Effectiveness of CRISPR-Cas in Sensitizing Bacterial Populations with Plasmid-Encoded Antimicrobial Resistance

The spread of bacteria resistant to antibiotics poses a serious threat to human health. Genes that encode antibiotic resistance are often harbored by plasmids, extra-chromosomal DNA molecules found in bacteria. The ability of plasmids to spread horizontally among bacteria facilitates the emergence and spread of multiresistant strains, outpacing the development of new antibiotics. CRISPR-Cas derived tools with their sequence specificity offer a promising new approach to combating antibiotic resistance. By introducing CRISPR-encoding plasmids that specifically target antibiotic resistance genes encoded on plasmids, the susceptibility of bacteria to conventional antibiotics can be restored. However, genetic variation within bacterial populations can hinder the effectiveness of such CRISPR-Cas tools by allowing some mutant strains to evade CRISPR-mediated cleaving or gene silencing.

In this study, we model the effectiveness of CRISPR-Cas in sensitizing bacterial populations and assess the success probability of a subsequent treatment with conventional antibiotics. We evaluate this probability according to the target interference mechanism, the copy number of the resistance-encoding plasmid and its compatibility with the CRISPR-encoding plasmid.

Our results identify promising approaches to revert antibiotic resistance with CRISPR-encoding plasmids: Cleaving by CRISPR systems on incompatible plasmids is most effective against AMR plasmids with a low copy number, while for higher copy numbers, gene silencing by CRISPR systems encoded on compatible plasmids offers the superior solution.