Elucidating effects of single and multiple resistance mechanisms on bacterial response to meropenem by quantitative and systems pharmacology modeling and population genomics

Meropenem is commonly used against Pseudomonas aeruginosa . Traditionally, the time unbound antibiotic concentration exceeds the MIC ( f T>MIC) is used to select carbapenem regimens. We aimed to: characterize the effects of different baseline resistance mechanisms on bacterial killing and resistance emergence; evaluate whether f T>MIC can predict these effects; and, develop a novel quantitative and systems pharmacology (QSP) model to describe effects of baseline resistance mechanisms on the time-course of bacterial response. Seven isogenic P. aeruginosa strains with a range of resistance mechanisms and MICs were used in 10-day hollow-fiber infection model studies. Meropenem pharmacokinetic profiles were simulated for various regimens (t1/2,meropenem=1.5h). All viable counts on drug-free, 3×MIC and 5×MIC meropenem-containing agar across all strains, five regimens and control (n=90 profiles) were simultaneously subjected to QSP modeling. Whole genome sequencing was completed for total population samples and emergent resistant colonies at 239h. Regimens achieving ≥98% f T>1xMIC suppressed resistance emergence of the mexR knockout strain. Even 100% f T>5xMIC failed to achieve this against the strain with OprD loss and the ampD and mexR double-knockout strain. Baseline resistance mechanisms affected bacterial outcomes, even for strains with the same MIC. Genomic analysis revealed that pre-existing resistant subpopulations drove resistance emergence. During meropenem exposure, mutations in mexR were selected in strains with baseline oprD mutations, and vice versa , confirming these as major mechanisms of resistance emergence. Secondary mutations occurred in lysS or argS , coding for lysyl and arginyl tRNA synthetases, respectively. The QSP model well characterized all bacterial outcomes of the seven strains simultaneously, which f T>MIC could not. ### Competing Interest Statement The authors have declared no competing interest.