Transcriptoma associado a sobrevivência de Klebsiella pneumoniae com resistência estendida sob estresse de meropenem

Abstract

Extensively drug-resistant Klebsiella pneumoniae is an opportunistic pathogen of high clinical relevance, whose resistance to carbapenems—especially meropenem—severely compromises available therapeutic options. This study aimed to elucidate, via transcriptomic analysis, the molecular adaptation mechanisms of a carbapenemase-producing strain subjected to the minimum inhibitory concentration (MIC) of meropenem. The strain, isolated from a tracheal aspirate of an ICU patient and identified by VITEK® 2, was characterized for antibiotic susceptibility by disk diffusion, broth microdilution, and automated methods, showing MICs of 64 µg/mL for ciprofloxacin, 256 µg/mL for gentamicin, and 256 µg/mL for meropenem. After exposure to meropenem at its MIC, growth was monitored until log phase, total RNA was extracted for rRNA depletion, cDNA library preparation, and sequencing on an Illumina platform. Differential expression analysis with DESeq2 (log₂ fold change ≥ 1 or ≤ –1; p < 0.05) identified 312 modulated genes: eight transcripts were significantly upregulated—including the ribosome‐associated inhibitor A, InsK transposase (IS150), D-ribose pyranase, penicillin insensitive transglycosylase/PBP-1C, and the septation protein Maf—while four were downregulated, such as ABC transporters and the membrane protein UPF0118. Moreover, marked metabolic reprogramming was observed: enhanced lipid and phospholipid biosynthesis to maintain membrane integrity; activation of carbohydrate degradation pathways and flexibility in carbon source utilization; increased expression of amino acid metabolism enzymes (alanine, glycine, glutamine); stimulation of anaerobic energy‐generating pathways and elevated NADPH production via the pentose-phosphate pathway; and concurrent repression of DNA synthesis routes and secretion systems. These findings reveal a multifaceted adaptive strategy by which XDR K. pneumoniae restructures metabolic functions and defense mechanisms to survive intense antibiotic pressure, highlighting potential targets for pharmacological intervention.