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

Abstract

In this study, we explored the clinical value of next-generation metagenome sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from patients with acid-fast staining (AFS) sputum smear-negative pulmonary tuberculosis (PTB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD). Data corresponding to hospitalized patients with pulmonary infection admitted to the hospital between July 2018 and July 2021, who were finally diagnosed with AFS sputum smear-negative PTB and NTM-PD, were retrospectively analyzed. Bronchoscopy data as well as mNGS, Xpert, AFS (BALF analysis), and T-SPOT (blood) data, were extracted from medical records. Thereafter, the diagnostic performances of these methods with respect to PTB and NTM-PD were compared. Seventy-one patients with PTB and 23 with NTM-PD were included in the study. The sensitivities of mNGS, Xpert, T-SPOT, and AFS for the diagnosis of PTB were 94.4% (67/71), 85.9% (61/71), 64.8% (46/71), and 28.2% (20/71), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (97.2%, 67/71). The specificity of Xpert was 100%, while those of AFS and T-SPOT were 73.9% (17/23) and 91.3% (21/23), respectively. Further, the 23 patients with NTM-PD could be identified using mNGS, and in the population with immunosuppression, the sensitivities of mNGS, Xpert, T-SPOT, and AFS were 93.5% (29/31), 80.6% (25/31), 48.4% (15/31), and 32.3% (10/31), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (100%, 31/31). The specificities of Xpert and T-SPOT in this regard were both 100%, while that of AFS was 40% (2/5). Furthermore, using mNGS, all the NTM samples could be identified. Thus, the analysis of BALF samples using mNGS has a high accuracy in the differential diagnosis of MTB and NTM. Further, mNGS combined with Xpert can improve the detection of MTB, especially in AFS sputum smear-negative samples from patients with compromised immune states or poor responses to empirical antibiotics.

The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform

“…M. tuberculosis was detected using the TB GENE XPERT test of BALF and mNGS. The result is consistent with that of previous studies ( Zhou et al, 2019 ; Xu et al, 2022 ), which showed that two platforms had a similar detection ability for M. tuberculosis when compared with TB GENE XPERT. However, because of the small sample sizes, these studies had limited power to detect effects; therefore, more evidence is needed.…”

Rapid diagnosis of non-tuberculous mycobacterial pulmonary diseases by metagenomic next-generation sequencing in non-referral hospitals

“…Several studies have validated the diagnostic performance of mNGS in the NTM pulmonary diseases. 281 One study ( Xu et al, 2022 ) stated that mNGS and acid-fast staining was positive in 23 and 6 NTM 282 samples, showing 100% and 26.08% sensitivity, separately. In our study, all 12 NTM samples can be identified by using mNGS with 100% sensitivity, too.…”

Evaluation of nucleotide MALDI-TOF MS on bronchoalveolar lavage fluid for pulmonary Tuberculosis: experience from a tertiary hospital in southwestern China

“…BALF is the most common used respiratory sample type for the diagnosis of PTB besides sputum, which is also preferred by clinicians due to its closer proximity to the lesion. Multiple studies have reported the capability of different molecular tests to diagnose PTB in BALFs, such as Xpert MTB/RIF assay, SAT-TB, LAMP, next-generation metagenome sequencing, nanopore sequencing, etc., with sensitivities raging from 45.18-94.4% [21][22][23][24][25][26] . The comparatively lower results of the Xpert MTB/RIF assay in our study than those previously studies may be related to several factors, including study site, sample source, and the operator, suggesting that we need to improve the level of testing within our hospital.…”