Development of detection method of Klebsiella pneumoniae based on digital LAMP-CRISPR/Cas12b
10.3760/cma.j.cn112309-20240531-00188
- VernacularTitle:基于数字LAMP-CRISPR/Cas12b的肺炎克雷伯菌检测方法的建立
- Author:
Shuting SUN
1
;
Tianchi ZHUANG
;
Yingqi YANG
;
Ning LI
;
Quan WANG
;
Minghui JI
Author Information
1. 南京医科大学第二临床医学院，南京 210011
- Publication Type:Journal Article
- Keywords:
Klebsiella pneumoniae;
Digital loop-mediated isothermal amplification (LAMP);
CRISPR;
Cas12b
- From:
Chinese Journal of Microbiology and Immunology
2025;45(6):485-492
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To develop a rapid, sensitive, and quantitative method for detecting Klebsiella pneumoniae using digital loop-mediated isothermal amplification(LAMP)-CRISPR/Cas12b. Methods:Five LAMP primers targeting the Kp-1 gene of Klebsiella pneumoniae and guide RNA (gRNA) for Cas12b were designed. The digital LAMP-CRISPR/Cas12b reaction mixture included 1×WarmStart ? LAMP master mix, 1×LAMP primers, 250 nmol/L Cas12b, 250 nmol/L gRNA, 3 μmol/L ssDNA reporter, 1 000 U/ml RNase inhibitor, 4 mmol/L Mg 2+, and DEPC water. After preparing the digital chip, it was incubated at 60℃ for one hour. Fluorescence distribution was then detected using a biochip analyzer to calculate the input DNA concentration. The specificity of the method was tested using genomic DNA from seven pathogenic microorganisms. The quantitative performance was assessed using serial dilutions of Klebsiella pneumoniae DNA ranging from 5-500 000 copies/μl. Clinical sputum samples were collected for comparison of quantitative performance with qPCR and qualitative performance with culture methods. Results:The digital LAMP-CRISPR/Cas12b method showed high specificity, yielding negative results for all six non-target pathogens. Quantitative performance tests indicated a sensitivity as low as 5 copies/μl, with a linear dynamic range of 5-50 000 copies/μl ( R2=0.927 4). Clinical sample quantitative testing showed that the correlation coefficient between digital LAMP-CRISPR/Cas12b and qPCR quantification was 0.917 0. Compared with the culture results of 72 samples, this method had a sensitivity of 100% and detected two additional samples with negative culture result, with a specificity of 91%; Compared with the culture method, qPCR had a sensitivity of 96% and a specificity of 83%. These results indicated that the digital LAMP-CRISPR/Cas12b method had good quantitative and qualitative detection performance for clinical sputum samples. Conclusions:This method offers advantages over qPCR, including rapidity, simplicity, and high precision. The digital LAMP-CRISPR/Cas12b method enables absolute quantification of Klebsiella pneumoniae in sputum samples, enhancing the accuracy of early screening for Klebsiella pneumoniae infections. These advantages make digital LAMP-CRISPR/Cas12b technology highly promising for the precise diagnosis of pathogenic microorganisms in field detection, primary healthcare, and resource-limited environments.
