Genome defense and acquired antibiotic resistance in Enterococcus faecalis and Enterococcus faecium

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 DESCRIPTION (provided by applicant): Enterococcus faecalis and E. faecium are normal human intestinal tract colonizers and opportunistic pathogens that are among the leading causes of hospital-acquired infections in the US. Specific phylogenetic lineages of E. faecalis and E. faecium cause hospital-acquired infections. These hospital enterococci are multidrug-resistant and possess dramatically expanded genomes relative to commensal enterococcal strains. Genome expansion is due to the acquisition of mobile genetic elements (MGEs) such as plasmids and phage. Interestingly, hospital enterococci lack CRISPR-Cas systems. CRISPR-Cas are prokaryotic genome defense systems that serve as molecular memories of past MGE encounters and that provide acquired immunity against MGEs. These results suggest that antibiotic treatment inadvertently selects for enterococci with enhanced abilities to acquire MGEs. The central hypothesis guiding this research is that compromised genome defense combined with strong selection for MGEs leads to the emergence of multidrug-resistant, genome- expanded enterococci endemic to clinical environments. In preliminary work supported by a NIAID K22 Research Scholar Development Award, we demonstrated that a CRISPR-Cas system in commensal E. faecalis acts as an impediment to the acquisition of antibiotic resistance. The research in this proposal investigates the function of a unique orphan CRISPR locus occurring in hospital E. faecalis strains, called CRISPR2, which regulates the antimicrobial stress response of those strains (Aim 1). We have observed that acquisition of an antibiotic resistance plasmid by commensal E. faecalis leads to molecular memory loss (CRISPR deletion) in plasmid-containing cells over time. Mechanisms by which the plasmid evades host CRISPR-Cas defense and induces molecular memory loss will be investigated (Aim 2). Finally, we investigate the hypothesis that hospital enterococci are dysfunctional for `self' versus non-self recognition; i.e. genome modification defense (Aim 3).