{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T22:08:32Z","timestamp":1790114912537,"version":"4.0.1"},"reference-count":40,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T00:00:00Z","timestamp":1750291200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"School of Medicine, University of Zagreb","award":["10106-24-1295"],"award-info":[{"award-number":["10106-24-1295"]}]},{"name":"School of Medicine, University of Zagreb","award":["20286539"],"award-info":[{"award-number":["20286539"]}]},{"name":"Faculty of Science, University of Zagreb","award":["10106-24-1295"],"award-info":[{"award-number":["10106-24-1295"]}]},{"name":"Faculty of Science, University of Zagreb","award":["20286539"],"award-info":[{"award-number":["20286539"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) Klebsiella pneumoniae is a major public health concern, and the role of CRISPR-Cas in its resistance is understudied. This study explored CRISPR-Cas associations with multidrug resistance in clinical K. pneumoniae. (2) Methods: 400 K. pneumoniae isolates (200 CR and 200 carbapenem susceptible (CS)) were analyzed. Carbapenemase genes (blaOXA-48, blaNDM-1, blaKPC-2), cas1, rpoB, and CRISPR1-3 loci were identified by PCR, while only CRISPR loci were sequenced. Genetic relatedness was assessed via PFGE, MLST, and spacer analysis. Statistical analysis utilized chi-squared and Fisher\u2019s exact tests. (3) Results: CRISPR-Cas was present in 15.8% of isolates, mainly subtypes I-E and I-E* (93.3%), with CRISPR3 loci showing the greatest spacer diversity. Clonal complexes ST14\/15\/101 (CR) and ST35 (CS) were identified. blaOXA-48 was linked to CRISPR-Cas-negative strains, while blaNDM-1 and blaKPC-2 were more frequent in CRISPR-Cas-positive strains (p &lt; 0.0001). Imipenem\/relebactam resistance was higher in CRISPR-Cas-negative isolates. (4) Conclusions: K. pneumoniae CRISPR-Cas systems correlate with specific carbapenemase profiles, suggesting pressure against blaOXA-48 acquisition. The coexistence of I-E and I-E* subtypes highlight synergies in targeting MGEs. CRISPR loci could be tools for subtyping organisms following MLST.<\/jats:p>","DOI":"10.3390\/pathogens14060604","type":"journal-article","created":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T06:11:07Z","timestamp":1750313467000},"page":"604","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible Klebsiella pneumoniae Clinical Isolates from a Croatian Tertiary Hospital"],"prefix":"10.3390","volume":"14","author":[{"given":"Ivana","family":"Juri\u0107","sequence":"first","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3554-3668","authenticated-orcid":false,"given":"Marko","family":"Jeli\u0107","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, University Hospital for Infectious Diseases \u201cFran Mihaljevi\u0107\u201d, Mirogojska 8, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manda","family":"Markanovi\u0107","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucija","family":"Kani\u017eaj","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zrinka","family":"Bo\u0161njak","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"},{"name":"School of Medicine, University of Zagreb, \u0160alata 3, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Budimir","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"},{"name":"School of Medicine, University of Zagreb, \u0160alata 3, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0895-5691","authenticated-orcid":false,"given":"Tomislav","family":"Kuli\u0161","sequence":"additional","affiliation":[{"name":"Department of Urology, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6232-1465","authenticated-orcid":false,"given":"Arjana","family":"Tambi\u0107-Andra\u0161evi\u0107","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, University Hospital for Infectious Diseases \u201cFran Mihaljevi\u0107\u201d, Mirogojska 8, 10000 Zagreb, Croatia"},{"name":"School of Medicine, University of Zagreb, \u0160alata 3, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2018-3150","authenticated-orcid":false,"given":"Ivana","family":"Ivan\u010di\u0107-Ba\u0107e","sequence":"additional","affiliation":[{"name":"Molecular Biology Department, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivana","family":"Marekovi\u0107","sequence":"additional","affiliation":[{"name":"Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Ki\u0161pati\u0107eva 12, 10000 Zagreb, Croatia"},{"name":"School of Medicine, University of Zagreb, \u0160alata 3, 10000 Zagreb, Croatia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,19]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Tang, M., Kong, X., Hao, J., and Liu, J. 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