Association of CRISPR-Cas System with the Antibiotic Resistance and Virulence Genes in Nosocomial Isolates of Enterococcus

Abstract

Purpose This study aimed to investigate the prevalence of the CRISPR-Cas system in nosocomial isolates of Enterococcus and their possible association with antibiotic resistance and virulence genes. Materials and Methods Identification and antimicrobial susceptibility of the microorganism were performed by the automatized VITEK 2 Compact system (bioMerieux, France). A total of 100 Enterococcus isolates were collected and identified by VITEK 2 Compact automatic microbial identification drug susceptibility analyzer. The prevalence of various CRISPR-Cas systems, antibiotic resistance genes and virulence genes were investigated by polymerase chain reaction (PCR). The prevalence of CRISPR-Cas systems associated with antibiotic resistance and virulence genes was performed by appropriate statistical tests. Results A total of 100 isolates of Enterococcus were identified and there were 62/100(62.0%) Enterococcus faecalis isolates and 38/100(38.0%) Enterococcus faecalis isolates. In total, 46 (46.0%) of 100 isolates had at least one CRISPR-Cas locus. CRISPR elements were more prevalent in Enterococcus faecalis isolates. The results of PCR demonstrated that CRISPR1-Cas, orphan CRISPR2, and CRISPR3-Cas were present in 23 (23.0%), 42 (42.0%) and 5 (5.0%) Enterococcus isolates, respectively. Compared with CRISPR-Casnegative isolates, the CRISPR-Cas positive isolates showed significant lower resistance rates against ampicillin, erythromycin, levofloxacin, tetracycline, vancomycin, gentamicin, streptomycin, and rifampicin. Presumably consistent with drug susceptibility, fewer CRISPR loci were identified in vanA, tetM, ermB, aac6’-aph(2”), aadE , and ant(6) positive isolates. There was a significant negative correlation between the CRISPR-Cas locus and the enterococcal virulence factors enterococcal surface protein ( esp ) gene. Conclusion In conclusion, the results indicated that the absence of the CRISPR-Cas system was negatively associated with some antibiotic resistance in clinical isolates of Enterococcus faecalis and Enterococcus faecium . Also, there was a negative correlation with the carriage of antibiotic resistance genes. Furthermore, CRISPR-Cas may prevent some isolates from acquiring certain virulence factors.

Analysis of genetic structure and function of clustered regularly interspaced short palindromic repeats loci in 110 Enterococcus strains

“…3389/fmicb.2023.1177841 Frontiers in Microbiology 08 frontiersin.org genes to further understand the function and drug resistance mechanism of the Enterococcus CRISPR system. The complete CRISPR detection rate of Enterococcus reported in this study was 35.45%, which was lower than that of Enterococcus nosocomial isolates (46%) (Tao et al, 2022) and Pseudomonas aeruginosa (61.6%) (van Belkum et al, 2015), but higher than Staphylococcus epidermidis (7%) (Li et al, 2016). The presence of CRISPR-Cas in the Enterococcus genome was all lower than the average carrier rate of bacteria (45%) (Watson et al, 2021), which may be related to the loss of the CRISPR system in Enterococcus under antibiotic selection pressure.…”

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

“…It has been described that multidrug-resistant E. faecium strains lack a functional CRISPR-Cas system (Alduhaidhawi et al 2022 ). This may imply that, in a hospital setting, these strains are subjected to a selective pressure favouring the survival of strains unable to decompose exogenous DNA; consequently, they can easily acquire mobile virulence and resistance genes, which may help them thrive in this environment (Tao et al 2022 ). This behaviour has been observed and described in VRE E. faecium and E. faecalis (Alduhaidhawi et al 2022 ).…”

Blunted blades: new CRISPR-derived technologies to dissect microbial multi-drug resistance and biofilm formation

“…Pathogenic E. faecalis strains largely lack functional CRISPR loci, a finding replicated in vivo with commensal E. faecalis in the mouse intestine ( 96 ). One such example is the vancomycin-resistant strain V583, which lost a functional CRISPR system while obtaining antibiotic resistance ( 97 – 99 ). Thus, CRISPRi systems may present an advantageous tool for the examination of MDR in E. faecalis clinical isolates.…”