Genome-driven identification of patient and bacterial drivers of resistance to novel beta-lactam/beta-lactamase inhibitor combination therapies

Project Summary Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent public health threat. Of greatest concern are epidemic CRKP lineages that have acquired multidrug resistance, rendering standard therapies ineffective. While new drugs are available, resistance has already been reported. Alarmingly, our preliminary analysis of resistance to novel β-lactam/β- lactamase inhibitor combination therapies in regional isolates collected from long-term acute care hospitals in 2014-2015 revealed that 14% of epidemic lineage CRKP sequence type (ST258) isolates were already resistant before the drugs were on the market. Maintaining the long-term efficacy of antibiotics is hindered by a limited understanding of the patient populations, clinical practices, and bacterial features that will ultimately drive the emergence and spread of resistance to newly approved antibiotics. This proposal’s objective is to identify patient and bacterial associated with the emergence and spread of resistance to two novel β-lactam/β-lactamase inhibitor therapies: meropenem-vaborbactam and imipenem- relebactam. The central hypothesis is that there is an interaction between strain background and clinical exposures that influence the propensity for resistance to emerge and subsequently spread via clonal expansion or plasmid transfer. This hypothesis will be tested using the following aims: (1) determine the potential for analysis of resistance drivers identified before the clinical deployment of β-lactam/β-lactamase inhibitor combination therapies to inform patterns of resistance emergence and spread once they begin being utilized and (2) determine the influence of genetic background on the emergence of resistance to β-lactam/β-lactamase inhibitor combination therapies. To accomplish these aims, the PI will leverage two isolate collections: (1) 390 clinical CRKP ST258 isolates collected from 12 California long-term acute care hospitals in 2014-15 and (2) ~1500 CRKP isolates collected from a 2021-23 follow-up study in the same facilities. Clinical data collection, antibiotic susceptibility testing, and whole-genome sequencing were performed on each isolate. Alongside bioinformatic analyses, experimental methods will be employed to validate resistance-associated genotypes and evaluate the contribution of genetic background on resistance emergence. The results from this proposal will improve our understanding of the patient and bacterial features that drive the evolution and spread of resistance to β-lactam/β- lactamase inhibitor combination therapies. Our results have the potential to inform surveillance efforts, infection prevention interventions, and the stewardship of antibiotics to slow the development of resistance. This proposal also serves as an excellent training program for the development of the critical thinking and multidisciplinary research skills needed to advance the PI’s pursuit of becoming an independent scientist who develops innovative solutions to combat antibiotic resistance by applying advanced genomic methods, data analysis methods, and wet lab experimentation to identify patient and bacterial features that drive the emergence and spread of antibiotic resistance.