Modeling CRISPR to Preserve Antibiotics

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DESCRIPTION (provided by applicant): The enterococci emerged as leading causes of multidrug resistant hospital acquired infection (HAI) in the 70's and 80's. They currently rank second only to the staphylococci, causing 12.1% of all HAI. Antibiotic resistant HAI add over $ 20 Billion annually in excess health care costs. Therefore $ 2.42 Billion annually, along with ~ 12,000 deaths are ascribable to HAI caused by enterococci, making it a leading public health concern. Moreover, they are now transmitting resistance to the last line drug, vancomycin, to the staphylococci. In preliminary data, we showed that the emergence of enterococci as leading hospital pathogens coincided with the outgrowth of strains in the 70's and 80's that lacked CRISPR defense against phage, plasmid and other mobile element entry into the genome. Our comparative genomics study indicated that under intense antibiotic pressure, enterococci without CRISPR were at an advantage for acquiring antibiotic resistance determinants. They became resistant to multiple antibiotics and proliferated in hospitals. Coinciding with the loss of CRISPR, phages lysogenized the hospital strains; and pathogenicity islands, transposons and other plasmids and mobile elements entered. As a result, hospital endemic enterococci have genomes over 25% larger than commensal strains, with a synergistic convergence of virulence traits and antibiotic resistances. In nature, most evidence indicates that phage pressure has selected for the occurrence and maintenance of the CRISPR defense over eons of evolution. However, the sudden and massive application of high levels of antibiotics in the last 50 years has selected for strains lacking that defense, with presumably enhanced ability to acquire new antibiotic resistances. In this exploratory R21 application, we propose to quantify the level of defense against plasmid and phage entry into Enterococcus faecalis accorded by the CRISPR locus, and to model using varying parameters, the tension between antibiotic selection and phage selection for the loss/maintenance of this locus. This will provide the preliminary data for a larger program to identify the optimum antibiotic use parameters for preserving CRISPR in the enterococcal population, thereby inhibiting transfer of antibiotic resistant elements, and preserving the shelf life of increasingly scarce, effective antibiotics.