CRISPR‐mediated removal of antibiotic resistance genes in Enterococcus faecalis populations

Abstract

Multidrug resistant infections caused by Enterococcus faecalis are serious threats in hospitals where immunocompromised individuals are at elevated risk of infection. A major cause for the rise of drug resistance in E. faecalis is the horizontal transfer of antibiotic resistance genes on mobile genetic elements including integrative and conjugative elements and the species‐specific pheromone‐responsive plasmids. The transfer of these potentially beneficial mobile elements among the population can be impeded by genome defense systems such as the prokaryotic adaptive immune system CRISPR‐Cas. However, multidrug‐resistant strains of E. faecalis circumvent this by compromising their genome defense systems, leaving them vulnerable to invasion by mobile DNA. In this study, the cas genes of a native E. faecalis CRISPR‐Cas system were introduced into a MDR strain, leading to the reactivation of host genome defenses. When self‐targeting CRISPR spacers were employed on conjugative elements in heterogenous populations of E. faecalis, we found that certain antibiotic resistance genes could be selectively removed from the population under pressure to maintain the conjugative element. Taken together, this study demonstrates that CRISPR‐mediated alteration of E. faecalis population structure may be a viable option for depleting undesirable traits from E. faecalis human gut populations.Support or Funding InformationThis project is supported by R01AI116610 to KP.