Modeling CRISPR to Preserve Antibiotics

描述（由申请人提供）：肠球菌在70年代和80年代成为多重耐药医院获得性感染（HAI）的主要原因。它们目前仅次于葡萄球菌，占所有HAI的12.1%。抗生素耐药的HAI每年增加超过200亿美元的额外卫生保健费用。因此，每年24.2亿美元以及约12,000例死亡可归因于肠球菌引起的HAI，使其成为主要的公共卫生问题。此外，它们现在正在将对最后一线药物万古霉素的耐药性传播给葡萄球菌。在初步数据中，我们发现肠球菌作为主要医院病原体的出现与70年代和80年代缺乏CRISPR防御噬菌体、质粒和其他移动元件进入基因组的菌株的生长相吻合。我们的比较基因组学研究表明，在强烈的抗生素压力下，没有CRISPR的肠球菌在获得抗生素耐药决定因素方面具有优势。它们对多种抗生素产生了耐药性，并在医院里激增。与…的损失同时发生

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.