flannagan SE, An FY. 2002. Enterococcal plasmid transfer: sex pheromones, transfer origins, relaxases, and the Staphylococcus aureus issue. Plasmid 48:193–201. [PubMed][CrossRef]
141. Weaver KE. 2014. The type I toxin-antitoxin par locus from Enterococcus faecalis plasmid pAD1: RNA regulation by both cis- and trans-acting elements. Plasmid. [Epub ahead of print.] doi:10.1016/j.plasmid.2014.10.001. [PubMed]
142. Grady R, Hayes F. 2003. Axe-Txe, a broad-spectrum proteic toxin-antitoxin system specified by a multidrug-resistant, clinical isolate of Enterococcus faecium. Mol Microbiol 47:1419–1432. [PubMed][CrossRef]
143. Halvorsen EM, Williams JJ, Bhimani AJ, Billings EA, Hergenrother PJ. 2011. Txe, an endoribonuclease of the enterococcal Axe-Txe toxin-antitoxin system, cleaves mRNA and inhibits protein synthesis. Microbiology 157:387–397. [PubMed][CrossRef]
144. Freitas AR, Coque TM, Novais C, Hammerum AM, Lester CH, Zervos MJ, Donabedian S, Jensen LB, Francia MV, Baquero F, Peixe L. 2011. Human and swine hosts share vancomycin-resistant Enterococcus faecium CC17 and CC5 and Enterococcus faecalis CC2 clonal clusters harboring Tn1546 on indistinguishable plasmids. J Clin Microbiol 49:925–931. [PubMed][CrossRef]
145. Werner G, Klare I, Witte W. 1999. Large conjugative vanA plasmids in vancomycin-resistant Enterococcus faecium. J Clin Microbiol 37:2383–2384. [PubMed]
146. Hasman H, Villadsen AG, Aarestrup FM. 2005. Diversity and stability of plasmids from glycopeptide-resistant Enterococcus faecium (GRE) isolated from pigs in Denmark. Microb Drug Resist 11:178–184. [PubMed][CrossRef]
147. Biavasco F, Foglia G, Paoletti C, Zandri G, Magi G, Guaglianone E, Sundsfjord A, Pruzzo C, Donelli G, Facinelli B. 2007. VanA-type enterococci from humans, animals, and food: species distribution, population structure, Tn1546 typing and location, and virulence determinants. Appl Environ Microbiol 73:3307–3319. [PubMed][CrossRef]
148. Laverde Gomez JA, van Schaik W, Freitas AR, Coque TM, Weaver KE, Francia MV, Witte W, Werner G. 2011. A multiresistance megaplasmid pLG1 bearing a hylEfm genomic island in hospital Enterococcus faecium isolates. Int J Med Microbiol 301:165–175. [PubMed][CrossRef]
149. Zhang X, Vrijenhoek JEP, Bonten MJM, Willems RJL, van Schaik W. 2011. A genetic element present on megaplasmids allows Enterococcus faecium to use raffinose as carbon source. Environ Microbiol 13:518–528. [PubMed][CrossRef]
150. Gordoncillo MJN, Donabedian S, Bartlett PC, Perri M, Zervos M, Kirkwood R, Febvay C. 2013. Isolation and molecular characterization of vancomycin-resistant Enterococcus faecium from swine in Michigan, USA. Zoonoses Public Health 60:319–326. [PubMed][CrossRef]
151. Johnson PDR, Ballard SA, Grabsch EA, Stinear TP, Seemann T, Young HL, Grayson ML, Howden BP. 2010. A sustained hospital outbreak of vancomycin-resistant Enterococcus faecium bacteremia due to emergence of vanB E. faecium sequence type 203. J Infect Dis 202:1278–1286. [PubMed][CrossRef]
152. Rosvoll TCS, Lindstad BL, Lunde TM, Hegstad K, Aasnaes B, Hammerum AM, Lester CH, Simonsen GS, Sundsfjord A, Pedersen T. 2012. Increased high-level gentamicin resistance in invasive Enterococcus faecium is associated with aac(6′)Ie-aph(2″)Ia-encoding transferable megaplasmids hosted by major hospital-adapted lineages. FEMS Immunol Med Microbiol 66:166–176. [PubMed][CrossRef]
153. Panesso D, Montealegre MC, Rincón S, Mojica MF, Rice LB, Singh KV, Murray BE, Arias CA. 2011. The hylEfm gene in pHylEfm of Enterococcus faecium is not required in pathogenesis of murine peritonitis. BMC Microbiol 11:20. [PubMed][CrossRef]
154. Kim DS, Singh KV, Nallapareddy SR, Qin X, Panesso D, Arias CA, Murray BE. 2010. The fms21 (pilA)-fms20 locus encoding one of four distinct pili of Enterococcus faecium is harboured on a large transferable plasmid associated with gut colonization and virulence. J Med Microbiol 59:505–507. [PubMed][CrossRef]
155. Boon E, Meehan CJ, Whidden C, Wong DH-J, Langille MGI, Beiko RG. 2014. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev 38:90–118. [PubMed][CrossRef]
156. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241–244. [PubMed][CrossRef]
157. Skippington E, Ragan MA. 2011. Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. BMC Genomics 12:532. [PubMed][CrossRef]
158. Baquero F, Coque TM, Canto R. 2003. Antibiotics, complexity, and evolution. ASM News 69:547–552.
159. Baquero F, Tedim AP, Coque TM. 2013. Antibiotic resistance shaping multilevel population biology of bacteria. Front Microbiol 4:1–15. [PubMed][CrossRef]
160. Baquero F, Lanza VF, Canton R, Coque TM. 2014. Public health evolutionary biology of antimicrobial resistance: priorities for intervention. Evol Appl. [Epub ahead of print.] doi:10.1111/eva.12235. [CrossRef]
161. Baquero F, Coque TM, Cantón R. 2014. Counteracting antibiotic resistance: breaking barriers among antibacterial strategies. Expert Opin Ther Targets 18:1–11. [PubMed][CrossRef]
162. Martínez JL. 2008. Antibiotics and antibiotic resistance genes in natural environments. Science 321:365–367. [PubMed][CrossRef]
163. Martínez JL. 2011. Bottlenecks in the transferability of antibiotic resistance from natural ecosystems to human bacterial pathogens. Front Microbiol 2:265. [PubMed]
164. Berryman DI, Rood JI. 1995. The closely related ermB-ermAM genes from Clostridium perfringens, Enterococcus faecalis (pAM beta 1), and Streptococcus agalactiae (pIP501) are flanked by variants of a directly repeated sequence. Antimicrob Agents Chemother 39:1830–1834. [PubMed][CrossRef]
165. Howden BP, Holt KE, Lam MMC, Seemann T, Ballard S, Coombs GW, Tong SYC, Grayson ML, Johnson PDR, Stinear TP. 2013. Genomic insights to control the emergence of vancomycin-resistant enterococci. MBio 4. doi:10.1128/mBio.00412-13. [PubMed][CrossRef]
166. Marvaud J-C, Mory F, Lambert T. 2011. Clostridium clostridioforme and Atopobium minutum clinical isolates with vanB-type resistance in France. J Clin Microbiol 49:3436–3438. [PubMed][CrossRef]
167. Ballard SA, Grabsch EA, Johnson PDR, Grayson ML. 2005. Comparison of three PCR primer sets for identification of vanB gene carriage in feces and correlation with carriage of vancomycin-resistant enterococci: interference by vanB-containing anaerobic bacilli. Antimicrob Agents Chemother 49:77–81. [PubMed][CrossRef]
168. Domingo M-C, Huletsky A, Boissinot M, Hélie M-C, Bernal A, Bernard KA, Grayson ML, Picard FJ, Bergeron MG. 2009. Clostridium lavalense sp. nov., a glycopeptide-resistant species isolated from human faeces. Int J Syst Evol Microbiol 59:498–503. [PubMed][CrossRef]
169. Marshall BM, Ochieng DJ, Levy SB. 2009. Commensals: underappreciated reservoir of antibiotic resistance. Microbe 4:231–238.
170. Maynard-Smith J. 1982. The century since Darwin. Nature 296:599–601. [PubMed][CrossRef]
171. Baquero F. 2014. Genetic hyper-codes and multidimensional Darwinism: replication modes and codes in evolutionary individuals of the bacterial world. In Trueba G (ed), Why does Evolution Matter? Cambridge Scholars Publishing, Newcastle Upon Tyne, UK.
172. Baquero F. 2004. From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat Rev Microbiol 2:510–518. [PubMed][CrossRef]
173. Okasha S. 2006. Evolution and the Levels of Selection. Clarendon Press, Oxford, UK. [CrossRef]
174. Paulsson J. 2002. Multileveled selection on plasmid replication. Genetics 161:1373–1384. [PubMed]
175. Cordero OX, Polz MF. 2014. Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol 12:263–273. [PubMed][CrossRef]
176. Norton B. 1996. Change, constancy, and creativity: the new ecology and some old problems. Duke Environ Law Policy Forum 7:49–70.
177. Hiramatsu K, Ito T, Tsubakishita S, Sasaki T, Takeuchi F, Morimoto Y, Katayama Y, Matsuo M, Kuwahara-Arai K, Hishinuma T, Baba T. 2013. Genomic basis for methicillin resistance in Staphylococcus aureus. Infect Chemother 45:117–136. [PubMed][CrossRef]
178. Haines AN, Gauthier DT, Nebergall EE, Cole SD, Nguyen KM, Rhodes MW, Vogelbein WK. 2013. First report of Streptococcus parauberis in wild finfish from North America. Vet Microbiol 166:270–275. [PubMed][CrossRef]
179. Richards VP, Palmer SR, Pavinski Bitar PD, Qin X, Weinstock GM, Highlander SK, Town CD, Burne RA, Stanhope MJ. 2014. Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol 6:741–753. [PubMed][CrossRef]
180. Gao X-Y, Zhi X-Y, Li H-W, Klenk H-P, Li W-J. 2014. Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups. PLoS One 9:e101229. doi:10.1371/journal.pone.0101229. [PubMed]
181. Jans C, Meile L, Lacroix C, Stevens MJA. 2014. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Infect Genet Evol. [Epub ahead of print.] doi:10.1016/j.meegid.2014.09.017. [PubMed][CrossRef]
182. Caufield PW, Saxena D, Fitch D, Li Y. 2007. Population structure of plasmid-containing strains of Streptococcus mutans, a member of the human indigenous biota. J Bacteriol 189:1238–1243. [PubMed][CrossRef]
183. Wescombe PA, Burton JP, Cadieux PA, Klesse NA, Hyink O, Heng NCK, Chilcott CN, Reid G, Tagg JR. 2006. Megaplasmids encode differing combinations of lantibiotics in Streptococcus salivarius. Antonie Van Leeuwenhoek 90:269–280. [PubMed][CrossRef]
184. Pepper K, Le Bouguénec C, de Cespédès G, Horaud T. 1986. Dispersal of a plasmid-borne chloramphenicol resistance gene in streptococcal and enterococcal plasmids. Plasmid 16:195–203. [PubMed][CrossRef]
185. Woodbury RL, Klammer KA, Xiong Y, Bailiff T, Glennen A, Bartkus JM, Lynfield R, Van Beneden C, Beall BW. 2008. Plasmid-borne erm(T) from invasive, macrolide-resistant Streptococcus pyogenes strains. Antimicrob Agents Chemother 52:1140–1143. [PubMed][CrossRef]
186. Whitehead TR, Cotta MA. 2001. Sequence analyses of a broad host-range plasmid containing ermT from a tylosin-resistant Lactobacillus sp. isolated from swine feces. Curr Microbiol 43:17–20. [PubMed][CrossRef]
187. DiPersio LP, DiPersio JR. 2006. High rates of erythromycin and clindamycin resistance among OBGYN isolates of group B Streptococcus. Diagn Microbiol Infect Dis 54:79–82. [PubMed][CrossRef]
188. Palmieri C, Magi G, Creti R, Baldassarri L, Imperi M, Gherardi G, Facinelli B. 2013. Interspecies mobilization of an ermT-carrying plasmid of Streptococcus dysgalactiae subsp. equisimilis by a coresident ICE of the ICESa2603 family. J Antimicrob Chemother 68:23–26. [PubMed][CrossRef]
189. Holden MTG, Hauser H, Sanders M, Ngo TH, Cherevach I, Cronin A, Goodhead I, Mungall K, Quail MA, Price C, Rabbinowitsch E, Sharp S, Croucher NJ, Chieu TB, Mai NTH, Diep TS, Chinh NT, Kehoe M, Leigh JA, Ward PN, Dowson CG, Whatmore AM, Chanter N, Iversen P, Gottschalk M, Slater JD, Smith HE, Spratt BG, Xu J, Ye C, Bentley S, Barrell BG, Schultsz C, Maskell DJ, Parkhill J. 2009. Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis. PLoS One 4:e6072. doi:10.1371/journal.pone.0006072. [CrossRef]
190. Cantin M, Harel J, Higgins R, Gottschalk M. 1992. Antimicrobial resistance patterns and plasmid profiles of Streptococcus suis isolates. J Vet Diagn Invest 4:170–174. [PubMed][CrossRef]
191. Wang Y, Li D, Song L, Liu Y, He T, Liu H, Wu C, Schwarz S, Shen J. 2013. First report of the multiresistance gene cfr in Streptococcus suis. Antimicrob Agents Chemother 57:4061–4063. [PubMed][CrossRef]
192. Chander Y, Oliveira SR, Goyal SM. 2011. Identification of the tet(B) resistance gene in Streptococcus suis. Vet J 189:359–360. [PubMed][CrossRef]
193. Lebreton F, Willems RJL, Gilmore MS. 2014. Enterococcus diversity, origins in nature, and gut colonization. In Gilmore MS, Clewell DB, Ike Y, Shankar N (ed), Enterococci: From Commensals to Leading Causes of Drug Resistant Infection. Massachusetts Eye and Ear Infirmary, Boston, MA.
194. Willems RJL, Top J, van Schaik W, Leavis H, Bonten M, Sirén J, Hanage WP, Corander J. 2012. Restricted gene flow among hospital subpopulations of Enterococcus faecium. MBio 3:e00151-12. doi:10.1128/mBio.00151-12. [PubMed][CrossRef]
195. Tedim AP, Ruiz-Garbajosa P, Corander J, Rodríguez CM, Cantón R, Willems R, Baquero F, Coque TM. 2014. Population biology of Enterococcus from intestinal colonization in hospitalized and non-hospitalized individuals in different age groups. Appl Environ Microbiol 81. [Epub ahead of print.] doi:10.1128/AEM.03661-14. [PubMed][CrossRef]
196. McBride SM, Fischetti VA, Leblanc DJ, Moellering RC, Gilmore MS. 2007. Genetic diversity among Enterococcus faecalis. PLoS One 2:e582. doi:10.1371/journal.pone.0000582. [PubMed][CrossRef]
197. Kuch A, Willems RJL, Werner G, Coque TM, Hammerum AM, Sundsfjord A, Klare I, Ruiz-Garbajosa P, Simonsen GS, van Luit-Asbroek M, Hryniewicz W, Sadowy E. 2012. Insight into antimicrobial susceptibility and population structure of contemporary human Enterococcus faecalis isolates from Europe. J Antimicrob Chemother 67:551–558. [PubMed][CrossRef]
198. López M, Tedim AP, Baquero F, Torres C, Coque TM. 2011. Plasmid diversity among Enterococcus spp from humans and animals (1991-2010) Poster presented at 4th Congress of European Microbiologist, FEMS. Geneva, Switzerland.
199. LeBlanc DJ, Inamine JM, Lee LN. 1986. Broad geographical distribution of homologous erythromycin, kanamycin, and streptomycin resistance determinants among group D streptococci of human and animal origin. Antimicrob Agents Chemother 29:549–555. [PubMed][CrossRef]
200. Murray BE, An FY, Clewell DB. 1988. Plasmids and pheromone response of the beta-lactamase producer Streptococcus ( Enterococcus) faecalis HH22. Antimicrob Agents Chemother 32:547–551. [PubMed][CrossRef]
201. Murray BE, Singh KV, Markowitz SM, Lopardo HA, Patterson JE, Zervos MJ, Rubeglio E, Eliopoulos GM, Rice LB, Goldstein FW. 1991. Evidence for clonal spread of a single strain of beta-lactamase-producing Enterococcus ( Streptococcus) faecalis to six hospitals in five states. J Infect Dis 163:780–785. [PubMed][CrossRef]
202. Patterson JE, Singh KV, Murray BE. 1991. Epidemiology of an endemic strain of beta-lactamase-producing Enterococcus faecalis. J Clin Microbiol 29:2513–2516. [PubMed]
203. Werner GDA, Strassmann JE, Ivens ABF, Engelmoer DJP, Verbruggen E, Queller DC, Noë R, Johnson NC, Hammerstein P, Kiers ET. 2014. Evolution of microbial markets. Proc Natl Acad Sci USA 111:1237–1244. [PubMed][CrossRef]
204. Datta N, Hughes VM. Plasmids of the same Inc groups in Enterobacteria before and after the medical use of antibiotics. Nature 306:616–617. [PubMed][CrossRef]
205. Wang X-M, Li X-S, Wang Y-B, Wei F-S, Zhang S-M, Shang Y-H, Du X-D. 2015. Characterization of a multidrug resistance plasmid from Enterococcus faecium that harbours a mobilized bcrABDR locus. J Antimicrob Chemother 70:609–611. [PubMed][CrossRef]
206. Devirgiliis C, Zinno P, Perozzi G. 2013. Update on antibiotic resistance in foodborne Lactobacillus and Lactococcus species. Front Microbiol 4:301. [PubMed][CrossRef]
207. Becker K, Heilmann C, Peters G. 2014. Coagulase-negative staphylococci. Clin Microbiol Rev 27:870–926. [PubMed][CrossRef]
208. Lindsay JA, Holden MTG. 2004. Staphylococcus aureus: superbug, super genome? Trends Microbiol 12:378–385. [PubMed][CrossRef]
209. Lindsay JA. 2010. Genomic variation and evolution of Staphylococcus aureus. Int J Med Microbiol 300:98–103. [PubMed][CrossRef]
210. Dethlefsen L, McFall-Ngai M, Relman DA. 2007. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449:811–818. [PubMed][CrossRef]
211. Lindsay JA, Knight GM, Budd EL, McCarthy AJ. 2012. Shuffling of mobile genetic elements (MGEs) in successful healthcare-associated MRSA (HA-MRSA). Mob Genet Elements 2:239–243. [PubMed][CrossRef]
212. Livermore DM. 2000. Antibiotic resistance in staphylococci. Int J Antimicrob Agents 16(Suppl 1) :S3–S10. [PubMed][CrossRef]
213. Sidhu MS, Heir E, Leegaard T, Wiger K, Holck A. 2002. Frequency of disinfectant resistance genes and genetic linkage with beta-lactamase transposon Tn552 among clinical staphylococci. Antimicrob Agents Chemother 46:2797–2803. [PubMed][CrossRef]
214. Willems RJL, Hanage WP, Bessen DE, Feil EJ. 2011. Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance. FEMS Microbiol Rev 35:872–900. [PubMed][CrossRef]
215. Lindsay JA, Holden MTG. 2006. Understanding the rise of the superbug: investigation of the evolution and genomic variation of Staphylococcus aureus. Funct Integr Genomics 6:186–201. [PubMed][CrossRef]
216. Lutz C, Erken M, Noorian P, Sun S, McDougald D. 2013. Environmental reservoirs and mechanisms of persistence of Vibrio cholerae. Front Microbiol 4:375. [PubMed][CrossRef]
217. Lindsay JA. 2014. Evolution of Staphylococcus aureus and MRSA during outbreaks. Infect Genet Evol 21:548–553. [PubMed][CrossRef]
218. McDougal LK, Fosheim GE, Nicholson A, Bulens SN, Limbago BM, Shearer JES, Summers AO, Patel JB. 2010. Emergence of resistance among USA300 methicillin-resistant Staphylococcus aureus isolates causing invasive disease in the United States. Antimicrob Agents Chemother 54:3804–3811. [PubMed][CrossRef]
219. McCarthy AJ, Witney AA, Gould KA, Moodley A, Guardabassi L, Voss A, Denis O, Broens EM, Hinds J, Lindsay JA. 2011. The distribution of mobile genetic elements (MGEs) in MRSA CC398 is associated with both host and country. Genome Biol Evol 3:1164–1174. [PubMed][CrossRef]
220. Alibayov B, Baba-Moussa L, Sina H, Zdeňková K, Demnerová K. 2014. Staphylococcus aureus mobile genetic elements. Mol Biol Rep 41:5005–5018. [PubMed][CrossRef]
221. Uhlemann A-C, Dordel J, Knox JR, Raven KE, Parkhill J, Holden MTG, Peacock SJ, Lowy FD. 2014. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci USA 111:6738–6743. [PubMed][CrossRef]
222. Rossi F, Diaz L, Wollam A, Panesso D, Zhou Y, Rincon S, Narechania A, Xing G, Di Gioia TSR, Doi A, Tran TT, Reyes J, Munita JM, Carvajal LP, Hernandez-Roldan A, Brandão D, van der Heijden IM, Murray BE, Planet PJ, Weinstock GM, Arias CA. 2014. Transferable vancomycin resistance in a community-associated MRSA lineage. N Engl J Med 370:1524–1531. [PubMed][CrossRef]
223. Strommenger B, Bartels MD, Kurt K, Layer F, Rohde SM, Boye K, Westh H, Witte W, De Lencastre H, Nübel U. 2014. Evolution of methicillin-resistant Staphylococcus aureus towards increasing resistance. J Antimicrob Chemother 69:616–622. [PubMed][CrossRef]
224. Locke JB, Zuill DE, Scharn CR, Deane J, Sahm DF, Goering RV, Jenkins SG, Shaw KJ. 2014. Identification and characterization of linezolid-resistant cfr-positive Staphylococcus aureus USA300 isolates from a New York City Medical Center. Antimicrob Agents Chemother 58:6949–6952. [PubMed][CrossRef]
225. Sung JM-L, Lloyd DH, Lindsay JA. 2008. Staphylococcus aureus host specificity: comparative genomics of human versus animal isolates by multi-strain microarray. Microbiology 154:1949–1959. [PubMed][CrossRef]
226. Holden MTG, Feil EJ, Lindsay JA, Peacock SJ, Day NPJ, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, Chillingworth C, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J, Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, James KD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, Stevens K, Whitehead S, Barrell BG, Spratt BG, Parkhill J. 2004. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci USA 101:9786–9791. [PubMed][CrossRef]
227. Robinson DA, Kearns AM, Holmes A, Morrison D, Grundmann H, Edwards G, O'Brien FG, Tenover FC, McDougal LK, Monk AB, Enright MC. 2005. Re-emergence of early pandemic Staphylococcus aureus as a community-acquired meticillin-resistant clone. Lancet 365:1256–1258. [PubMed][CrossRef]
228. Yutin N, Galperinr MY. 2014. A genomic update on clostridial phylogeny: Gram-negative spore-formers and other misplaced clostridia. Environ Microbiol 15:2631–2641. [PubMed]
229. Magot M. 1984. Physical characterization of the Clostridium perfringens tetracycline-chloramphenicol resistance plasmid pIP401. Ann Microbiol 135B:269–282. [PubMed][CrossRef]
230. Lyras D, Adams V, Ballard SA, Teng WL, Howarth PM, Crellin PK, Bannam TL, Songer JG, Rood JI. 2009. tISCpe8, an IS1595-family lincomycin resistance element located on a conjugative plasmid in Clostridium perfringens. J Bacteriol 191:6345–6351. [PubMed][CrossRef]
231. Bannam TL, Teng WL, Bulach D, Lyras D, Rood JI. 2006. Functional identification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens. J Bacteriol 188:4942–4951. [PubMed][CrossRef]
232. Gurjar A, Li J, McClane BS. 2010. Characterization of toxin plasmids in Clostridium perfringens type C isolates. Infect Immun 78:4860–4869. [PubMed][CrossRef]
233. Nowell VJ, Kropinski AM, Songer JG, MacInnes JI, Parreira VR, Prescott JF. 2012. Genome sequencing and analysis of a type A Clostridium perfringens isolate from a case of bovine clostridial abomasitis. PLoS One 7:e32271. doi:10.1371/journal.pone.0032271. [PubMed][CrossRef]
234. Sasaki Y, Yamamoto K, Tamura Y, Takahashi T. 2001. Tetracycline-resistance genes of Clostridium perfringens, Clostridium septicum and Clostridium sordellii isolated from cattle affected with malignant edema. Vet Microbiol 83:61–69. [PubMed][CrossRef]
235. Franciosa G, Scalfaro C, Di Bonito P, Vitale M, Aureli P. 2011. Identification of novel linear megaplasmids carrying a ß-lactamase gene in neurotoxigenic Clostridium butyricum type E strains. PLoS One 6:e21706. doi:10.1371/journal.pone.0021706. [PubMed][CrossRef]
236. Slavić D, Boerlin P, Fabri M, Klotins KC, Zoethout JK, Weir PE, Bateman D. 2011. Antimicrobial susceptibility of Clostridium perfringens isolates of bovine, chicken, porcine, and turkey origin from Ontario. Can J Vet Res 75:89–97. [PubMed]
237. Farrow KA, Lyras D, Rood JI. 2000. The macrolide-lincosamide-streptogramin B resistance determinant from Clostridium difficile 630 contains two erm(B) genes. Antimicrob Agents Chemother 44:411–413. [PubMed][CrossRef]
238. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. [PubMed][CrossRef]
239. Li W, Godzik A. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659. [PubMed][CrossRef]
240. Lederberg J. 1998. Plasmid (1952–1997). Plasmid 39:1–9. [PubMed][CrossRef]
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/content/journal/microbiolspec/10.1128/microbiolspec.PLAS-0039-2014
2015-04-03
2019-08-25

Abstract:

The phylum is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.

The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among , , and species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a “single centric” perspective (“gene tracking” or “vehicle centric” in “single host-single pathogen” systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.

This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.

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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials
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Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The plasmidome of firmicutes: impact on the emergence and the spread of resistance to antimicrobials. microbiolspec 3(2): doi:10.1128/microbiolspec.PLAS-0039-2014
/content/microbiolspec/10.1128/microbiolspec.PLAS-0039-2014.fig1
FIGURE 1
Protein content network (PCN) of AbR proteins found in plasmids and chromosomes of and . To determine the AbR protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the ARG-ANNOT database (http://en.mediterranee-infection.com/article.php?laref=283&titre=arg-annot) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive AbR proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blast search (blastp, 1e-30 E-value and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes; each color indicates one genus) and AbR proteins (square nodes). Nodes were connected by an edge when a positive hit between AbR proteins and one or more strains of a given species were identified. Edges further indicate the location of the AbR genes associated with each AbR protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When an AbR gene was located in both chromosomes and plasmids, both lines were plotted.
microbiolspec/3/2/PLAS-0039-2014-fig1_thmb.gif
microbiolspec/3/2/PLAS-0039-2014-fig1.gif
Image of FIGURE 1

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FIGURE 1

Protein content network (PCN) of AbR proteins found in plasmids and chromosomes of and . To determine the AbR protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the ARG-ANNOT database (http://en.mediterranee-infection.com/article.php?laref=283&titre=arg-annot) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive AbR proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blast search (blastp, 1e-30 E-value and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes; each color indicates one genus) and AbR proteins (square nodes). Nodes were connected by an edge when a positive hit between AbR proteins and one or more strains of a given species were identified. Edges further indicate the location of the AbR genes associated with each AbR protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When an AbR gene was located in both chromosomes and plasmids, both lines were plotted.

Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.PLAS-0039-2014
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FIGURE 2
PCN of metal-biocide (Met/Bc) proteins found in plasmids and chromosomes of and . To determine the Met/Bc protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the BacMet database (http://bacmet.biomedicine.gu.se/) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive Met/Bc proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blastp search (blastp, 1e-30 evalue and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes) and Met/Bc proteins (triangular nodes). Nodes were connected by an edge when a positive hit between Met/Bc proteins on one or more strains of a given species was identified. Edges further indicate the location of the Met/Bc genes associated with each Met/Bc protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When a Met/Bc gene was located in both chromosomes and plasmids, both lines were plotted.
microbiolspec/3/2/PLAS-0039-2014-fig2_thmb.gif
microbiolspec/3/2/PLAS-0039-2014-fig2.gif
Image of FIGURE 2

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FIGURE 2

PCN of metal-biocide (Met/Bc) proteins found in plasmids and chromosomes of and . To determine the Met/Bc protein catalog of Gram-positive strains (chromosomes and plasmids), a Blastp search was performed of all their proteomes against the BacMet database (http://bacmet.biomedicine.gu.se/) using a cut-off of 1e-30 and 85% of identity. The presence of the Gram-positive Met/Bc proteins identified above in all bacterial species (only complete sequences, not partial) was determined using a similar Blastp search (blastp, 1e-30 evalue and 85% identity) against the NCBI GenBank database. The nodes correspond to bacterial species (circular nodes) and Met/Bc proteins (triangular nodes). Nodes were connected by an edge when a positive hit between Met/Bc proteins on one or more strains of a given species was identified. Edges further indicate the location of the Met/Bc genes associated with each Met/Bc protein of the Gram-positive catalog. Solid lines represent chromosomal location, and dotted lines represent plasmid location. When a Met/Bc gene was located in both chromosomes and plasmids, both lines were plotted.

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FIGURE 3
Plasmid homology network. The genomic homology network was performed using “All-versus-All” genomic Megablast ( 238 ) of 1,326 fully sequenced plasmids from low G+C bacterial species ( and phyla) available at public gene databases. The nodes correspond to bacterial plasmids (circular nodes; different colors representing different genera). Two nodes are connected by an edge if they share homologous DNA.
microbiolspec/3/2/PLAS-0039-2014-fig3_thmb.gif
microbiolspec/3/2/PLAS-0039-2014-fig3.gif
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FIGURE 3

Plasmid homology network. The genomic homology network was performed using “All-versus-All” genomic Megablast ( 238 ) of 1,326 fully sequenced plasmids from low G+C bacterial species ( and phyla) available at public gene databases. The nodes correspond to bacterial plasmids (circular nodes; different colors representing different genera). Two nodes are connected by an edge if they share homologous DNA.

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FIGURE 4
PCN of AbR and Met/Bc proteins located on plasmids of and . PCN of AbR and Met proteins found in Gram-positive plasmids. We formed the PCN by representing plasmids as circular nodes, AbR as square nodes, and Met/Bc as triangular nodes, connecting two nodes (plasmid and AbR or Met/Bc) if one plasmid has this AbR or Met/Bc. The presence of the Met/Bc gene was determined by blasp of all plasmid proteins against the BacMet database. The presence of the AbR gene was determined by blasp of all plasmid proteins against the ARG-ANNOT database. The colors for the genus are the same as those in Fig. 3 .
microbiolspec/3/2/PLAS-0039-2014-fig4_thmb.gif
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FIGURE 4

PCN of AbR and Met/Bc proteins located on plasmids of and . PCN of AbR and Met proteins found in Gram-positive plasmids. We formed the PCN by representing plasmids as circular nodes, AbR as square nodes, and Met/Bc as triangular nodes, connecting two nodes (plasmid and AbR or Met/Bc) if one plasmid has this AbR or Met/Bc. The presence of the Met/Bc gene was determined by blasp of all plasmid proteins against the BacMet database. The presence of the AbR gene was determined by blasp of all plasmid proteins against the ARG-ANNOT database. The colors for the genus are the same as those in Fig. 3 .

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FIGURE 5
Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. PriCT_1; *One of these plasmids (GenBank accession number NC_013381) has a truncated rep_pKH21 (rep_1) gene, and no other known RIPs were identified. **Two of these plasmids (GenBank accession number NC_016054 and NC_019144) appear to have two copies of the MOB gene. One of these plasmids (GenBank accession number NC_008354) has two copies of the gene. One plasmid (GenBank accession number NC_001393) has a truncated copy of the gene. One plasmid (GenBank accession number NC_010419) has a truncated copy of the gene. The plasmid (GenBank accession number NC_005076) appears to have two copies of the MOB gene. One plasmid (GenBank accession number NC_018959) has a truncated copy of the gene. Two plasmids (GenBank accession numbers NC_007931 and NC_016942) have two copies of the and genes. This plasmid (GenBank accession number NC_013320) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_005004) has a truncated copy of the gene. Three plasmids (GenBank accession numbers NC_013321, NC_019007, and NC_018976) have a truncated copy of the gene. Eleven of these plasmids have a truncated copy of the gene (GenBank accession numbers NC_020531, NC_020538, NC_013337, NC_020534, NC_020565, NC_020567, NC_020530, NC_020539, NC_017352, NC_013323, and NC_022610). One plasmid (GenBank accession number NC_013334) has a truncated copy of the gene. This plasmid (GenBank accession number NC_020237) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_022598) appears to have two copies of the MOB gene. Abbreviations: MRIP, Multi-RIP; S, spp; Sar, ; Sa, ; Sc, ; Se, ; Sha, ; Shy, ; Sle, ; Slu, ; Sp, ; Ssa, ; Ssc, ; Ssi, ; Sw, .
microbiolspec/3/2/PLAS-0039-2014-fig5_thmb.gif
microbiolspec/3/2/PLAS-0039-2014-fig5.gif
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FIGURE 5

Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. PriCT_1; *One of these plasmids (GenBank accession number NC_013381) has a truncated rep_pKH21 (rep_1) gene, and no other known RIPs were identified. **Two of these plasmids (GenBank accession number NC_016054 and NC_019144) appear to have two copies of the MOB gene. One of these plasmids (GenBank accession number NC_008354) has two copies of the gene. One plasmid (GenBank accession number NC_001393) has a truncated copy of the gene. One plasmid (GenBank accession number NC_010419) has a truncated copy of the gene. The plasmid (GenBank accession number NC_005076) appears to have two copies of the MOB gene. One plasmid (GenBank accession number NC_018959) has a truncated copy of the gene. Two plasmids (GenBank accession numbers NC_007931 and NC_016942) have two copies of the and genes. This plasmid (GenBank accession number NC_013320) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_005004) has a truncated copy of the gene. Three plasmids (GenBank accession numbers NC_013321, NC_019007, and NC_018976) have a truncated copy of the gene. Eleven of these plasmids have a truncated copy of the gene (GenBank accession numbers NC_020531, NC_020538, NC_013337, NC_020534, NC_020565, NC_020567, NC_020530, NC_020539, NC_017352, NC_013323, and NC_022610). One plasmid (GenBank accession number NC_013334) has a truncated copy of the gene. This plasmid (GenBank accession number NC_020237) appears to have two copies of the MOB gene. This plasmid (GenBank accession number NC_022598) appears to have two copies of the MOB gene. Abbreviations: MRIP, Multi-RIP; S, spp; Sar, ; Sa, ; Sc, ; Se, ; Sha, ; Shy, ; Sle, ; Slu, ; Sp, ; Ssa, ; Ssc, ; Ssi, ; Sw, .

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FIGURE 6
Hierarchical clustering dendrogram of plasmids from enterococci. The matrix distance used for building the UPGMA dendrogram is based on the Raup-Crick distance of the orthologous protein profile of each plasmid. For each plasmid, a presence/absence protein profile was made using cut-off values of 80% identity and 80% coverage. Protein clustering was made by using CD-HIT ( 239 ). Different background colors are used to emphasize branches of related plasmids and are the same as those defined in Fig. 5 . Names to the left of the dendrogram indicate the RIP family. Background colors were used to point out plasmid groups frequently involved in mobility of AbR genes and pheromone-responsive plasmids. Circles indicate RIPs identified in each plasmid according to data shown in Fig. 7 .
microbiolspec/3/2/PLAS-0039-2014-fig6_thmb.gif
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FIGURE 6

Hierarchical clustering dendrogram of plasmids from enterococci. The matrix distance used for building the UPGMA dendrogram is based on the Raup-Crick distance of the orthologous protein profile of each plasmid. For each plasmid, a presence/absence protein profile was made using cut-off values of 80% identity and 80% coverage. Protein clustering was made by using CD-HIT ( 239 ). Different background colors are used to emphasize branches of related plasmids and are the same as those defined in Fig. 5 . Names to the left of the dendrogram indicate the RIP family. Background colors were used to point out plasmid groups frequently involved in mobility of AbR genes and pheromone-responsive plasmids. Circles indicate RIPs identified in each plasmid according to data shown in Fig. 7 .

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FIGURE 7
Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. Rep_2; *One of these plasmids (GenBank accession number NC_015849) has a truncated rep_AUS0004_p2 (Rep_1) gene, and no other known replication initiator proteins were found. **This plasmid (GenBank accession number NC_017962) has two copies of Tn; in one of them the gene is not truncated; this plasmid also appears to have two copies of the MOB gene. These two plasmids (GenBank accession numbers NC_008768 and NC_008821) have a truncated copy of the gene. Abbreviations: MRIP, multi-RIP; Efm, ; Efc, ; Emu, ; Edu, ; Ehi, .
microbiolspec/3/2/PLAS-0039-2014-fig7_thmb.gif
microbiolspec/3/2/PLAS-0039-2014-fig7.gif
Image of FIGURE 7

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FIGURE 7

Plasmids from spp. The presence of an orange border in the RIP family indicates that the corresponding RIP is truncated. Rep_2; *One of these plasmids (GenBank accession number NC_015849) has a truncated rep_AUS0004_p2 (Rep_1) gene, and no other known replication initiator proteins were found. **This plasmid (GenBank accession number NC_017962) has two copies of Tn; in one of them the gene is not truncated; this plasmid also appears to have two copies of the MOB gene. These two plasmids (GenBank accession numbers NC_008768 and NC_008821) have a truncated copy of the gene. Abbreviations: MRIP, multi-RIP; Efm, ; Efc, ; Emu, ; Edu, ; Ehi, .

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FIGURE 8
Plasmids from spp. Rep_trans; This plasmid (GenBank accession number NC_015219) has two similar replication genes belonging to the Rep_3 family. This plasmid (GenBank accession number NC_006979) has two similar replication genes belonging to the PriCT_1 family. Abbreviations: MRIP, Multi-RIP; Sag, ; Sdy, ; Sga, ; Siu, ; Sin, ; Sma, ; Smu, ; Spa, ; Spn, ; Sps, ; Spy, ; Ssu, ; Sth,
microbiolspec/3/2/PLAS-0039-2014-fig8_thmb.gif
microbiolspec/3/2/PLAS-0039-2014-fig8.gif
Image of FIGURE 8

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FIGURE 8

Plasmids from spp. Rep_trans; This plasmid (GenBank accession number NC_015219) has two similar replication genes belonging to the Rep_3 family. This plasmid (GenBank accession number NC_006979) has two similar replication genes belonging to the PriCT_1 family. Abbreviations: MRIP, Multi-RIP; Sag, ; Sdy, ; Sga, ; Siu, ; Sin, ; Sma, ; Smu, ; Spa, ; Spn, ; Sps, ; Spy, ; Ssu, ; Sth,

Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.PLAS-0039-2014
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FIGURE 9
Plasmids from spp. rep_3. One plasmid (GenBank NC_013767) has two copies of the gene, one of which is truncated. One plasmid (GenBank NC_018888) has a truncated copy of the gene. This plasmid (GenBank NC_022045) has two copies of the operon. Abbreviations: MRIP, multi-RIP; Lm, ; Lg, ; Li,
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FIGURE 9

Plasmids from spp. rep_3. One plasmid (GenBank NC_013767) has two copies of the gene, one of which is truncated. One plasmid (GenBank NC_018888) has a truncated copy of the gene. This plasmid (GenBank NC_022045) has two copies of the operon. Abbreviations: MRIP, multi-RIP; Lm, ; Lg, ; Li,

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FIGURE 10
Plasmids from LAB. Rep_1. Rep_trans. PriCT_1. *This plasmid (GenBank accession number NC_010540) has two copies of the gene. **One of these plasmids (GenBank accession number NC_010603) has a truncated copy of the gene. One of these plasmids (GenBank accession number NC_014133) appears to have three copies of the MOB gene. One of these plasmids (GenBank accession number NC_022123) appears to have two copies of the MOB gene. Abbreviations: MRip, multi-RIP; Lb, spp; Lca, ; Lam, ; Lbr, ; Lbu, ; Lca, ; Lfe ; Lpa, ; Lpl, ; Lre, ; Lsa, Lga, ; Lla, ; Lcm, ; Lci, ; Lki, ; Lme,
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FIGURE 10

Plasmids from LAB. Rep_1. Rep_trans. PriCT_1. *This plasmid (GenBank accession number NC_010540) has two copies of the gene. **One of these plasmids (GenBank accession number NC_010603) has a truncated copy of the gene. One of these plasmids (GenBank accession number NC_014133) appears to have three copies of the MOB gene. One of these plasmids (GenBank accession number NC_022123) appears to have two copies of the MOB gene. Abbreviations: MRip, multi-RIP; Lb, spp; Lca, ; Lam, ; Lbr, ; Lbu, ; Lca, ; Lfe ; Lpa, ; Lpl, ; Lre, ; Lsa, Lga, ; Lla, ; Lcm, ; Lci, ; Lki, ; Lme,

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FIGURE 11
Similarity of -like sequences encoding RIPs of the Rep_1 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_1 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .
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FIGURE 11

Similarity of -like sequences encoding RIPs of the Rep_1 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_1 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .

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FIGURE 12
Similarity of -like sequences encoding RIPs of the Rep_trans family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_trans family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. **Similar to and . Abbreviations: ND, not determined.
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FIGURE 12

Similarity of -like sequences encoding RIPs of the Rep_trans family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_trans family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different backgrounds colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. **Similar to and . Abbreviations: ND, not determined.

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FIGURE 13
Similarity of -like sequences encoding RIPs of the Rep_2 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_2 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .
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FIGURE 13

Similarity of -like sequences encoding RIPs of the Rep_2 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_2 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .

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FIGURE 14
Similarity of -like sequences encoding RIPs of the Rep_L family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_L family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .
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FIGURE 14

Similarity of -like sequences encoding RIPs of the Rep_L family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_L family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 .

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FIGURE 15
Similarity of -like sequences encoding RIPs of the Rep_3 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_3 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.
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FIGURE 15

Similarity of -like sequences encoding RIPs of the Rep_3 family. A neighbor-joining tree of gene sequences coding for RIPs of the Rep_3 family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.

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FIGURE 16
Similarity of -like sequences encoding RIPs with the PriCT_1 domain. A neighbor-joining tree of gene sequences coding for RIPs with PriCT_1 domains was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.
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FIGURE 16

Similarity of -like sequences encoding RIPs with the PriCT_1 domain. A neighbor-joining tree of gene sequences coding for RIPs with PriCT_1 domains was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . Abbreviations: ND, not determined.

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FIGURE 17
Similarity of -like sequences encoding RIPs of the RepA_N family. A neighbor-joining tree of gene sequences coding for replication initiator proteins of the RepA_N family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. Similar to and . Abbreviations: ND, not determined.
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FIGURE 17

Similarity of -like sequences encoding RIPs of the RepA_N family. A neighbor-joining tree of gene sequences coding for replication initiator proteins of the RepA_N family was built using MEGA 6.06. A cut-off equal to or higher than 80% and a bootstrap analysis based on 1,000 permutations were applied to the analysis. Alignment of nucleotide sequences was performed using ClustalW2 (http://www.ebi.ac.uk/Tools/phylogeny/clustalw2_phylogeny/), and sequences showing an identity equal to or higher than 80% were clustered in groups that were highlighted by different background colors. Black dots indicate the RIP of the plasmid used for further comparison in Figs. 5 to 10 . *Truncated gene. Similar to and . Abbreviations: ND, not determined.

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Tables

The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials
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Citation: Lanza V, Tedim A, Martínez J, Baquero F, Coque T. 2015. The plasmidome of firmicutes: impact on the emergence and the spread of resistance to antimicrobials. microbiolspec 3(2): doi:10.1128/microbiolspec.PLAS-0039-2014
/content/microbiolspec/10.1128/microbiolspec.PLAS-0039-2014.T1
TABLE 1
Fully characterized plasmids from low G+C bacteria available in GenBank database (updated September 2014)
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TABLE 1

Fully characterized plasmids from low G+C bacteria available in GenBank database (updated September 2014)

Source: microbiolspec April 2015 vol. 3 no. 2 doi:10.1128/microbiolspec.PLAS-0039-2014

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