CRISPR Elements and Their Association with Macrolide and Aminoglycoside Resistance Genes in Enterococci

CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems are common among enterococci and may prevent the acquisition of mobile genetic elements carrying antimicrobial resistance genes. In this study, we correlate the presence of CRISPR with genes associated with macrolide resistance and high-level resistance to aminoglycosides (HLR-A) among 216 Enterococcus faecalis and 82 Enterococcus faecium isolates. We used PCR to detect genes associated with macrolide resistance, HLR-A, and type II-A CRISPR elements. We used two-tailed Fisher's exact test to evaluate correlation between CRISPR and resistance genes. One hundred and seven (35.9%) isolates had at least one HLR-A gene; the prevalent genes were aac(6')-Ie-aph(2″)-Ia and ant(6)-Ia found in 61 (57%) and 46 (43%) isolates, respectively. The macrolide resistance genes erm(A) and erm(B) were found in 116 (38.9%) isolates. Overall, 174 (58.4%) isolates had at least one CRISPR element; the predominant one was CRISPR3-Cas (n = 117; 39.2%). The presence of three genes, two related to HLR-A [aph(2″)-Ic and ant(6)-Ia] and one macrolide resistance gene [erm(B)], was associated with the absence of CRISPR (p < 0.05), mainly in E. faecalis lacking CRISPR3-Cas. We observed the association between the absence of CRISPR and the presence of major aminoglycoside and macrolide resistance determinants, contributing to the understanding of the evolution of resistance in enterococci.