CRISPR-based rapid and ultra-sensitive diagnostic test for Mycobacterium tuberculosis

Emerg Microbes Infect. 2019;8(1):1361-1369. doi: 10.1080/22221751.2019.1664939.

Abstract

Rapid and simple-to-use diagnostic methods for tuberculosis are urgently needed. Recent development has unveiled the diagnostic power of the CRISPR system in the detection of viral infections. However, its potential use in detecting the Mycobacterium tuberculosis complex (MTB) remained unexplored. We developed a rapid CRISPR-based assay for TB detection and conducted a retrospective cohort study of 179 patients to evaluate the CRISPR-MTB test for identifying MTB in various forms of direct clinical samples. Its diagnostic performance was compared, in parallel with culture and the GeneXpert MTB/RIF assay (Xpert). The CRISPR-MTB test is highly sensitive with a near single-copy sensitivity, demands less sample input and offers shorter turnaround time than Xpert. When evaluated in the clinical cohort of both pulmonary and extra-pulmonary tuberculosis, the CRISPR-MTB test exhibited an overall improved sensitivity over both culture (79% vs 33%) and Xpert (79% vs 66%), without comprise in specificity (62/63, 98%). The CRISPR-MTB test exhibits an improved overall diagnostic performance over culture and Xpert across a variety of sample types, and offers great potential as a new diagnostic technique for both pulmonary and extra-pulmonary tuberculosis.

Keywords: complex (MTB); CRISPR-MTB; GeneXpert MTB/RIF; diagnosis; tuberculosis.

MeSH terms

  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Humans
  • Molecular Diagnostic Techniques*
  • Mycobacterium tuberculosis / genetics
  • Mycobacterium tuberculosis / isolation & purification*
  • Reagent Kits, Diagnostic / standards
  • Retrospective Studies
  • Sensitivity and Specificity
  • Sputum / microbiology
  • Tuberculosis / diagnosis*
  • Tuberculosis / microbiology
  • Tuberculosis, Pulmonary / diagnosis*
  • Tuberculosis, Pulmonary / microbiology

Substances

  • Reagent Kits, Diagnostic

Grants and funding

This work was supported by the New and Advanced Technology Project of Shanghai Municipal Hospital: Application of next generation sequencing technique in precise diagnosis of infectious diseases under Grant SHDC12017104; Key Technologies Research and Development Program for Infectious Diseases of China under Grant 2018ZX10305-409-001-003; Active Design Project of Hangzhou Science and Technology Bureau under Grant 20162013A04; and the Joint Medical Research Program of Shanghai Jing’an District Science and Technology Commission and Health Commission under grant number 2016QN02.