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resistance","volume":"10","author":"CA Arias","year":"2012","journal-title":"Nat Rev Microbiol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"4904","DOI":"10.1128\/AEM.02945-08","article-title":"Dispersion of multidrug-resistant <italic>Enterococcus faecium<\/italic> isolates belonging to major clonal complexes in different Portuguese settings","volume":"75","author":"AR Freitas","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1093\/jac\/dkr544","article-title":"Insight into antimicrobial susceptibility and population structure of contemporary human <italic>Enterococcus faecalis<\/italic> isolates from Europe","volume":"67","author":"A Kuch","year":"2012","journal-title":"J Antimicrob Chemother"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"5709","DOI":"10.1128\/JB.187.16.5709-5718.2005","article-title":"Molecular characterization of a widespread, pathogenic, and antibiotic 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faecalis<\/italic>","volume":"2","author":"SM McBride","year":"2007","journal-title":"PLoS ONE"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1471-2180-11-3","article-title":"Comparative genomic analysis reveals significant enrichment of mobile genetic elements and genes encoding surface structure-proteins in hospital-associated clonal complex 2 <italic>Enterococcus faecalis<\/italic>","volume":"11","author":"M Solheim","year":"2011","journal-title":"BMC Microbiol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1128\/JB.01293-09","article-title":"Comparative genomics and transduction potential of <italic>Enterococcus faecalis<\/italic> temperate bacteriophages","volume":"192","author":"A Yasmin","year":"2010","journal-title":"J Bacteriol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"e1001029","DOI":"10.1371\/journal.pcbi.1001029","article-title":"Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases","volume":"6","author":"RJ Fieldhouse","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1111\/j.1749-6632.1980.tb27987.x","article-title":"A theory of modular evolution for bacteriophages","volume":"354","author":"D Botstein","year":"1980","journal-title":"Ann N Y Acad Sci"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1146\/annurev.mi.48.100194.001205","article-title":"Comparative molecular biology of lambdoid phages","volume":"48","author":"A Campbell","year":"1994","journal-title":"Annu Rev Microbiol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/s00253-011-3519-5","article-title":"Site-specific recombinases as tools for heterologous gene integration","volume":"92","author":"N Hirano","year":"2011","journal-title":"Appl Microbiol 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Palmer","year":"2012","journal-title":"MBio"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"2775","DOI":"10.1111\/j.1462-2920.2009.01970.x","article-title":"Position paper: The creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea","volume":"11","author":"AM Kropinski","year":"2009","journal-title":"Environmental Microbiology"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"17621","DOI":"10.1073\/pnas.1206136109","article-title":"A composite bacteriophage alters colonization by an intestinal commensal bacterium","volume":"109","author":"BA Duerkop","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1128\/jb.152.1.284-290.1982","article-title":"Interference of plasmid pCM194 with lysogeny of bacteriophage SP02 in <italic>Bacillus subtilis<\/italic>","volume":"152","author":"R Marrero","year":"1982","journal-title":"J 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Dearborn","year":"2012","journal-title":"Bacteriophage"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.genet.39.073003.113656","article-title":"Switches in bacteriophage lambda development","volume":"39","author":"AB Oppenheim","year":"2005","journal-title":"Annu Rev Genet"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1016\/j.mib.2009.06.018","article-title":"Role of reactive oxygen species in antibiotic action and resistance","volume":"12","author":"DJ Dwyer","year":"2009","journal-title":"Curr Opin Microbiol"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1111\/j.1365-2958.2007.05703.x","article-title":"Mechanism of cell surface expression of the <italic>Streptococcus mitis<\/italic> platelet binding proteins PblA and PblB","volume":"64","author":"J Mitchell","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.virol.2006.04.001","article-title":"Induction of the SOS response by bacteriophage lytic development in <italic>Salmonella enterica<\/italic>","volume":"351","author":"S Campoy","year":"2006","journal-title":"Virology"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/S1369-5274(03)00086-9","article-title":"Phage as agents of lateral gene transfer","volume":"6","author":"C Canchaya","year":"2003","journal-title":"Curr Opin Microbiol"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1111\/j.1472-765X.2011.03043.x","article-title":"Bacteriophage-mediated transduction of antibiotic resistance in enterococci","volume":"52","author":"R Mazaheri Nezhad Fard","year":"2011","journal-title":"Lett Appl Microbiol"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tim.2004.07.003","article-title":"Antibiotic-induced lateral transfer of antibiotic resistance","volume":"12","author":"PJ Hastings","year":"2004","journal-title":"Trends Microbiol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1128\/AAC.50.1.171-177.2006","article-title":"Ciprofloxacin and trimethoprim cause phage induction and virulence modulation in <italic>Staphylococcus aureus<\/italic>","volume":"50","author":"C Goerke","year":"2006","journal-title":"Antimicrob Agents Chemother"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1086\/315239","article-title":"Quinolone antibiotics induce Shiga toxin-encoding bacteriophages, toxin production, and death in mice","volume":"181","author":"X Zhang","year":"2000","journal-title":"J Infect Dis"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1111\/j.1365-2958.2005.04584.x","article-title":"Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci","volume":"56","author":"C Ubeda","year":"2005","journal-title":"Mol Microbiol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"1234","DOI":"10.1073\/pnas.0809600106","article-title":"Killing niche competitors by remote-control bacteriophage induction","volume":"106","author":"L Selva","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"802","DOI":"10.3201\/eid0808.010418","article-title":"Antecedent treatment with different antibiotic agents as a risk factor for vancomycin-resistant <italic>Enterococcus<\/italic>","volume":"8","author":"Y Carmeli","year":"2002","journal-title":"Emerg Infect Dis"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1016\/j.cub.2006.08.089","article-title":"Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare","volume":"16","author":"SP Brown","year":"2006","journal-title":"Curr Biol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/ismej.2010.153","article-title":"Phage-induced lysis enhances biofilm formation in <italic>Shewanella oneidensis<\/italic> MR-1","volume":"5","author":"J Godeke","year":"2011","journal-title":"Isme J"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/ismej.2008.109","article-title":"The biofilm life cycle and virulence of <italic>Pseudomonas aeruginosa<\/italic> are dependent on a filamentous prophage","volume":"3","author":"SA Rice","year":"2009","journal-title":"Isme J"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"e15678","DOI":"10.1371\/journal.pone.0015678","article-title":"Prophage spontaneous activation promotes DNA release enhancing biofilm formation in <italic>Streptococcus pneumoniae<\/italic>","volume":"5","author":"M Carrolo","year":"2010","journal-title":"PLoS One"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1128\/JB.00773-06","article-title":"C-terminal WxL domain mediates cell wall binding in <italic>Enterococcus faecalis<\/italic> and other gram-positive bacteria","volume":"189","author":"S Brinster","year":"2007","journal-title":"J Bacteriol"},{"key":"ref89","unstructured":"Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2<sup>nd<\/sup> ed. Cold Spring Harbor. Cold Spring Harbor Laboratory Press."},{"key":"ref90","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.femsle.2004.11.006","article-title":"Enterococcal surface protein Esp does not facilitate intestinal colonization or translocation of <italic>Enterococcus faecalis<\/italic> in clindamycin-treated mice","volume":"242","author":"NJ Pultz","year":"2005","journal-title":"FEMS Microbiology Letters"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"e34398","DOI":"10.1371\/journal.pone.0034398","article-title":"Transcriptional regulator PerA influences biofilm-associated, platelet binding, and metabolic gene expression in <italic>Enterococcus faecalis<\/italic>","volume":"7","author":"SM Maddox","year":"2012","journal-title":"PLoS One"}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1003539","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,24]],"date-time":"2022-02-24T06:25:23Z","timestamp":1645683923000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1003539"}},"subtitle":[],"editor":[{"given":"Diarmaid","family":"Hughes","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2013,6,6]]},"references-count":91,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2013,6,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1003539","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,6,6]]}}}