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Antimicrob Agents Chemother. 2019 Oct 22;63(11). pii: e01454-19. doi: 10.1128/AAC.01454-19. Print 2019 Nov.

Conjugative Delivery of CRISPR-Cas9 for the Selective Depletion of Antibiotic-Resistant Enterococci.

Author information

1
Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA.
2
Department of Immunology & Microbiology, The University of Colorado School of Medicine, Aurora, Colorado, USA.
3
Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA kelli.palmer@utdallas.edu breck.duerkop@cuanschutz.edu.
4
Department of Immunology & Microbiology, The University of Colorado School of Medicine, Aurora, Colorado, USA kelli.palmer@utdallas.edu breck.duerkop@cuanschutz.edu.

Abstract

The innovation of new therapies to combat multidrug-resistant (MDR) bacteria is being outpaced by the continued rise of MDR bacterial infections. Of particular concern are hospital-acquired infections (HAIs) that are recalcitrant to antibiotic therapies. The Gram-positive intestinal pathobiont Enterococcus faecalis is associated with HAIs, and some strains are MDR. Therefore, novel strategies to control E. faecalis populations are needed. We previously characterized an E. faecalis type II CRISPR-Cas system and demonstrated its utility in the sequence-specific removal of antibiotic resistance determinants. Here, we present work describing the adaption of this CRISPR-Cas system into a constitutively expressed module encoded on a pheromone-responsive conjugative plasmid that efficiently transfers to E. faecalis for the selective removal of antibiotic resistance genes. Using in vitro competition assays, we show that these CRISPR-Cas-encoding delivery plasmids, or CRISPR-Cas antimicrobials, can reduce the occurrence of antibiotic resistance in enterococcal populations in a sequence-specific manner. Furthermore, we demonstrate that deployment of CRISPR-Cas antimicrobials in the murine intestine reduces the occurrence of antibiotic-resistant E. faecalis by several orders of magnitude. Finally, we show that E. faecalis donor strains harboring CRISPR-Cas antimicrobials are immune to uptake of antibiotic resistance determinants in vivo Our results demonstrate that conjugative delivery of CRISPR-Cas antimicrobials may be adaptable for future deployment from probiotic bacteria for exact targeting of defined MDR bacteria or for precision engineering of polymicrobial communities in the mammalian intestine.

KEYWORDS:

CRISPR-Cas; Enterococcus faecalis ; antibiotic resistance; conjugation; intestinal colonization; pheromone; plasmid

PMID:
31527030
PMCID:
PMC6811441
[Available on 2020-04-22]
DOI:
10.1128/AAC.01454-19

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