Enterococcus faecalis CRISPR-Cas Is a Robust Barrier to Conjugative Antibiotic Resistance Dissemination in the Murine Intestine

• Published in: mSphere Vol. 4; no. 4
• Main Authors: Price, Valerie J, McBride, Sara W, Hullahalli, Karthik, Chatterjee, Anushila, Duerkop, Breck A, Palmer, Kelli L
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 24-07-2019
• Subjects: Acids; Animals; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacteria; Biofilms; Conjugation, Genetic; CRISPR; CRISPR-Cas; CRISPR-Cas Systems; Drug resistance; Drug Resistance, Bacterial; Ecological and Evolutionary Science; Enterococcus faecalis; Enterococcus faecalis - drug effects; Enterococcus faecalis - genetics; Experiments; Feces; Gene transfer; Gene Transfer, Horizontal; Genes; Gram-positive bacteria; Hypotheses; Immune system; Infectious diseases; intestinal colonization; Intestinal microflora; Intestine; Intestines - microbiology; Mice; Mice, Inbred C57BL; Microbiota; Plasmids; Plasmids - genetics; United States > US; Enterococcus faecalis; CRISPR-Cas; plasmids; intestinal colonization; antibiotic resistance
• ISSN: 2379-5042; 2379-5042
• DOI: 10.1128/msphere.00464-19

CRISPR-Cas systems are barriers to horizontal gene transfer (HGT) in bacteria. Little is known about CRISPR-Cas interactions with conjugative plasmids, and studies investigating CRISPR-Cas/plasmid interactions in
models relevant to infectious disease are lacking. These are significant gaps in knowledge because conjugative plasmids disseminate antibiotic resistance genes among pathogens
, and it is essential to identify strategies to reduce the spread of these elements. We use enterococci as models to understand the interactions of CRISPR-Cas with conjugative plasmids.
is a native colonizer of the mammalian intestine and harbors pheromone-responsive plasmids (PRPs). PRPs mediate inter- and intraspecies transfer of antibiotic resistance genes. We assessed
CRISPR-Cas anti-PRP activity in the mouse intestine and under different
conditions. We observed striking differences in CRISPR-Cas efficiency
versus
With few exceptions, CRISPR-Cas blocked intestinal PRP dissemination, while
, the PRP frequently escaped CRISPR-Cas defense. Our results further the understanding of CRISPR-Cas biology by demonstrating that standard
experiments do not adequately model the
antiplasmid activity of CRISPR-Cas. Additionally, our work identifies several variables that impact the apparent
antiplasmid activity of CRISPR-Cas, including planktonic versus biofilm settings, different donor-to-recipient ratios, production of a plasmid-encoded bacteriocin, and the time point at which matings are sampled. Our results are clinically significant because they demonstrate that barriers to HGT encoded by normal (healthy) human microbiota can have significant impacts on
antibiotic resistance dissemination.
CRISPR-Cas is a type of immune system in bacteria that is hypothesized to be a natural impediment to the spread of antibiotic resistance genes. In this study, we directly assessed the impact of CRISPR-Cas on antibiotic resistance dissemination in the mammalian intestine and under different
conditions. We observed a robust effect of CRISPR-Cas on
but not
dissemination of antibiotic resistance plasmids in the native mammalian intestinal colonizer
We conclude that standard
experiments currently do not appropriately model the
conditions where antibiotic resistance dissemination occurs between
strains in the intestine. Moreover, our results demonstrate that CRISPR-Cas present in native members of the mammalian intestinal microbiota can block the spread of antibiotic resistance plasmids.