Clinical Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage in the Diagnosis and Management of Pneumonia

Zhou, Hua; Larkin, Paige M.K.; Zhao, Dongdong; Ma, Qiang; Yao, Yake; Wu, Xiaohong; Wang, Jiaoli; Xiao-hu, Zhou; Li, Yaqing; Wang, Gang; Feng, Malong; Wu, Lei; Chen, Jinyin; Zhou, Changsheng; Hua, Xiaoting; Zhou, Jianying; Yang, Shangxin; Yu, Yunsong

doi:10.1016/j.jmoldx.2021.06.007

Cited by 54 publications

(46 citation statements)

References 36 publications

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“… 17 MALDI-TOF MS can quickly and accurately identify strains, and high-throughput sequencing technology also has unique advantages in etiological diagnosis. 18 Drug sensitivity test was important in antibiotic selection. This was an important defect of this study.…”

Section: Discussionmentioning

confidence: 99%

Clinical Features of Pulmonary Nocardiosis in Patients with Different Underlying Diseases: A Case Series Study

Zhong¹,

Huang²,

Zhan³

et al. 2022

IDR

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Objective To investigate the clinical features of pulmonary nocardiosis (PN) in patients with different underlying diseases. Methods Clinical, imaging, treatment and prognosis data from patients diagnosed with PN from July 2011 to June 2021 at the First Affiliated Hospital, Zhejiang University School of Medicine were collected and analyzed. According to different underlying diseases, patients were grouped into immunocompromised host (ICH) group and immunocompetent host (ICO) group, and clinical characteristics were compared between the two groups. Results There were 64 patients with PN, including 42 males, aged from 21 to 86 (57.1 ± 15.7) years. The most common clinical manifestations were cough, expectoration, fever. There were 41 cases in the ICH group and 23 cases in the ICO group. There were 11 cases with underlying pulmonary diseases in the ICH group, including 2 cases of bronchiectasis, 4 cases of chronic obstructive pulmonary disease (COPD), etc. There were 11 cases of underlying pulmonary basic diseases in ICO group, including 7 cases of bronchiectasis and COPD, 1 case of bronchiectasis, 1 case of COPD, etc. The proportion of patients with bronchiectasis and COPD in the ICO group was significantly higher (P < 0.05). Extrapulmonary nocardiosis infection occurred in 6 patients of the ICH group. During the period of hospitalization, 87.0% patients in ICO group received SMZ/TMP therapy, 73.2% of patients in ICH group received two drug combination therapy. In the ICH group, mortality at 28 days was 14.6% and 8.7% in the ICO group. Conclusion PN mainly occurred in ICH patients, but also occurred in the ICO cases to a lesser extent, especially in patients with bronchiectasis and/or COPD. Complicated with extrapulmonary infections mainly occurred in ICH population and combination of two antibiotics was often used in ICH group. The case fatality rates were 14.6% in ICH and 8.7% in ICO cases, respectively.

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Section: Discussionmentioning

confidence: 99%

Clinical Features of Pulmonary Nocardiosis in Patients with Different Underlying Diseases: A Case Series Study

Zhong¹,

Huang²,

Zhan³

et al. 2022

IDR

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“…ENNGS recommended > 10 million reads per sample for virus diagnostics due to the generally low proportion of viral reads in clinical samples [33] . For the diagnosis of LRIs, the sequencing depth varied from 2 to 25 million reads has been reported [14] , [27] , [66] , [67] . At the sequencing depth of 20 million read pairs for each sample, Chen et al evaluated the clinical utility of laboratory-developed mNGS tests for the diagnosis of LRIs and analysis of the host immune response [14] .…”

Section: Challenges Of Mngs For Lower Respiratory Infectionmentioning

confidence: 99%

Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections

Diao

Han

Zhang

et al. 2022

Journal of Advanced Research

104

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“…The timely and accurate initiation of anti-infective treatment is vital to the clinical outcomes, which depends on the rapid and accurate pathogen identification. In real-world clinical practice, conventional detection methods (CDM) have a lower sensitivity and a relatively long turn-around time for detecting opportunistic pathogens such as Pneumocystis jirovecii, mycobacteria, Nocardia spp., fungi, and other atypical pathogens (5)(6)(7). Moreover, it is difficult to distinguish non-infectious diseases from infections because the clinical manifestations and radiologic characteristics are non-specific in LTRs (8)(9)(10).…”

Section: Introductionmentioning

confidence: 99%

Metagenomic Next-Generation Sequencing for Diagnosing Infections in Lung Transplant Recipients: A Retrospective Study

et al. 2022

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Background: Accurate identification of pathogens is essential for the diagnosis and control of infections. We aimed to compare the diagnostic performance of metagenomic next-generation sequencing (mNGS) and conventional detection methods (CDM) in lung transplant recipients (LTRs).Methods: We retrospectively analyzed 107 LTRs with suspected infection of pulmonary, blood, central nervous system or chest wall between March 2018 and November 2020. Bronchoalveolar lavage fluid and other body fluids were subject to pathogen detection by both mNGS and CDM.Results: Of the 163 specimens, 84 (51.5%) tested positive for both mNGS and culture, 19 (11.7%) of which were completely consistent, 44 (27.0%) were partially congruent, and 21 (12.9%) were discordant (kappa = .215; p = .001). Compared with CDM, mNGS detected a higher diversity of pathogens. Moreover, the turn-around time was significantly shorter for mNGS compared with culture (2.7 ± .4 vs. 5.5 ± 1.6 days, p < .001). As an auxiliary method, treatment strategies were adjusted according to mNGS findings in 31 cases (29.0%), including eight patients with non-infectious diseases, who were finally cured.Conclusion: mNGS can identify pathogens with a shorter turn-around time and therefore provide a more accurate and timely diagnostic information to ascertaining pulmonary infections. mNGS might have a role in differentiating infectious from non-infectious lung diseases in LTRs.

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Clinical Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage in the Diagnosis and Management of Pneumonia

Cited by 54 publications

References 36 publications

Clinical Features of Pulmonary Nocardiosis in Patients with Different Underlying Diseases: A Case Series Study

Clinical Features of Pulmonary Nocardiosis in Patients with Different Underlying Diseases: A Case Series Study

Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections

Metagenomic Next-Generation Sequencing for Diagnosing Infections in Lung Transplant Recipients: A Retrospective Study

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