Investigating the prevalence of CRISPR-Cas systems and their association with antibiotic resistance in Enterococcus faecalis and Enterococcus faecium isolated from hospitalized patients

BACKGROUND AND OBJECTIVESEnterococcus faecalis and Enterococcus faecium, are an important cause of nosocomial infections. Antibiotic resistance of Enterococci is a challenge in the clinical setting and increases the difficulty of treating Enterococcal infectious diseases.Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune system involved in specific defenses against the invasion of foreign elements. Three Type II CRISPR systems (CRISPR۱-cas, CRISPR۲ and CRISPR۳-cas) have been identified in Enterococci isolates. This study aimed to evaluate the presence of CRISPR-Cas system genes and their possible association with antibiotic resistance patterns of E. faecalis and E.faecium species isolated from hospitalized patients.MATERIALS AND METHODSIn this study, a total of ۶۲ isolates of E. faecalis and E. faecium were collected from urinary tract infections (UTI), Blood infections, Wound infections and other sources. The isolation and identification of Enterococci species were performed by standard bacteriology tests and polymerase chain reaction (PCR). Antibiotic susceptibility profiles were determined by the disc diffusion method and studied using standard CLSI protocols. The presence of various CRISPR-Cas systems was investigated by PCR. The association of the occurrence of CRISPR-Cas systems with antibiotic resistance was analyzed with appropriate statistical tests.RESULTS AND DISCUSSION The results of PCR confirmed the prevalence of ۳۲ (۵۱.۶%) E. faecalis and ۳۰ (۴۸.۳%) E. faecium, respectively. In total, ۵۳ (۸۵.۴%) of ۶۲ isolates showed the presence of CRISPR-Cas loci. The incidence of CRISPR-Cas was more common in E. faecalis. CRISPR۱, CRISPR۲, and CRISPR۳ were present in ۱۵ (۲۴.۱%), ۵۲ (۸۳.۸%), and ۱۲ (۱۹.۳%) Enterococci isolates, respectively. The CRISPR-Cas positive isolates showed significant lower resistance rates against Linzolid and Chloramphenicol in comparison with CRISPR-Cas negative isolates. The results showed that the presence of CRISPR-Cas genes was lower in multidrug-resistant (MDR) isolates (۷۷.۱%, n=۲۷/۳۵) compared to the non-MDR enterococci isolates (۹۶.۲%, n = ۲۶/۲۷).CONCLUSION According to our study, the lack of CRISPR-Cas genes was associated with more antibiotic resistance rates and multidrug resistance in E. faecalis and E. faecium isolated form clinical samples.