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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-Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference ( p -value &lt; 10 -5 ). We found a negative correlation between the number of CRISPR-Cas systems and genome size (r = -0.397, p -value &lt; 10 -5 ) and a positive correlation between the genome %GC content and the number of CRISPR-Cas systems (r = 0.215, p -value &lt; 10 -5 ). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR-Cas systems in E. faecium , known to deactivate the endonucleases' 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-Cas, the presence of the anti-CRISPR ardA gene and the acquisition of vancomycin resistance genes.

microorganisms

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