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. 2020 Aug;12(8):4014-4024.
doi: 10.21037/jtd-20-1232.

Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis

Peixin Chen  1   2 , Wenwen Sun  3 , Yayi He  1
Affiliations

Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB/RIF assay in the diagnosis of tuberculosis

Peixin Chen et al. J Thorac Dis. 2020 Aug.

Abstract

Background: With a high incidence rate and mortality rate, tuberculosis (TB) is a major public health concern worldwide. There is an urgent need to develop the rapid, reliable and affordable diagnostic test for the detection of Mycobacterium tuberculosis (Mtb). Metagenomic next-generation sequencing (mNGS) showed promising values in the rapid diagnosis of clinical TB, while studies on the application of mNGS in pulmonary and extrapulmonary TB remain scarce.

Methods: In this study, we collected the results of both mNGS and culture of 70 specimens from suspected TB patients at the Shanghai Pulmonary Hospital of Tongji University. Results of GeneXpert MTB/RIF assay (Xpert) were obtained from 19 patients. We also assessed the diagnostic performance, relationship and consistency between mNGS, traditional culture method, and Xpert.

Results: Overall, 36 of 70 suspected patients were finally diagnosed with TB. The sensitivity, specificity, positive predictive value, negative predictive value and the Youden index of mNGS in all clinical TB specimens were calculated as 66.7% (95% CI: 0.489-0.809), 97.1% (95% CI: 0.829-0.998), 96.0% (95% CI: 0.777-0.998), 73.3% (95% CI: 0.578-0.849), 63.8%, respectively. The sensitivity of mNGS was much superior to that of conventional culture method (66.7%, 95% CI: 0.489-0.809 vs. 36.1%, 95% CI: 0.213-0.538) and Xpert (76.9%, 95% CI: 0.460-0.938 vs. 61.5%, 95% CI: 0.323-0.849). In pulmonary TB cases, mNGS, culture, and Xpert all demonstrated better diagnostic capacity for TB when compared with extrapulmonary TB cases. Among all methods and sample classifications, the Youden index of parallel diagnostic test in pulmonary samples was outstanding (mNGS/culture 88.2%; mNGS/Xpert 100%). Furthermore, the correlation and concordance between mNGS and culture method in all types of specimens was statistically significant (both P<0.001).

Conclusions: With high sensitivity and specificity, mNGS showed remarkable diagnostic performance in various samples from suspected TB patients. Combining mNGS and culture or Xpert method had the potential for clinical application in TB.

Keywords: GeneXpert MTB/RIF assay (Xpert); Metagenomic next-generation sequencing (mNGS) technology; Mycobacterium tuberculosis (Mtb); culture method; tuberculosis (TB).

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Conflict of interest statement

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/jtd-20-1232). The authors have no conflicts of interest to declare.

Figures

Figure 1
Figure 1
Study flowchart showing patient enrollment.
Figure 2
Figure 2
Venn diagrams in different classification of clinical samples. (A) The same Mtb outcomes of both mNGS and culture method were observed in 29 of 37 cases with pulmonary samples; (B) the same Mtb outcomes of both mNGS and culture method were observed in 25 of 33 cases with extrapulmonary samples.
See this image and copyright information in PMC

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