Elsevier

Journal of Infection

Volume 81, Issue 4, October 2020, Pages 567-574
Journal of Infection

Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis

https://doi.org/10.1016/j.jinf.2020.08.004Get rights and content

Highlights

  • mNGS produces a similar sensitivity with xpert and culture for TB detection.

  • mNGS detects NTM and other pathogens with a higher sensitivity than conventional microbiological testing.

  • mNGS is highly efficient in the diagnosis of infectious pathogens, with shorter turnaround time.

Summary

Objectives:

The aim of this study is to investigate the clinical usefulness of metagenomic Next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples to discriminate pulmonary tuberculosis (PTB) from Non-TB community-acquired pneumonia (CAP) in PTB suspects.

Methods:

We investigate the performance of mNGS on BALF samples from 110 PTB suspects, in comparison with conventional microbiological testing (solid media culture, acid-fast bacilli staining (AFS), Xpert) of BALF or sputum samples and final clinical diagnosis.

Results:

We finally clinically diagnosed 48 cases of pulmonary tuberculosis patients and 62 cases of non-tuberculosis patients. Comparing to the final clinical diagnosis, mNGS produced a sensitivity of 47.92%, which was similar to that of Xpert (45.83%) and culture (46.81%), but much higher than that of AFS (29.17%) for TB diagnosis in BALF samples. Apart from detecting Mycobacterium tuberculosis, mNGS also identified mixed infections in PTB patients, including 3 fungal cases and 1 bacteria case. Meanwhile, mNGS efficiently identified 14 of 22 (63.63%) cases of non-tuberculous mycobacteria (NTM), 7 cases of fungi, 1 case of viral infection, and other common bacterial pathogens in Non-PTB group. Finally, mNGS identified 67.23% infection cases within 3 days, while the conventional methods identified 49.58% infection cases for over 90 days.

Conclusion:

Our data show that mNGS of BALF represents a potentially effective tool for the rapid diagnosis of PTB suspects.

Introduction

Tuberculosis (TB), which is caused by the bacillus Mycobacterium tuberculosis (MTB), remains a leading cause of death from infectious disease. According to the 2019 World Health Organization global report, TB was one of the top 10 causes of death worldwide, ranking above acquired immune deficiency syndrome. There were an estimated 10.0 million newly diagnosed TB cases worldwide in 2018, with a high incidence and mortality in developing countries.1,2 Although effective treatment has been available for decades, the difficulty faced by physicians has been the issue of rapid and reliable diagnosis. Currently, the Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA. USA) has been endorsed by the WHO for the initial diagnosis of TB suspects.3 However, the presumptive diagnosis of TB mainly relies on an examination of clinical symptoms, radiological findings, and acid-fast staining (AFS). The nonspecific symptoms and signs of pulmonary TB often overlap with common pulmonary infections, which may delay the diagnosis of pulmonary TB and increase TB-related death.4,5 Therefore, alternative rapid and hypothesis-free diagnostic approaches are urgently required to accurately discriminate pulmonary TB from other common pulmonary infections in the early stages of the diagnostic process.

Recent advances and lower costs of next-generation sequencing (NGS) technologies have allowed NGS to be applied to diagnostic microbiology, with the advantages of hypothesis-free, culture-independent and unbiased pathogen detection directly from clinical specimens.6 To date, clinical metagenomics next-generation sequencing (mNGS) has been applied in diagnosis of pathogens causing a variety of infectious syndromes, including respiratory tract infection,7,8 bloodstream infection,9,10 meningitis and encephalitis.11,12 However, published reports describing the usefulness of mNGS in pulmonary TB suspects are limited to individual patients or small, retrospective studies.13, 14, 15, 16 The question remains whether the diagnostic performance of clinical mNGS testing for pulmonary TB justifies its wider adoption by the healthcare community.

Here, we performed a prospective, single-center study involving hospitalized patients with suspicion of active pulmonary TB infections. This study was designed to evaluate the clinical performance and effect of the mNGS assay in comparison with conventional microbiological testing in patient-care scenarios in which the tests, including Xpert, solid media culture, acid-fast bacilli staining (AFS), are likely to be used.

Section snippets

Study population and specimen

As a tertiary hospital, the Infectious Diseases Hospital of Soochow University admitted suspected tuberculosis patients. We enrolled 110 patients with suspected tuberculosis who underwent bronchoscopy and were tested for both Xpert and mNGS of alveolar lavage fluid from June 1, 2019, to January 31, 2020.

The patient's attending physician judged the patient with suspected tuberculosis based on clinical manifestations and imaging tests. Patients' sputum test methods included AFS (Ziehl–Neelsen

Diagnosis and demographic baseline

A total of 116 patients initially suspected of having active TB infection underwent bronchoscopy during hospitalization and received clinical lavage fluid or other tissue specimens were obtained for Xpert and mNGS tests. Six patients, with 9 specimens total, were excluded, including 4 endobronchial ultrasound (EBUS) tissue specimens, 1 cerebrospinal fluid specimen, 1 pleural fluid specimen and 3 tissue specimens. Finally, 110 patients were enrolled, and 48 patients were eventually diagnosed

Discussion

In this study, we enrolled a cohort of 110 patients with suspicious pulmonary TB infection. Forty-eight patients were diagnosed with PTB, and the rest were non-TB patients. Compared with the non-tuberculosis patients, the patients with pulmonary tuberculosis had no specific clinical features. The utility of clinical symptoms for screening PTB is hard to characterize, with rather low sensitivity and unsatisfactory specificity.23 TSPOT-TB is a widely used indicator for detecting tuberculosis

Declaration of Competing Interest

We declare that we do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted.

Acknowledgments

We thank Meng Xiang from Shanghai Genskey Technology Co., Ltd for the technical support with NGS sample processing and Library construction.

This work was supported by grants from the Science and Technology Plan of Suzhou, China (SYS201778, X.Y.; SYSD2018193, C.S.; SYS2019111, M.W.; and SS201880, J.Z.), and High-level Health Talents in Jiangsu Province (LGY2019014, P.T.). Our research sponsors had no role in the research design, data collection, data analysis, data interpretation, or report

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    These authors contributed equally to this work.

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