Precise Combination Strategies Targeting Carbapenem-Resistant Klebsiella pneumoniae

PROJECT SUMMARY/ABSTRACT: Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) cause life-
threatening infections that are associated with unacceptably high mortality rates. CR-Kp is particularly
challenging to treat since it often possesses a myriad of molecular resistance determinants that enable it to grow
in the presence of most antibiotics. New β-lactam/β-lactamase inhibitors (BL/BLI), such as ceftazidime-
avibactam, are not a sustainable therapeutic solution for CR-Kp as monotherapy since there is potential for
development of resistance and clinical failure rates remain remarkably high when used alone. Up to 95% of CR-
Kp still remain susceptible to at least one of the aminoglycosides (AMG). However, nearly all CR-Kp isolates
harbor at least one of the aminoglycoside-modifying enzymes (AME), which inactivate a subset of the AMGs.
Thus, selecting an AMG that is tailored to the AMEs and other AMG-resistance determinants (strain-specific
AMG) is innovative and provides the foundation for this application, which is focused on development of
molecularly precise AMG-based combinations for CR-Kp. Our central hypothesis is that novel combination
regimens including short-courses of an optimally dosed, strain-specific AMG and a BL/BLI can maximize killing
and resistance suppression of CR-Kp. Our promising preliminary data are highly supportive of our innovative
and mechanistic approach. We developed a preliminary model to predict the strain-specific AMG based on an
isolate’s AMG-resistance genes. We generated the first data for the combination of the strain-specific AMG with
a BL/BLI (ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam) against CR-Kp in both
the hollow fiber infection model (HFIM) and the mouse pneumonia model, where the combination was highly
synergistic. We have also developed a novel assay to quantify intracellular AMG concentrations. Leveraging our
latest assays, we will elucidate the mechanisms responsible for synergy of the combination between a strain-
specific AMG and BL/BLI in CR-Kp to rationally optimize them for future clinical trials. In Aim 1, the precise
influence of each AMG-resistance determinant on AMG activity will be defined and novel predictors of AMG-
resistance will be elucidated. In Aim 2, we will design novel short-course AMG treatment regimens that are
efficacious. We will define the time-course of AMG-tolerance and resistance emergence using systems
pharmacology and protein synthesis assays. In Aim 3, we will rationally optimize AMG and BL/BLI combinations
by identifying mechanisms of synergy and assessing antibiotic target site concentrations. The HFIM will be used
to define the pharmacodynamics of combinations and determine optimal timing of antibiotic administration. In
Aim 4, we will develop quantitative and systems pharmacology (QSP) models that integrate our mechanistic
data and rationally optimize AMG-based combination dosing strategies based on AMG-resistance determinants
in CR-Kp. QSP-optimized combinations will be prospectively validated in mouse pneumonia models. This project
will develop novel, molecularly precise AMG-based combinations to combat the urgent threat of CR-Kp.

Grant Number: 5R01AI173064-04
NIH Institute/Center: NIH
Principal Investigator: Zackery Bulman