Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 18 1 2026 02 14 1 13 Samira Saedi Department of Medical Microbiology, Khalkhal University of Medical Sciences, Khalkhal, Iran Javad Nezhadi Department of Medical Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran Hadi Feizi Deparment of Medical Microbiology, Alinasab Hospital, Sccial Security Organization, Tabriz, Iran Mohammad Yousef Memar Infectious and Tropical Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran Vahid Arefi Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran Hiva Kadkhoda Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Microbiology, Mahabad Faculty of Medical Sciences, Urmia University of Medical Sciences, Urmia, Iran 2025 08 21 2026 01 08 Background and Objectives: Klebsiella pneumoniae is a major cause of healthcare-associated infections, particularly in immunocompromised patients. This study compares the CRISPR systems, virulence factors, and antibiotic resistance genes in carbapenem-sensitive (CSKP) and carbapenem-resistant (CRKP) clinical isolates. Materials and Methods: Carbapenemase-producing isolates were identified by mCIM/eCIM. PCR and RT-qPCR detected key genes, including cas3, involved in CRISPR-Cas function. In silico analyses included STRING for protein interactions, CRISPRCasdb for CRISPR subtype distribution, and Phyre2/AlphaFold for cas3 structure prediction. Results: Among the isolates, 35.2% were resistant to carbapenems. Among CRKP strains, high prevalence of bla-NDM-1 (82%) and bla-OXA-48 (64%) was observed. The cas3 expression was significantly upregulated in resistant isolates (P = 0.002). CRISPR subtype I-E was identified in 16% of CRKP and 36% of CSKP isolates. Structural-functional analysis supported the integrity of Cas3 and revealed interactions with regulatory and iron acquisition proteins. Statistically significant differences in virulence and resistance gene profiles were found between CRKP and CSKP groups (P < 0.05). Conclusion: This study highlights key differences between CRKP and CSKP isolates, particularly in CRISPR-Cas systems, resistance, and virulence. The findings suggest that cas3 plays a critical role in genomic adaptation and resistance mechanisms in K. pneumoniae, offering insights for future therapeutic strategies. https://ijm.tums.ac.ir/index.php/ijm/article/view/5720 https://ijm.tums.ac.ir/index.php/ijm/article/download/5720/1856