CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital
(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) <i>Klebsiella pneumoniae</i> is a major public health concern, and the role of CRISPR-Cas in its resistance is unde...
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MDPI AG
2025-06-01
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| author | Ivana Jurić Marko Jelić Manda Markanović Lucija Kanižaj Zrinka Bošnjak Ana Budimir Tomislav Kuliš Arjana Tambić-Andrašević Ivana Ivančić-Baće Ivana Mareković |
| author_facet | Ivana Jurić Marko Jelić Manda Markanović Lucija Kanižaj Zrinka Bošnjak Ana Budimir Tomislav Kuliš Arjana Tambić-Andrašević Ivana Ivančić-Baće Ivana Mareković |
| author_sort | Ivana Jurić |
| collection | DOAJ |
| description | (1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) <i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i>. (2) Methods: 400 <i>K. pneumoniae</i> isolates (200 CR and 200 carbapenem susceptible (CS)) were analyzed. Carbapenemase genes (<i>bla</i><sub>OXA-48</sub>, <i>bla</i><sub>NDM-1</sub>, <i>bla</i><sub>KPC-2</sub>), <i>cas1</i>, <i>rpoB</i>, 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’s 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. <i>bla</i><sub>OXA-48</sub> was linked to CRISPR-Cas-negative strains, while <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>KPC-2</sub> were more frequent in CRISPR-Cas-positive strains (<i>p</i> < 0.0001). Imipenem/relebactam resistance was higher in CRISPR-Cas-negative isolates. (4) Conclusions: <i>K. pneumoniae</i> CRISPR-Cas systems correlate with specific carbapenemase profiles, suggesting pressure against <i>bla</i><sub>OXA-48</sub> 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. |
| format | Article |
| id | doaj-art-f6bfe6ffca6e4d4c9aa4c12e1dadbf89 |
| institution | OA Journals |
| issn | 2076-0817 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj-art-f6bfe6ffca6e4d4c9aa4c12e1dadbf892025-08-20T02:21:52ZengMDPI AGPathogens2076-08172025-06-0114660410.3390/pathogens14060604CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary HospitalIvana Jurić0Marko Jelić1Manda Markanović2Lucija Kanižaj3Zrinka Bošnjak4Ana Budimir5Tomislav Kuliš6Arjana Tambić-Andrašević7Ivana Ivančić-Baće8Ivana Mareković9Clinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, CroatiaDepartment of Clinical Microbiology, University Hospital for Infectious Diseases “Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, CroatiaClinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, CroatiaClinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, CroatiaClinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, CroatiaClinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, CroatiaDepartment of Urology, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, CroatiaDepartment of Clinical Microbiology, University Hospital for Infectious Diseases “Fran Mihaljević”, Mirogojska 8, 10000 Zagreb, CroatiaMolecular Biology Department, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, CroatiaClinical Microbiology, Infection Prevention and Control Department, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) <i>Klebsiella pneumoniae</i> 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 <i>K. pneumoniae</i>. (2) Methods: 400 <i>K. pneumoniae</i> isolates (200 CR and 200 carbapenem susceptible (CS)) were analyzed. Carbapenemase genes (<i>bla</i><sub>OXA-48</sub>, <i>bla</i><sub>NDM-1</sub>, <i>bla</i><sub>KPC-2</sub>), <i>cas1</i>, <i>rpoB</i>, 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’s 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. <i>bla</i><sub>OXA-48</sub> was linked to CRISPR-Cas-negative strains, while <i>bla</i><sub>NDM-1</sub> and <i>bla</i><sub>KPC-2</sub> were more frequent in CRISPR-Cas-positive strains (<i>p</i> < 0.0001). Imipenem/relebactam resistance was higher in CRISPR-Cas-negative isolates. (4) Conclusions: <i>K. pneumoniae</i> CRISPR-Cas systems correlate with specific carbapenemase profiles, suggesting pressure against <i>bla</i><sub>OXA-48</sub> 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.https://www.mdpi.com/2076-0817/14/6/604<i>Klebsiella pneumoniae</i>CRISPR-Cas systemCRISPR locisubtypes I-E and I-E*carbapenemase genescarbapenem resistance |
| spellingShingle | Ivana Jurić Marko Jelić Manda Markanović Lucija Kanižaj Zrinka Bošnjak Ana Budimir Tomislav Kuliš Arjana Tambić-Andrašević Ivana Ivančić-Baće Ivana Mareković CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital Pathogens <i>Klebsiella pneumoniae</i> CRISPR-Cas system CRISPR loci subtypes I-E and I-E* carbapenemase genes carbapenem resistance |
| title | CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital |
| title_full | CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital |
| title_fullStr | CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital |
| title_full_unstemmed | CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital |
| title_short | CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible <i>Klebsiella pneumoniae</i> Clinical Isolates from a Croatian Tertiary Hospital |
| title_sort | crispr cas dynamics in carbapenem resistant and carbapenem susceptible i klebsiella pneumoniae i clinical isolates from a croatian tertiary hospital |
| topic | <i>Klebsiella pneumoniae</i> CRISPR-Cas system CRISPR loci subtypes I-E and I-E* carbapenemase genes carbapenem resistance |
| url | https://www.mdpi.com/2076-0817/14/6/604 |
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