CRISPR-Cas Based Plasmid Design for Multidrug Resistant Klebsiella Pneumoniae Isolates

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Baba S., Öncül M. O., Aktaş Z.

FEMS MICROBIOLOGY LETTERS, sa.0378-1097 , ss.1-2, 2026 (Hakemli Dergi)

Özet

Antimicrobial resistance (AMR) is a major global health concern that requires innovative therapeutic strategies. This study aimed to address this challenge by designing Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein (CRISPR-Cas)-based plasmid systems for potential genome editing applications in multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates. Minimum inhibitory concentrations (MICs) of imipenem, meropenem, and ertapenem were determined according to EUCAST guidelines. All isolates (n = 5) were resistant, with MIC ranges of 4-128 μg/mL for imipenem, 8-64 μg/mL for meropenem, and 8-256 μg/mL for ertapenem. Resistance gene analysis revealed blaOXA-48-like and blaCTX-M-15 in all isolates, while blaNDM-1 was detected in one isolate. Two CRISPR-based plasmid systems, CRISPR-Cas9 and CRISPR-assisted cytidine deaminase, were designed. Target genes were amplified by PCR, and guide RNA (gRNA) sequences were designed from selected regions. Apramycin (50 μg/mL) was identified as a suitable selection marker. The pSGKP-AmpR(Pro)-ApmR plasmid was successfully constructed, whereas Cas9 and APOBEC constructs could not be cloned. Overall, this study highlights technical challenges in developing CRISPR-based tools for MDR K. pneumoniae and emphasizes the need for isolate-specific plasmid design and gRNA optimization.