Recurrent emergence of Klebsiella pneumoniae carbapenem resistance mediated by an inhibitory ompK36 mRNA secondary structure

Abstract

Outer membrane porins in Gram-negative bacteria facilitate antibiotic influx. In Klebsiella pneumoniae , modifications in the porin OmpK36 are implicated in increasing resistance to carbapenems. An analysis of large K. pneumoniae genome collections, encompassing major healthcare-associated clones, revealed the recurrent emergence of a synonymous cytosine-to-thymine transition at position 25 (25c > t) in ompK36. We show that the 25c > t transition increases carbapenem resistance through depletion of OmpK36 from the outer membrane. The mutation attenuates K. pneumoniae in a murine pneumonia model, which accounts for its limited clonal expansion observed by phylogenetic analysis. However, in the context of carbapenem treatment, the 25c > t transition tips the balance toward treatment failure, thus accounting for its recurrent emergence. Mechanistically, the 25c > t transition mediates an intramolecular messenger RNA (mRNA) interaction between a uracil encoded by 25t and the first adenine within the Shine–Dalgarno sequence. This specific interaction leads to the formation of an RNA stem structure, which obscures the ribosomal binding site thus disrupting translation. While mutations reducing OmpK36 expression via transcriptional silencing are known, we uniquely demonstrate the repeated selection of a synonymous ompK36 mutation mediating translational suppression in response to antibiotic pressure.

Insight into the Mechanisms of Carbapenem Resistance in Klebsiella pneumoniae: A Study on IS26 Integrons, Beta-Lactamases, Porin Modifications, and Plasmidome Analysis

“…Although our study does not directly investigate the comparative fitness or virulence of the endemic strains in Taiwan, some factors may contribute to their potential for increased robustness or risk to human health. The presence of specific resistance genes, plasmids (such as IncC), and outer membrane protein mutations (e.g., in OmpK36) may enhance the survival and adaptability of these strains in the presence of antibiotics, facilitating their persistence and transmission in various environments [ 2 , 24 ]. Additionally, certain virulence factors, such as hypermucoviscosity, siderophore production, and capsule synthesis, have been associated with increased pathogenicity in some CRKP strains [ 25 , 26 ].…”

The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance inEnterobacterales

“…The ratio of ertapenem to meropenem MIC predicts resistance mechanism better than either MIC alone, perhaps because the periplasmic permeability of ertapenem is more strongly affected by porin disruption than that of meropenem (6,44,54), while both are hydrolyzed at similar rates by carbapenemases (64,65). Predicting porin function has been a major challenge for genomic resistance prediction (66)(67)(68)(69)(70)(71), as polymorphisms are frequently found but challenging to functionally interpret. Given the differential impact of porin mutations on each carbapenem, the ertapenem-to-meropenem MIC ratio may offer a phenotypic reflection of porin function.…”

Diverse Database and Machine Learning Model to Narrow the Generalization Gap in RNA Structure Prediction

“…The first step in this module is constructing the pair representation. The one-hot encoded sequence is transformed using a Kronecker outer product (specified here [3.]) to create an LxLx17 pair representation.…”

“…Beyond its primary sequence, RNA harbors a second layer of information in its ability to form secondary structures that can conceal or expose crucial regulatory binding sites for proteins, microRNAs, and other RNAs. These secondary structures, dictated by Watson-Crick base pairings, are pivotal in RNA’s lifecycle, affecting localization, translation, degradation, and more [1, 2, 3, 4]. While X-ray crystallography, Nuclear Magnetic Resonance (NMR), and CryoEM are adept at elucidating RNA’s tertiary structure, their applicability is limited for long RNA sequences.…”

“…translation), RNA harbors a second layer of information—its ability to form secondary structures. These structures can conceal or expose crucial regulatory binding sites for proteins, microRNAs, and other RNAs [1., 2., 3., 4.]. While X-ray crystallography, Nuclear Magnetic Resonance (NMR), and CryoEM are adept at elucidating RNA’s tertiary structure, their applicability is limited for long RNA sequences (>200nt).…”