CRISPR elements and their association with antimicrobial resistance and virulence genes among vancomycin-resistant and vancomycin-susceptible enterococci recovered from human and food sources

Abstract We aimed to investigate the occurrence of CRISPR elements in the genomes of vancomycin-resistant (VRE) and vancomycin-susceptible (VSE) enterococci and their association with the presence of antimicrobial resistance and virulence genes. We analyzed 180 isolates, including 91 VRE and 89 VSE. Isolates were identified by PCR or MALDI-TOF. Antimicrobial susceptibility and MICs for vancomycin were determined by the disk-diffusion method and E-test®, respectively. The presence of resistance and virulence genes, as well as CRISPR elements, was investigated by PCR. We identified 95 (53%) E. faecalis, 78 (43%) E. faecium, five (2.8%) E. gallinarum, and one (0.6% each) E. casseliflavus and E. durans. The highest and the lowest non-susceptibility frequencies were observed for erythromycin (n = 152; 84.4%) and fosfomycin (n = 5; 2.8%), respectively. Most erythromycin-resistant isolates had the erm(B) gene (106/152; 69.7%). Of 118 (65.6%) isolates with high-level resistance to aminoglycoside, 69 (58.5%) had at least one aminoglycoside resistance gene, mostly ant(6)-Ia and aac(6′)-Ie + aph(2″)-Ia. We found at least one virulence gene among 135 (75%) isolates, mostly gelE (79/180; 43.9%). Ninety-two (51.1%) isolates had at least one CRISPR element, especially CRISPR3 (62/92; 67.4%). CRISPR elements were more common among E. faecalis, in which we observed a relationship between the absence of CRISPR and the presence of the vanA resistance gene, and the hyl and esp virulence genes. Among VRE. faecium, a relationship was found between the absence of CRISPR and the hyl gene. In conclusion, we found evident associations between the lack of CRISPR elements with species, multidrug resistance, and major resistance- and virulence-associated genes.