{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T00:56:30Z","timestamp":1790470590976,"version":"4.1.0"},"reference-count":47,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T00:00:00Z","timestamp":1621555200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007356","name":"Fondation M\u00e9diterran\u00e9e Infection","doi-asserted-by":"publisher","award":["10-IAHU-03"],"award-info":[{"award-number":["10-IAHU-03"]}],"id":[{"id":"10.13039\/100007356","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 1591) and E. faecium (n = 1981) and investigated the association between the presence or absence of CRISPR-Cas systems, endonuclease\/anti-endonuclease systems and the acquisition of antimicrobial resistance, especially vancomycin resistance genes. Most of the analysed Enterococci were isolated from humans and less than 14% of them were from foods and animals. We analysed and detected CRISPR\u2013Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference (p-value &lt; 10\u22125). We found a negative correlation between the number of CRISPR\u2013Cas systems and genome size (r = \u22120.397, p-value &lt; 10\u22125) and a positive correlation between the genome %GC content and the number of CRISPR\u2013Cas systems (r = 0.215, p-value &lt; 10\u22125). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR\u2013Cas systems in E. faecium, known to deactivate the endonucleases\u2019 protective activities and enable the E. faecium genome to be versatile in acquiring mobile genetic elements, including carriers of antimicrobial resistance genes, especially vanB. Most importantly, we observed that there was a direct association between the absence of CRISPR\u2013Cas, the presence of the anti-CRISPR ardA gene and the acquisition of vancomycin resistance genes.<\/jats:p>","DOI":"10.3390\/microorganisms9061118","type":"journal-article","created":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T00:01:20Z","timestamp":1621814480000},"page":"1118","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Extensive Comparative Genomic Analysis of Enterococcus faecalis and Enterococcus faecium Reveals a Direct Association between the Absence of CRISPR\u2013Cas Systems, the Presence of Anti-Endonuclease (ardA) and the Acquisition of Vancomycin Resistance in E. faecium"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3162-0371","authenticated-orcid":false,"given":"Kodjovi D.","family":"Mlaga","sequence":"first","affiliation":[{"name":"Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Garcia","sequence":"additional","affiliation":[{"name":"Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6285-0308","authenticated-orcid":false,"given":"Philippe","family":"Colson","sequence":"additional","affiliation":[{"name":"Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France"},{"name":"IHU-Mediterranee Infection, Aix-Marseille University, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raymond","family":"Ruimy","sequence":"additional","affiliation":[{"name":"Department of Bacteriology at Nice Academic Hospital, Nice Medical University, 06003 Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Marc","family":"Rolain","sequence":"additional","affiliation":[{"name":"Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France"},{"name":"IHU-Mediterranee Infection, Aix-Marseille University, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6466-2324","authenticated-orcid":false,"given":"Seydina M.","family":"Diene","sequence":"additional","affiliation":[{"name":"Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, France"},{"name":"IHU-Mediterranee Infection, Aix-Marseille University, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,5,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1128\/MMBR.00023-12","article-title":"Enterococci in the environment","volume":"76","author":"Byappanahalli","year":"2012","journal-title":"Microbiol. 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