Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital

Wu, Jin; Pan, Jue; Miao, Qi; Ma, Yu; Zhang, Yao; Huang, Yingnan; Yao, Yao; Su, Yi; Wang, Qingqing; Wang, Mengran; Li, Bing; Bao, Rong; Gao, Xiaodong; Wu, Honglong; Hu, Bijie

doi:10.21037/atm-20-2274

Cited by 16 publications

(19 citation statements)

References 16 publications

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“…High-quality data were obtained by removing low-quality bases, linker sequences, and short sequences (< 35 bp). The process of subtracting the human host sequence and aligning the remaining sequences were described in the previous study (Jin et al, 2020). The remaining data by removal of low-complexity reads were classified by simultaneously aligning to Pathogens metagenomics Database (PMDB).…”

Section: Bioinformatic Analysis and Criteria For Positive Resultsmentioning

confidence: 99%

Clinical performance of metagenomic next-generation sequencing for the rapid diagnosis of talaromycosis in HIV-infected patients

Mao

Shen

Yang

et al. 2022

Front. Cell. Infect. Microbiol.

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BackgroundTalaromycosis is an invasive endemic mycosis caused by the dimorphic fungus Talaromyces marneffei (T. marneffei, TM). It mainly affects immunodeficient patients, especially HIV-infected individuals, which causes significant morbidity and mortality. Culture-based diagnosis takes a long turnaround time with low sensitivity, leading to treatment delay. In this study, we aimed to evaluate the performance of Metagenomic Next-Generation Sequencing (mNGS) for the rapid diagnosis of talaromycosis in HIV-infected patients.MethodsRetrospectively analysis was conducted in HIV-infected cases at Changsha First Hospital (China) from January 2021 to March 2022. Patients who underwent routine microbiological examination and mNGS testing in parallel were enrolled. The clinical final diagnosis was used as a reference standard, and cases were classified into the TM group (60 cases) and the non-TM group (148 cases). The clinical performances of mNGS were compared with culture and serum Galactomannan (GM). The mixed infections detected by mNGS were analyzed. The impact of mNGS detection on treatment was also investigated.ResultsThe sensitivity of mNGS test reached 98.3% (95% CI, 89.8-99.9), which was significantly higher than culture (66.7% [95% CI, 53.2-77.9], P < 0.001) and serum GM (83.3% [95% CI, 71.0-91.2], P < 0.05). The specificity of 98.6% (95% CI, 94.7-99.7) was similar to culture (100.0% [95% CI, 96.8-100.0], P = 0.156), and superior to serum GM (91.9% [95% CI, 85.9-95.5], P < 0.05). In bronchoalveolar lavage fluid (BALF) samples, the positive rate of mNGS was 97.6%, which was significantly higher than culture (28.6%, P <0.001). mNGS has excellent performance in the identification of mixed infection in TM group patients. Cytomegalovirus, Epstein-Barr virus and Pneumocystis jirovecii were the most common concurrent pathogens. In summary, 60.0% (36/60) patients were added or adjusted to antimicrobial therapy after mNGS test.ConclusionmNGS is a powerful technique with high specificity and sensitivity for the rapid diagnosis of talaromycosis. mNGS of BALF samples may be a good option for early identification of T. marneffei in HIV-infected individuals with manifestations of infection. Moreover, mNGS shows excellent performance in mixed infection, which benefits timely treatment and potential mortality reduction.

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Section: Bioinformatic Analysis and Criteria For Positive Resultsmentioning

confidence: 99%

Clinical performance of metagenomic next-generation sequencing for the rapid diagnosis of talaromycosis in HIV-infected patients

Mao

Shen

Yang

et al. 2022

Front. Cell. Infect. Microbiol.

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“…For instance, Chen et al found that mNGS improved the diagnosis rate of Chlamydia psittaci through a retrospective analysis of nine cases of psittacosis pneumonia, 13 while Jin et al showed that the overall sensitivity of mNGS was superior to that of culture (49.6% vs 35.2%, respectively) in the diagnosis of 125 cases of active tuberculosis. 14 mNGS was also reported to improve the diagnosis rate of viral infections in plasma samples, and to identify dengue virus 1 and…”

Section: Discussionmentioning

confidence: 99%

Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections

et al. 2022

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Objective Metagenomic next-generation sequencing (mNGS) has the potential to overcome the shortcomings of traditional culture methods. This study aimed to assess the diagnostic value of mNGS in patients with lower respiratory tract infections (LRTIs). Methods This retrospective observational study sequentially enrolled 47 patients with LRTIs admitted to Shenzhen Hospital of Southern Medical University between February 2019 and November 2020. Pathogens in bronchoalveolar lavage fluid (BALF) samples were investigated to compare diagnoses by mNGS with culture methods. Results Compared with culture methods, mNGS had a diagnostic sensitivity of 80% and a specificity of 35.13% with an agreement rate of 44.68% between these two methods. mNGS significantly increased the pathogen detection rate. Conclusions mNGS may show some advantages in identifying a wide range of LRTI pathogens, improving the sensitivity for viruses and atypical pathogens. The clinical application of NGS technology is worth looking forward to.

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“…Another retrospective study has indicated that the diagnostic accuracy of mNGS in detecting active TB is higher than that of culture on liquid medium (the MGIT 960 system) (49.6% vs 35.2%). In addition, the turnaround time of mNGS detection, 32-36 hours, is markedly shorter than the 2-6 weeks required for the MGIT 960 system [14].…”

Section: Application Of Mngs In Detecting M Tuberculosismentioning

confidence: 99%

The Role of Metagenomic Next-Generation Sequencing as a Promising Technology for Diagnosing HIV-TB Coinfection

Liao

Yang

et al. 2022

Zoonoses

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The human immunodeficiency virus (HIV) pandemic has caused a resurgence of tuberculosis (TB), thus increasing morbidity and mortality. Moreover, HIV-TB coinfection leads to difficulties in diagnosis. Sputum smear microscopy, mycobacterial culture and GeneXpert MTB/RIF assays are generally endorsed to detect Mycobacterium tuberculosis (M. tuberculosis) in HIV-TB coinfection. However, these methods cannot diagnose TB in an accurate and timely manner, thus increasing the rates of HIV-associated morbidity and mortality in patients with TB. Hence, a considerable need exists for better diagnostic tools for patients with HIV-TB coinfection. Metagenomic next-generation sequencing (mNGS) is a novel detection platform widely used to assess infectious disease, antimicrobial resistance, the microbiome and human host gene expression. Herein, we summarize the advantages of mNGS for infectious disease diagnostics. We then assess the efficiency of mNGS in the detection of M. tuberculosis in different specimens and several cases of HIV-TB coinfection. We conclude that mNGS is an acceptable diagnostic method for HIV-TB coinfection, although limited research is available.

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Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital

Abstract: Background: To evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for active tuberculosis (TB).

Cited by 16 publications

References 16 publications

Clinical performance of metagenomic next-generation sequencing for the rapid diagnosis of talaromycosis in HIV-infected patients

Clinical performance of metagenomic next-generation sequencing for the rapid diagnosis of talaromycosis in HIV-infected patients

Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections

The Role of Metagenomic Next-Generation Sequencing as a Promising Technology for Diagnosing HIV-TB Coinfection

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