Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations

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Abstract

CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. It was of interest to investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes E. faecalis populations. Here, we demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains. Interestingly, we observe that E. faecalis transiently maintains CRISPR targets despite active CRISPR-Cas systems. Subsequently, if selection for the CRISPR target is present, toxic CRISPR spacers are lost over time, while in the absence of selection, CRISPR targets are lost over time. We find that forced maintenance of CRISPR targets induces a fitness cost that can be exploited to alter heterogeneous E. faecalis populations.

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Karthik Hullahalli

Department of Biological Sciences, The University of Texas at Dallas, Richardson, United States

Competing interests
The authors declare that no competing interests exist.
Marinelle Rodrigues

Department of Biological Sciences, The University of Texas at Dallas, Richardson, United States

Competing interests
The authors declare that no competing interests exist.
Kelli L Palmer

Department of Biological Sciences, The University of Texas at Dallas, Richardson, United States

For correspondence
kelli.palmer@utdallas.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-7343-9271

Funding

National Institutes of Health (R01 AI116610)

Kelli L Palmer

American Society for Microbiology (Undergraduate Research Fellowship)

Karthik Hullahalli

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.