Extensive Comparative Genomic Analysis of Enterococcus faecalis and Enterococcus faecium Reveals a Direct Association between the Absence of CRISPR–Cas Systems, the Presence of Anti-Endonuclease (ardA) and the Acquisition of Vancomycin Resistance in E. faecium

Abstract

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^-5). We found a negative correlation between the number of CRISPR-Cas systems and genome size (r = -0.397, <i>p</i>-value < 10^-5) and a positive correlation between the genome %GC content and the number of CRISPR-Cas systems (r = 0.215, <i>p</i>-value < 10^-5). 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.