TB-QUICK: CRISPR-Cas12b-assisted rapid and sensitive detection of Mycobacterium tuberculosis

I Kuan Sam; Ying-Ying Chen; Jun Ma; Shi-Yuan Li; Ruo-Yan Ying; Lin-Xian Li; Ping Ji; Shu-Jun Wang; Jie Xu; Yu-Jie Bao; Guo-Ping Zhao; Hua-Jun Zheng; Jin Wang; Wei Sha; Ying Wang

doi:10.1016/j.jinf.2021.04.032

TB-QUICK: CRISPR-Cas12b-assisted rapid and sensitive detection of Mycobacterium tuberculosis

J Infect. 2021 Jul;83(1):54-60. doi: 10.1016/j.jinf.2021.04.032. Epub 2021 May 2.

Authors

I Kuan Sam¹, Ying-Ying Chen¹, Jun Ma², Shi-Yuan Li³, Ruo-Yan Ying², Lin-Xian Li⁴, Ping Ji¹, Shu-Jun Wang¹, Jie Xu⁵, Yu-Jie Bao⁵, Guo-Ping Zhao⁶, Hua-Jun Zheng⁷, Jin Wang⁸, Wei Sha⁹, Ying Wang¹⁰

Affiliations

¹ Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
² Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China.
³ Shanghai TOLO Biotechnology Company Limited, Shanghai 200233, China.
⁴ Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China.
⁵ Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
⁶ Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200032, China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
⁷ Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.
⁸ Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China. Electronic address: wangj01@hotmail.com.
⁹ Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China. Electronic address: shfksw@126.com.
¹⁰ Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100), Shanghai, China. Electronic address: ywang@sibs.ac.cn.

PMID: 33951419
DOI: 10.1016/j.jinf.2021.04.032

Abstract

Objectives: Tuberculosis (TB) remains one of the public health problems worldwide. Rapid, sensitive and cost-effective diagnosis of Mycobacterium tuberculosis (M.tb) is critical for TB control.

Methods: We developed a novel M.tb DNA detection platform (nominated as TB-QUICK) which combined loop-mediated isothermal amplification (LAMP) and CRISPR-Cas12b detection. TB-QUICK was performed on pulmonary or plasma samples collected from 138 pulmonary TB (PTB) patients, 21 non-TB patients and 61 close contacts to TB patients. Acid-fast bacillus (AFB) smear, M.tb culture and GeneXpert MTB/RIF (Xpert) assays were routinely conducted in parallel.

Results: By targeting M.tb IS6110, TB-QUICK platform could detect as low as 1.3 copy/μL M.tb DNA within 2 h. In pulmonary TB samples, TB-QUICK exhibited improved overall sensitivity of 86.8% over M.tb culture (66.7%) and Xpert (70.4%), with the specificity of 95.2%. More significantly, TB-QUICK exhibited a superior sensitivity in AFB-negative samples (80.5%) compared to Xpert (57.1%) and M.tb culture (46.2%). In the detection of plasma M.tb DNA by TB-QUICK, 41.2% sensitivity for AFB-positive and 31.7% for AFB-negative patients were achieved.

Conclusion: In conclusion, TB-QUICK exhibits rapidity and sensitivity for M.tb DNA detection with the superiority in smear-negative paucibacillary TB patients. The clinical application of TB-QUICK in TB diagnosis needs to be further validated in larger cohort.

Keywords: CRISPR-Cas12b; Diagnosis; IS6110; Mycobacterium tuberculosis; TB-QUICK; Tuberculosis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Clustered Regularly Interspaced Short Palindromic Repeats
Humans
Molecular Diagnostic Techniques
Mycobacterium tuberculosis* / genetics
Nucleic Acid Amplification Techniques
Rifampin
Sensitivity and Specificity
Sputum
Tuberculosis*

Substances

Rifampin

Supplementary concepts

LAMP assay