  CRISPR-Cas systems are an adaptive immunity that protects prokaryotes against
foreign genetic elements. Genetic templates acquired during past infection
events enable DNA-interacting enzymes to recognize foreign DNA for destruction.
Due to the programmability and specificity of these genetic templates,
CRISPR-Cas systems are potential alternative antibiotics that can be engineered
to self-target antimicrobial resistance genes on the chromosome or plasmid.
However, several fundamental questions remain to repurpose these tools against
drug-resistant bacteria. For endogenous CRISPR-Cas self-targeting,
antimicrobial resistance genes and functional CRISPR-Cas systems have to
co-occur in the target cell. Furthermore, these tools have to outplay DNA
repair pathways that respond to the nuclease activities of Cas proteins, even
for exogenous CRISPR-Cas delivery. Here, we conduct a comprehensive survey of
CRISPR-Cas genomes. First, we address the co-occurrence of CRISPR-Cas systems
and antimicrobial resistance genes in the CRISPR-Cas genomes. We show that the
average number of these genes varies greatly by the CRISPR-Cas type, and some
CRISPR-Cas types (IE and IIIA) have over 20 genes per genome. Next, we
investigate the DNA repair pathways of these CRISPR-Cas genomes, revealing that
the diversity and frequency of these pathways differ by the CRISPR-Cas type.
The interplay between CRISPR-Cas systems and DNA repair pathways is essential
for the acquisition of new spacers in CRISPR arrays. We conduct simulation
studies to demonstrate that the efficiency of these DNA repair pathways may be
inferred from the time-series patterns in the RNA structure of CRISPR repeats.
This bioinformatic survey of CRISPR-Cas genomes elucidates the necessity to
consider multifaceted interactions between different genes and systems to
design effective CRISPR-based antimicrobials.
