Comparison of Metagenomic Second- and Third-Generation Sequencing by Diagnostic Sensitivity and Specificity in Tuberculosis Patients

Background: The third-generation sequencing (TGS) of Mycobacterium tuberculosis (MTB) is rarely reported in clinical practice. This study aims to compare the efficacy difference between next-generation sequencing (NGS) and TGS in the diagnosis of MTB and share the experience of NGS/TGS in the diagnosis of PTB. Methods: The past cases of suspected pulmonary tuberculosis (PTB) in our hospital were reviewed. Patients suspected of PTB who had undergone NGS/TGS detection, MTB culture, and molecular biology detection were included in the study. The clinical data of patients were reviewed, and the clinical comprehensive diagnosis of patients was used as the gold standard to analyze the efficacy of four methods for diagnosis of MTB infection, namely, metagenomic sequencing, MTB culture, molecular biology, and MTB culture + molecular biology. Then, we analyzed the results of NGS and TGS and compared the efficacy of the two metagenomic sequencing methods in the diagnosis of MTB infection. Results: Ninety patients suspected of PTB were included in the study. 37 patients (41.11%) completed NGS and 53 patients (58.89%) completed TGS. Sixty-five patients (72.11%) had MTB infection in the lung or other parts of the body, and the remaining 25 patients (27.89%) had no MTB infection. Traditional laboratory tests such as MTB culture have low sensitivity and accuracy in diagnosing MTB. The sensitivity, specificity, and detection accuracy of metagenomic sequencing are significantly higher than those of other detection methods. The diagnostic accuracy of TGS reached 88.68%, which is significantly higher than that of NGS (64.86%). Conclusions: Compared with NGS, TGS has higher sensitivity and specificity in the diagnosis of MTB. In clinical practice, TGS is a better choice for patients who are suspected of MTB infection but cannot be diagnosed by traditional laboratory indicators.