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In this study, we aimed to assess the prevalence of the CRISPR-Cas systems and their association with antibiotic resistance in one of the most challenging bacterial pathogens, <jats:italic>Klebsiella pneumoniae<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Materials and methods<\/jats:title>\n                <jats:p>A total of 105 <jats:italic>K. pneumoniae<\/jats:italic> isolates were collected from various clinical infections. Extended-spectrum \u03b2-lactamases (ESBLs) phenotypically were detected and the presence of ESBL, aminoglycoside-modifying enzymes (AME), and CRISPR-Cas system subtype genes were identified using PCR. Moreover, the diversity of the isolates was determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Phenotypically, 41.9% (44\/105) of the isolates were found to be ESBL producers. A significant inverse correlation existed between the subtype I-E CRISPR-Cas system\u2019s presence and ESBL production in <jats:italic>K. pneumoniae<\/jats:italic> isolates. Additionally, the frequency of the ESBL genes <jats:italic>bla<\/jats:italic><jats:sub><jats:italic>CTX\u2212M1<\/jats:italic><\/jats:sub> (3%), <jats:italic>bla<\/jats:italic><jats:sub><jats:italic>CTX\u2212M9<\/jats:italic><\/jats:sub> (12.1%), <jats:italic>bla<\/jats:italic><jats:sub><jats:italic>SHV<\/jats:italic><\/jats:sub> (51.5%), and <jats:italic>bla<\/jats:italic><jats:sub><jats:italic>TEM<\/jats:italic><\/jats:sub> (33.3%), as well as some AME genes such as <jats:italic>aac(3)-Iva<\/jats:italic> (21.2%) and <jats:italic>ant(2\u2019\u2019)-Ia<\/jats:italic> (3%) was significantly lower in the isolates with the subtype I-E CRISPR-Cas system in comparison to CRISPR-negative isolates. There was a significant inverse correlation between the presence of ESBL and some AME genes with subtype I-E CRISPR-Cas system.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The presence of the subtype I-E CRISPR-Cas system was correlated with the antibiotic-resistant gene (ARGs). The isolates with subtype I-E CRISPR-Cas system had a lower frequency of ESBL genes and some AME genes than CRISPR-negative isolates.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12879-024-09451-5","type":"journal-article","created":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T13:02:01Z","timestamp":1717419721000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Prevalence of the CRISPR-cas system and its association with antibiotic resistance in clinical Klebsiella pneumoniae isolates"],"prefix":"10.1186","volume":"24","author":[{"given":"Hiva","family":"Kadkhoda","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pourya","family":"Gholizadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reza","family":"Ghotaslou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tahereh","family":"Pirzadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Ahangarzadeh Rezaee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edris","family":"Nabizadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hadi","family":"Feizi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hossein","family":"Samadi Kafil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Aghazadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,6,3]]},"reference":[{"issue":"9","key":"9451_CR1","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1038\/nrmicro1235","volume":"3","author":"LS Frost","year":"2005","unstructured":"Frost LS, Leplae R, Summers AO, Toussaint A. 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