Towards the Translation of Synergistic Phage-Polymyxin Combination Therapy against Pandrug-resistant Klebsiella pneumoniae: A Systems Approach

Antimicrobial resistance (AMR) has become one of the greatest global threats to human health. Pandrug- resistant (PDR) Klebsiella pneumoniae has been identified by the World Health Organization as one of the 3 top- priority pathogens urgently requiring new treatments. Polymyxins are often used as the last option; however, plasmid-mediated polymyxin resistance highlights the urgency to develop novel therapeutics to treat PDR K. pneumoniae. Bacteriophage (i.e. phage) has recently attracted substantial attention as a promising option to treat PDR bacterial infections; unfortunately, resistance to phage monotherapy in K. pneumoniae can rapidly develop. Optimal phage-antibiotic combinations provide a superior approach; however, there is a significant lack of knowledge on the pharmacokinetics/pharmacodynamics/toxicodynamics (PK/PD/TD) of phage therapy. This situation has severely hindered the optimization of phage therapy against bacterial 'superbugs' and limited their clinical utility. Traditional PK/PD/TD plays a critical role in optimizing antibiotic dosage regimens, but lacks systems and mechanistic information. Furthermore, antibiotic PK/PD/TD cannot be easily extrapolated to phage therapy, mainly due to their unique PK, host specificity and self-amplification. As phage-antibiotic synergy also depends on the dynamics of infection and host responses, innovative strategies incorporating systems pharmacology and host-pathogen-phage-antibiotic interactions have the significant potential to optimize their clinical use. Excitingly, we have isolated a number of phages with superior activity against PDR K. pneumoniae, and identified several novel phage-antibiotic combinations (e.g. with polymyxins) that synergistically kill PDR K. pneumoniae in vitro and in animals without any regrowth. Considering the urgent need to optimize phage therapy and minimize resistance to the last-line polymyxins, it is essential to develop superior phage-polymyxin combinations using a systems approach by integrating PK/PD/TD and multi-omics. Therefore, the Specific Aims of this application are: (1) To identify superior synergistic combinations of phage and polymyxin B, and evaluate their PK/PD/TD against PDR K. pneumoniae using in vitro and animal infection models; (2) To elucidate the mechanisms of synergistic bacterial killing by the superior phage-polymyxin combinations and the host- pathogen-phage-polymyxin interactions using correlative multi-omics; and (3) To develop novel QSP models integrating PK/PD/TD and multi-omics data for the superior phage-polymyxin combinations targeting PDR K. pneumoniae, and propose optimal dosage regimens for future clinical trials. Our innovative multi-disciplinary project will generate urgently needed information for rational optimization of novel phage-polymyxin combinations. Importantly, this proposal aligns perfectly with the present NIAID RFA for exploiting phages to kill 'superbugs' and responds in a timely manner to the recent 2019 NIAID Antibiotic Resistance Framework to protect global health security.