Tuberculosis Diagnosis by Metagenomic Next-generation Sequencing on Bronchoalveolar Lavage Fluid: a cross-sectional analysis

Abstract

Background: Metagenomic next-generation sequencing (mNGS) is an effective diagnostic method for infectious diseases, however, its clinical utility for tuberculosis (TB) diagnosis remains to be demonstrated. Methods: A total of 322 bronchoalveolar lavage fluid (BALF) samples were collected from 311 suspected and confirmed pulmonary TB patients and tested by mNGS, acid-fast bacillus (AFB) smear by microscopy, Xpert 1 MTB/RIF (Xpert), mycobacterium culture and bacterial/fungal culture. Diagnostic performance of mNGS was compared with conventional methods for detection of Mycobacterium tuberculosis complex (MTBC) and other pathogens in BALF. Underlying factors associated with positive detection in pulmonary TB patients were investigated. Results: mNGS, Xpert and culture presented a high proportion of complete matching for MTBC detection (244/322, 75.8%). In pulmonary TB patients pre-treatment the sensitivity of MTBC detection by mNGS, Xpert, culture and smear was 59.9% (85/142), 69.0% (98/142), 59.9% (85/142) and 24.6% (35/142), respectively, and 79.6% overall; MTBC was detected by mNGS in 33.2% (5/34) Xpert and culture negative samples. Positive MTBC detection by mNGS was affected by Vitamin D, erythrocyte sedimentation rate, TB initial treatment/ retreatment, and cavity in chest imaging (χ 2 = 37.42, P < 0.001), but not by prior anti-TB therapy within 3 months. mNGS was able to detect new potential pathogens in 8.7% (28/322) of samples. Conclusions: Combining mNGS with conventional detection methods could increase the detection rate for MTBC. Additionally, mNGS could identify pathogens in a non-targeted approach for better diagnosis of coinfection.

Next-Generation Metagenome Sequencing Shows Superior Diagnostic Performance in Acid-Fast Staining Sputum Smear-Negative Pulmonary Tuberculosis and Non-tuberculous Mycobacterial Pulmonary Disease

“…However, its sensitivity is only approximately 50-60% (Young et al, 2008;Deshwal et al, 2019). In this regard, some authors have proposed that AFS using bronchoalveolar lavage fluid (BALF) samples can be performed in patients with negative sputum smears; however, the sensitivity of this test still needs to be improved (Shi et al, 2020;Liu et al, 2021). Further, whether using sputum or BALF smears, the major challenge associated with TB diagnosis using AFS is that a non-tuberculous mycobacteria (NTM) infection can be mistaken for an Mycobacterium tuberculosis (MTB) infection, resulting in patients receiving incorrect treatment.…”

Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients

“…Of these, 123 patients were enrolled in this study following strict criteria, including 1) new diagnosis, 2) no treatment, 3) no antibiotic exposure in the last two weeks, 4) no pulmonary infection except Mtb ( Figure 1 ). By combining the results of conventional bacterial detection and mNGS, 101 (82%) TB patients in our cohort were identified as bacteriologically confirmed (BC) ( Liu et al, 2020 ); the BC rate is higher that of the WHO 2019 report (55%) ( WHO, 2019 ). Significant differences were detected in cavity on the chest radiography, monocyte, and alanine aminotransferase (ALT) between BC and BN groups ( Table 1 ).…”

The Diagnostic Value of Metagenomic Next–Generation Sequencing in Lower Respiratory Tract Infection

“…However, the sensitivity of both decrease significantly after more than 3 months of anti-TB treatment, possibly due to the undetectable tuberculous bacterial load after long-term treatment (Zhou et al, 2019). Liu et al showed that the sensitivities of mNGS, Xpert, culture, and smear for detecting tuberculosis were 59.9%, 69.0%, 59.9%, and 24.6%, respectively (Liu et al, 2020). Before antituberculosis treatment, the combined application of mNGS and conventional methods can increase the detection rate to 79.6% since mNGS is more advantageous in detecting mixed infections.…”

“…Liu et al. showed that the sensitivities of mNGS, Xpert, culture, and smear for detecting tuberculosis were 59.9%, 69.0%, 59.9%, and 24.6%, respectively ( Liu et al., 2020 ). Before anti-tuberculosis treatment, the combined application of mNGS and conventional methods can increase the detection rate to 79.6% since mNGS is more advantageous in detecting mixed infections.…”