Genomic Features Associated with the Degree of Phenotypic Resistance to Carbapenems in Carbapenem-Resistant <named-content content-type='genus-species'>Klebsiella pneumoniae</named-content>

Carbapenem-resistant Klebsiella pneumoniae strains cause severe infections that are difficult to treat. The production of carbapenemases such as the K. pneumoniae carbapenemase (KPC) is a common mechanism by which these strains resist killing by the carbapenems. However, the degree of phenotypic carbapenem resistance (MIC) may differ markedly between isolates with similar carbapenemase genes, suggesting that our understanding of the underlying mechanisms of carbapenem resistance remains incomplete. To address this problem, we determined the whole-genome sequences of 166 K. pneumoniae clinical isolates resistant to meropenem, imipenem, or ertapenem. Multiple linear regression analysis of this collection of largely blaKPC-3-containing sequence type 258 (ST258) isolates indicated that blaKPC copy number and some outer membrane porin gene mutations were associated with higher MICs to carbapenems. A trend toward higher MICs was also observed with those blaKPC genes carried by the d isoform of Tn4401. In contrast, ompK37 mutations were associated with lower carbapenem MICs, and extended spectrum b-lactamase genes were not associated with higher or lower MICs in carbapenem-resistant K. pneumoniae. A machine learning approach based on the whole-genome sequences of these isolates did not result in a substantial improvement in prediction of isolates with high or low MICs. These results build upon previous findings suggesting that multiple factors influence the overall carbapenem resistance levels in carbapenem-resistant K. pneumoniae isolates. IMPORTANCE Klebsiella pneumoniae can cause severe infections in the blood, urinary tract, and lungs. Resistance to carbapenems in K. pneumoniae is an urgent public health threat, since it can make these isolates difficult to treat. While individual contributors to carbapenem resistance in K. pneumoniae have been studied, few reports explore their combined effects in clinical isolates. We sequenced 166 clinical carbapenem-resistant K. pneumoniae isolates to evaluate the contribution of known genes to carbapenem MICs and to try to identify novel genes associated with higher carbapenem MICs. The blaKPC copy number and some outer membrane porin gene mutations were associated with higher carbapenem MICs. In contrast, mutations in one specific porin, ompK37, were associated with lower carbapenem MICs. Machine learning did not result in a substantial improvement in the prediction of carbapenem resistance nor did it identify novel genes associated with carbapenem resistance. These findings enhance our understanding of the many contributors to carbapenem resistance in K. pneumoniae. Citation Bulman ZP, Krapp F, Pincus NB, Wenzler E, Murphy KR, Qi C, Ozer EA, Hauser AR. 2021. Genomic features associated with the degree of phenotypic resistance to carbapenems in carbapenem-resistant Klebsiella pneumoniae. mSystems 6:e00194-21. https://doi.org/10.1128/mSystems.00194-21. Editor Christopher W. Marshall, Marquette University Copyright © 2021 Bulman et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Zackery P. Bulman, bulman@uic.edu, or Fiorella Krapp, fiorella.krapp@upch.pe. * Present address: Fiorella Krapp, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru. * Present address: Katherine R. Murphy, Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA. Mutations in outer membrane porin genes and blaKPC copy number are associated with variations in carbapenem MICs in a large collection of clinical carbapenem-resistant Klebsiella pneumoniae isolates. Received 19 February 2021 Accepted 19 August 2021 Published September/October 2021 Volume 6 Issue 5 e00194-21 msystems.asm. org 1 RESEARCH ARTICLE