Abstract
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 < 10−5). We found a negative correlation between the number of CRISPR–Cas systems and genome size (r = −0.397, p-value < 10−5) and a positive correlation between the genome %GC content and the number of CRISPR–Cas systems (r = 0.215, p-value < 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.
Highlights
Enterococci are an ancient genus of Enterococcaceae that have adapted to living in complex environments and surviving in harsh conditions [1,2]
The aim of this study was to investigate the presence of recombination sites in both E. faecalis and E. faecium as evidence of mobile genetic elements (MGEs) transfer and the association between the absence or presence of a CRISPR–Cas system, an endonuclease and antiendonuclease system and the acquisition of antimicrobial resistance genes—especially the vancomycin resistance genes vanA, vanB and vanC—using sequenced genomes of E. faecalis from Marseille and publicly available genomes of both species
We found that the presence of a CRISPR–Cas system is protective for E. faecalis in acquiring specific mobile genetic elements carrying the vancomycin resistance genes vanA and vanB
Summary
Enterococci are an ancient genus of Enterococcaceae that have adapted to living in complex environments and surviving in harsh conditions [1,2]. Enterococcus faecalis and Enterococcus faecium, are the leading cause of the vast majority of hospital-acquired Enterococci infections in humans [4]. The plasticity of the Enterococcus genomes allows them to rapidly respond and adapt to the environment by acquiring genetic determinants. It increases their ability to colonise and infect their host and cause diseases [3]. The success of E. faecium and E. faecalis in evolving as multi-resistant nosocomial pathogens is associated with their capacity to harbour and spray adaptive genetic materials, including antimicrobial resistance genes encoded by Microorganisms 2021, 9, 1118.
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