CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible Klebsiella pneumoniae Clinical Isolates from a Croatian Tertiary Hospital.

IF 3.3 3区医学 Q2 MICROBIOLOGY

Pathogens Pub Date : 2025-06-19 DOI:10.3390/pathogens14060604

Ivana Jurić, Marko Jelić, Manda Markanović, Lucija Kanižaj, Zrinka Bošnjak, Ana Budimir, Tomislav Kuliš, Arjana Tambić-Andrašević, Ivana Ivančić-Baće, Ivana Mareković

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引用次数: 0

Abstract

(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 (bla_OXA-48, bla_NDM-1, bla_KPC-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'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. bla_OXA-48 was linked to CRISPR-Cas-negative strains, while bla_NDM-1 and bla_KPC-2 were more frequent in CRISPR-Cas-positive strains (p < 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 bla_OXA-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.

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克罗地亚某三级医院耐碳青霉烯和敏感碳青霉烯肺炎克雷伯菌临床分离株的CRISPR-Cas动态

(1)背景：CRISPR-Cas系统对携带抗菌素耐药性（AMR）基因的移动遗传元件（MGEs）提供适应性免疫。耐碳青霉烯（CR）肺炎克雷伯菌是一个主要的公共卫生问题，CRISPR-Cas在其耐药中的作用尚未得到充分研究。本研究探讨了CRISPR-Cas与临床肺炎克雷伯菌多药耐药的关系。(2)方法：对400株肺炎克雷伯菌（200株CR和200株碳青霉烯类敏感菌）进行分析。碳青霉烯酶基因（blaOXA-48、blaNDM-1、blaKPC-2）、cas1、rpoB和CRISPR -1位点通过PCR鉴定，仅对CRISPR位点进行测序。通过PFGE、MLST和间隔分析评估遗传相关性。统计分析采用卡方检验和费雪精确检验。(3)结果：15.8%的分离株中存在CRISPR-Cas，主要为I-E和I-E*亚型（93.3%），其中CRISPR3位点的间隔多样性最大。克隆复合物ST14/15/101 （CR）和ST35 （CS）得到鉴定。blaOXA-48与crispr - cas阴性菌株相关，blaNDM-1和blaKPC-2在crispr - cas阳性菌株中更常见（p < 0.0001）。crispr - cas阴性菌株对亚胺培南/relebactam的耐药性较高。(4)结论：肺炎克雷伯菌CRISPR-Cas系统与特异性碳青霉烯酶谱相关，提示抗blaOXA-48获取的压力。I-E和I-E*亚型的共存突出了靶向MGEs的协同作用。CRISPR基因座可以作为MLST后生物分型的工具。

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来源期刊

Pathogens Medicine-Immunology and Allergy

CiteScore

6.40

自引率

8.10%

发文量

1285

审稿时长

17.75 days

期刊介绍： Pathogens (ISSN 2076-0817) publishes reviews, regular research papers and short notes on all aspects of pathogens and pathogen-host interactions. There is no restriction on the length of the papers. Our aim is to encourage scientists to publish their experimental and theoretical research in as much detail as possible. Full experimental and/or methodical details must be provided for research articles.