Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics

Abstract

In this era of rising antibiotic resistance, in contrast to our increasing understanding of mechanisms that cause resistance, our understanding of mechanisms that influence the propensity to evolve resistance remains limited. Here, we identified genetic factors that facilitate the evolution of resistance to carbapenems, the antibiotic of 'last resort,' in Klebsiella pneumoniae, the major carbapenem resistant species. In clinical isolates, we found that high-level transposon insertional mutagenesis plays an important role in contributing to high-level resistance frequencies in several major and emerging carbapenem-resistant lineages. A broader spectrum of resistance-conferring mutations for select carbapenems such as ertapenem also enables higher resistance frequencies and importantly, creates stepping-stones to achieve high-level resistance to all carbapenems. These mutational mechanisms can contribute to the evolution of resistance, in conjunction with the loss of systems that restrict horizontal resistance gene uptake, such as the CRISPR-Cas system. Given the need for greater antibiotic stewardship, these findings argue that in addition to considering the current efficacy of an antibiotic for a clinical isolate in antibiotic selection, considerations of future efficacy are also important. The genetic background of a clinical isolate and the exact antibiotic identity can and should also be considered as it is a determinant of a strain's propensity to become resistant. Together, these findings thus provide a molecular framework for understanding acquisition of carbapenem resistance in K. pneumoniae with important implications for diagnosing and treating this important class of pathogens.

Systematic Analysis of Mobile Genetic Elements Mediating β-lactamase Gene Amplification in Non-Carbapenemase-Producing Carbapenem Resistant Enterobacterales Bloodstream Infections

“…Our findings along with other data (43, 45, 46) suggest carbapenem non-susceptible Enterobacterales reside along a spectrum mediated to a major degree by changes in porin function and β-lactamase gene copy number. It is likely that unconfirmed CNSE consist of a heterogenous population of ESBL-positive, carbapenem-adapting strains with β-lactamase gene amplifications/porin disruptions which may give different phenotypic results depending on the particular colony tested (47).…”

New Delhi Metallo-Beta-Lactamase Facilitates the Emergence of Cefiderocol Resistance in Enterobacter cloacae

“…The idea of transposon insertional mutagenesis as a means of resistance acquisition is not completely novel but is not yet well investigated. Transposon insertional mutagenesis has been described to play an important role in contributing to high-level resistance toward ertapenem ( 27 ). In their experiments, Ma et al ( 27 ) demonstrated that a reversible transposon insertion into the ompK36 gene, encoding one of the major porins of Klebsiella pneumoniae , could be identified in ertapenem-resistant isolates.…”

“…Transposon insertional mutagenesis has been described to play an important role in contributing to high-level resistance toward ertapenem ( 27 ). In their experiments, Ma et al ( 27 ) demonstrated that a reversible transposon insertion into the ompK36 gene, encoding one of the major porins of Klebsiella pneumoniae , could be identified in ertapenem-resistant isolates. In contrast, in our case, the cefiderocol resistance was not reverted by serial passaging in the absence of antibiotic pressure, indicating the stability of the transposon insertion (data not shown).…”

“…Fitness costs associated with the transposon insertion may explain this discrepancy. In the experiments of Ma et al ( 27 ), the IS1 transposon insertion correlated with higher fitness costs such that, in the absence of antibiotic pressure, this insertion may be reverted to restore growth efficiency ( 27 ). In our case, the cirA disruption was not associated with an increased fitness cost and iron could be acquired via other means such that the mutation is not counter-selected.…”

Genomic Features Associated with the Degree of Phenotypic Resistance to Carbapenems in Carbapenem-Resistant Klebsiella pneumoniae

“…Previous studies have shown that bla ESBL genes such as bla CTX-M or bla SHV-5 in combination with outer membrane porin deficits can cause carbapenem resistance in K. pneumoniae isolates that do not coharbor carbapenemase genes ( 13 , 14 ). Similarly, bla ESBL gene duplications have been shown to increase carbapenem MICs in isolates without a carbapenemase ( 46 ). However, the present study suggests, for the first time, that neither the presence of an bla ESBL nor the bla ESBL gene copy number appreciably increases the carbapenem MICs in isolates that coharbor carbapenemase genes, which is supported by the absence of these genomic features in the final multivariate models.…”