Mechanisms of Resistance and Clinical Outcomes of non-Carbapenemase Producing Carbapenem-Resistant Klebsiella pneumoniae Infections - PROJECT SUMMARY Carbapenem resistant Klebsiella pneumoniae (CR-Kpn) have been identified by the World Health Organization as a critical threat on the Priority Pathogens List. Novel diagnostics and therapeutic drug discovery have largely been focused on carbapenemase-producing isolates, however, non-carbapenemase producing carbapenem resistant K. pneumoniae (NCP-Kpn) account for a growing proportion of CR-Kpn clinical isolates. Clinical data on the outcomes of infections due to NCP-Kpn is limited, however, recent studies suggest that rates of mortality may be equal to or even higher than infections due to carbapenemase producing isolates. Carbapenemase independent carbapenem resistance in Kpn has been associated with the alteration or loss of outer membrane porins OmpK35 and OmpK36, and increases in the expression or gene copy number of Extended Spectrum β-lactamases (ESBLs) or plasmid encoded cephalosporinases (AmpC). These changes compromise the entry and concentration of carbapenems in the periplasmic space, and disproportionately impact ertapenem as compared to meropenem or imipenem. In an international cohort of NCP-Kpn isolates, susceptibility to individual carbapenems varied substantially, with all isolates resistant to ertapenem, 67% resistant to meropenem, and 25% resistant to imipenem, respectively. The majority of these isolates had alteration or disruption of the OmpK35/OmpK36 porins with increases in β-lactamase gene copy number. However, the specific drivers that accounted for the discordance between meropenem and imipenem remain to be elucidated. Further, increases in gene copy number expansion also correlated with increasing minimum inhibitory concentration of the β-lactam/β-lactamase inhibitor (BL/BLI) ceftazidime-avibactam, suggesting newer BL/BLI combinations may also be vulnerable to these mechanisms. This proposal seeks to investigate the hypothesis that the specific combination of porin mutations along with the presence, Ambler type, and gene copy number of β-lactamases mediates the differential in vitro phenotypes and can inform optimal treatment selection for NCP-Kpn. In the first aim, a large international collection of NCP-Kpn isolates will be characterized using whole genome sequencing, to investigate the genomic factors associated with discordant carbapenem susceptibility phenotypes. Using a 1-compartment in vitro model, isolates from each NCP-Kpn class will be evaluated for the emergence of resistance to carbapenems and BL/BLI combinations. In the second aim, the clinical impact of NCP-Kpn will be assessed in the cohort of patients with bacteremia. Using a desirability of outcomes ranking (DOOR), differences in mortality, relapse, and emergence of resistance will be compared across infections due to isolates stratified by meropenem susceptibility and underlying mechanism of resistance. The data from this proposal will help to inform the rational selection of antibiotics for treatment of NCP-Kpn infections, and form the basis for the design of larger prospective trials in the future.
