The Value of Single-Molecule Nanopore DNA Sequencing in the Clinical Diagnosis of Suspected Tuberculosis Patients.

Abstract

Background: Early diagnosis of Mycobacterium tuberculosis (MTB) infection is of great significance for the clinical management of tuberculosis (TB). We first explored the efficacy of single-molecule nanopore DNA sequencing in the early diagnosis of suspected TB patients and analyzed the advantages in differentiating and diagnosing MTB and non-tuberculous Mycobacteria (NTM).

Methods: In this cohort study, we reviewed the clinical data of suspected TB patients admitted from December 1, 2021, through April 15, 2022. All patients underwent 3 - 6 times acid-fast bacilli smear examinations of sputum, all of which were negative. To make a definitive diagnosis, we extracted specimens from the patients and performed specimen culture, Xpert MTB/Rif assay, and single-molecule nanopore DNA sequencing. The efficacy of different diagnostic methods in diagnosing suspected TB patients was compared using "Diagnostic Criteria for Pulmonary Tuberculosis" (WS288-2017) as the gold standard.

Results: Among the 25 patients, 15 were infected with MTB, 5 were infected with NTM, 1 had mixed MTB and NTM infection, and 4 were negative. The accuracy of single-molecule nanopore DNA sequencing in diagnosing mycobacterial infection (MTB + NTM) was 92.0%, with a sensitivity of 90.5% and a specificity of 100%; the accuracy of diagnosing MTB infection was also 92.0%, with a sensitivity of 87.5% and a specificity of 100%. Single-molecule nanopore DNA sequencing showed an accuracy of 100% in differentiating MTB and NTM. However, the diagnostic accuracy and sensitivity of specimen culture and Xpert MTB/Rif assay were relatively low (≤ 52%) compared to "specimen culture + Xpert MTB/Rif assay". The diagnostic efficacy of single-molecule nanopore DNA sequencing was not affected by the source of tissue samples, while specimen culture and Xpert MTB/Rif assay could not diagnose mycobacterial infection using extrapulmonary specimens.

Conclusions: As a third-generation sequencing technology, single-molecule nanopore DNA sequencing has significant application value in diagnosing suspected TB patients. Compared to traditional diagnostic methods, such as specimen culture and Xpert MTB/Rif assay, single-molecule nanopore DNA sequencing exhibits high diagnostic efficacy, low error rate, and convenient detection.