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Extensive Comparative Genomic Analysis of <i>Enterococcus faecalis</i> and <i>Enterococcus faecium</i> Reveals a Direct Association between the Absence of CRISPR–Cas Systems, the Presence of Anti-Endonuclease (ardA) and the Acquisition of Vancomycin Resistance in <i>E. faecium</i>
oleh: Kodjovi D. Mlaga, Vincent Garcia, Philippe Colson, Raymond Ruimy, Jean-Marc Rolain, Seydina M. Diene
Format: | Article |
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Diterbitkan: | MDPI AG 2021-05-01 |
Deskripsi
Here, we performed a comparative genomic analysis of all available genomes of <i>E. faecalis</i> (<i>n</i> = 1591) and <i>E. faecium</i> (<i>n</i> = 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–Cas systems in 75.36% of <i>E. faecalis</i> genomes and only 4.89% of <i>E. faecium</i> genomes with a significant difference (<i>p</i>-value < 10<sup>−5</sup>). We found a negative correlation between the number of CRISPR–Cas systems and genome size (r = −0.397, <i>p</i>-value < 10<sup>−5</sup>) and a positive correlation between the genome %GC content and the number of CRISPR–Cas systems (r = 0.215, <i>p</i>-value < 10<sup>−5</sup>). Our findings showed that the presence of the anti-endonuclease <i>ardA</i> gene may explain the decrease in the number of CRISPR–Cas systems in <i>E. faecium</i>, known to deactivate the endonucleases’ protective activities and enable the <i>E. faecium</i> genome to be versatile in acquiring mobile genetic elements, including carriers of antimicrobial resistance genes, especially <i>vanB</i>. Most importantly, we observed that there was a direct association between the absence of CRISPR–Cas, the presence of the anti-CRISPR <i>ardA</i> gene and the acquisition of vancomycin resistance genes.