Investigate the Relationship between the Presence of the CRISPR-Cas System and Antimicrobial Resistance in Klebsiella pneumoniae

Abstract BACKGROUND: The CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) serves as an adaptive immune defense mechanism in Klebsiella pneumoniae . The aim of the study was to evaluate the correlation between the presence of the CRISPR-Cas system and antimicrobial resistance profiles in K. pneumoniae isolates. METHODS: This study included patients of all ages and genders, with histories recorded (name, age, gender, and sample type blood, sputum, and urine) and conducted at Al-Hilla Teaching Hospitals, Babylon City (February–August 2024); 200 clinical samples were cultured on various media and identified through biochemical tests and VITEK®2. Antibiotic susceptibility was assessed using the Kirby–Bauer method per CLSI 2024 guidelines. Tested antibiotics included imipenem, augmentin, amikacin, tetracycline, ceftriaxone, gentamicin, chloramphenicol, cefotaxime, ceftazidime, and colistin. DNA was extracted using a Geneaid kit, and polymerase chain reaction detected Cas1A and Cas1B genes with specific primers. Statistical analyses were performed using IBM SPSS Statistics, version 25.0 (IBM Corp., Armonk, NY, USA). Data were presented in the form of tables, charts, and graphs. A P < 0.05 was considered statistically significant. Categorical variables were compared using t -tests, while Pearson’s correlation coefficient ( r ) was used to assess associations. RESULTS: The present study analyzed 200 clinical samples (blood, sputum, and urine) from Al-Hillah Teaching Hospital, identifying K. pneumoniae in 12.5% of cases, aligning with previous studies. Molecular detection confirmed CRISPR-Cas systems, with Cas1 type A in 68% and Cas1 type B in 60% of isolates. Antibiotic susceptibility testing revealed multidrug resistance, though isolates with CRISPR-Cas Type I-E showed higher susceptibility to antibiotics such as amikacin, aztreonam, and imipenem ( P ≤ 0.01). The CRISPR-Cas system appears to limit horizontal gene transfer of resistance genes but does not fully mitigate intrinsic resistance, underscoring its complex role in antimicrobial resistance management. CONCLUSIONS: This study highlights CRISPR-Cas systems’ role in K. pneumoniae , with Cas1 type A and Cas1 type B detected in 68% and 60% of isolates, respectively. CRISPR-Cas Type I-E isolates showed increased susceptibility to amikacin, aztreonam, and imipenem, suggesting a potential role in resistance gene modulation and antimicrobial resistance management.