基于ERA-CRISPR/Cas12a的肺炎克雷伯菌检测方法的建立

Establishment of a detection method for Klebsiella pneumoniae based on ERA-CRISPR/Cas12a

  • 摘要: 目的 建立一种基于酶促重组等温扩增-成簇规律间隔短回文重复序列Cas12a蛋白(ERA-CRISPR/Cas12a)的肺炎克雷伯菌(KP)核酸检测方法。方法 针对KP(fimI)基因设计3条CRISPR RNA(crRNA),以含该基因的质粒为模板进行ERA扩增,通过CRISPR/Cas12a荧光反应筛选出最佳的crRNA。设计3对靶序列的ERA引物并构建9组引物组合,从中筛选出一组作为ERA-CRISPR/Cas12a反应的最佳引物,结合消线法核酸检测试纸技术(ERASE)建立完整检测体系。以十倍梯度稀释的fimI基因质粒为模板检测方法灵敏度; 同时对KP和其他4种临床常见革兰阴性杆菌进行检测评价其特异性; 检测34株临床分离株核酸,并与荧光定量PCR(qPCR)结果对比。结果 成功建立ERA-CRISPR/Cas12a检测体系,灵敏度试验中,质粒模板的荧光检测最低检出限(LOD)为1 copy/μl,ERASE试纸为10 copies/μl,均优于qPCR(100 copies/μl); 特异性试验中,仅KP检测结果呈阳性; 34株临床分离株中30株KP均被检出,与qPCR结果一致。结论 本研究成功建立了一种简便、经济且兼具高灵敏度与高特异性的KP核酸检测方法,该方法适用于经济欠发达地区的基层卫生机构开展核酸检测工作。

     

    Abstract: OBJECTIVE To establish a nucleic acid detection method for Klebsiella pneumoniae (KP) based on enzymatic recombinant isothermal amplification - clustered regularly interspaced short palindromic repeats (ERA-CRISPR/Cas12a) protein. METHODS Three CRISPR RNAs (crRNAs) were designed for KP (fimI) gene. The plasmids containing the KP gene were used as templates for ERA amplification, and the best crRNA was selected by CRISPR/Cas12a fluorescence reaction. Three pairs of ERA primers were designed and 9 primer combinations were constructed. One set of primers was selected as the best one for ERA-CRISPR/Cas12a reaction. A complete detection system was established by combining the easy-readout and sensitive enhanced (ERASE) nucleic acid test strip technology. Tenfold gradient dilution of fimI gene plasmid was used as a template to detect the sensitivity of the method. At the same time, the specificity of the method in detection of KP and other four types of common gram-negative bacilli was evaluated. The nucleic acid test was performed for 34 clinical isolates, and the result was compared with the result of quantitative real-time PCR (qPCR). RESULTS The ERA-CRISPR/Cas12a detection system was successfully established. The result of sensitivity experiment showed that the minimum detection limit of detection (LOD) of the plasmid template was 1 copy/μl, with the ERASE dipstick 10 copies/μl, both were superior to qPCR (100 copies/μl). The result of the specificity test showed that only KP was tested positive. All of the KP strains were detected from the 34 clinical isolates, which was consistent with the results of qPCR. CONCLUSIONS A simple, economical, highly sensitive and specific nucleic acid detection method is successfully established for KP. The method is suitable for nucleic acid detection in primary health institutions in economically underdeveloped areas.

     

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