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>
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, endonucle...
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MDPI AG
2021-05-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/6/1118 |
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| author | Kodjovi D. Mlaga Vincent Garcia Philippe Colson Raymond Ruimy Jean-Marc Rolain Seydina M. Diene |
| author_facet | Kodjovi D. Mlaga Vincent Garcia Philippe Colson Raymond Ruimy Jean-Marc Rolain Seydina M. Diene |
| author_sort | Kodjovi D. Mlaga |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T11:10:37Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T11:10:37Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-bdda1a28070a489993687fdd5f6109bb2023-11-21T20:51:22ZengMDPI AGMicroorganisms2076-26072021-05-0196111810.3390/microorganisms9061118Extensive 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>Kodjovi D. Mlaga0Vincent Garcia1Philippe Colson2Raymond Ruimy3Jean-Marc Rolain4Seydina M. Diene5Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, FranceAix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, FranceAix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, FranceDepartment of Bacteriology at Nice Academic Hospital, Nice Medical University, 06003 Nice, FranceAix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, FranceAix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranee Infection, 13005 Marseille, FranceHere, 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.https://www.mdpi.com/2076-2607/9/6/1118comparative genomics<i>E. faecalis</i><i>E. faecium</i>CRISPR–Casvancomycin resistancerecombinations |
| spellingShingle | Kodjovi D. Mlaga Vincent Garcia Philippe Colson Raymond Ruimy Jean-Marc Rolain Seydina M. Diene 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> Microorganisms comparative genomics <i>E. faecalis</i> <i>E. faecium</i> CRISPR–Cas vancomycin resistance recombinations |
| title | 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> |
| title_full | 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> |
| title_fullStr | 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> |
| title_full_unstemmed | 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> |
| title_short | 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> |
| title_sort | 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 |
| topic | comparative genomics <i>E. faecalis</i> <i>E. faecium</i> CRISPR–Cas vancomycin resistance recombinations |
| url | https://www.mdpi.com/2076-2607/9/6/1118 |
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