Enterococcus faecalisstrains with compromised CRISPR-Cas defense emerge under antibiotic selection for a CRISPR-targeted plasmid

Enterococcus faecalisis a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR)E. faecalisstrains have emerged that are replete with mobile genetic elements (MGEs). Non-MDRE. faecalisstrains frequently possess CRISPR-Cas systems, which reduce the frequency of mobile genetic element (MGE) acquisition. We demonstrated in previous studies thatE. faecalispopulations can transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze these populations. In the presence of antibiotic selection for the plasmid, mutants with compromised CRISPR-Cas defense and enhanced ability to acquire a second antibiotic resistance plasmid emerged. Conversely, in the absence of selection, the plasmid was lost from wild-typeE. faecalispopulations, but notE. faecalispopulations that lacked thecas9gene. Our results indicate thatE. faecalisCRISPR-Cas can become compromised under antibiotic selection, generating populations with enhanced abilities to undergo horizontal gene transfer.