Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid on Antimicrobial Stewardship in Patients With Lower Respiratory Tract Infections: A Retrospective Cohort Study

Yan, Mengwei; Zou, Xiaohui; Wang, Yeming; Wang, Chenhui; Wang, Yimin; Liu, Zhibo; Shang, Lianhan; Cui, Xiaojing; Cao, Bin

doi:10.1093/infdis/jiad296

Cited by 5 publications

(3 citation statements)

References 31 publications

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“…discovered that incorporating mNGS tests into conventional microbiologic methods was related to lower rates of antibiotic escalation and may potentially aid in cessation of empirical antiviral therapies in lower respiratory tract infections (LRTIs) patients. 22 Meanwhile, mNGS could benefit the patients after allogeneic hematopoietic stem cell transplantation by lowering the mortality of pulmonary complications on account of its early accurate diagnosis and the ability to discern the pathogens. 23 In this study, we evaluated the potential application value of mNGS negative results in patients with corticosteroid-responsive DPLD.…”

Section: Discussionmentioning

confidence: 99%

“…mNGS reported all the microorganism detected in the sample, encompassing opportunistic pathogen and resident flora in the respiratory tract. 22 Yuan et al. utilize mNGS to uncover the relationship between lung microbiota and lung diseases in patients with pneumoconiosis and pulmonary infection, implying that lung microbiota could be biomarkers in lung diseases.…”

Section: Discussionmentioning

confidence: 99%

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Optimizing treatment administration strategies using negative mNGS results in corticosteroid-sensitive diffuse parenchymal lung diseases

Jing,

Ding,

Zhou

et al. 2024

iScience

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Optimizing treatment administration strategies using negative mNGS results in corticosteroid-sensitive diffuse parenchymal lung diseases

Jing,

Ding,

Zhou

et al. 2024

iScience

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“…The results also showed that mNGS could potentially improve outcomes for patients with LRTIs. Yan et al 12 showed that the use of mNGS was associated with lower rates of antibiotic escalation and may facilitate the cessation of antivirals in patients with LRTIs. Zhao et al 13 demonstrated that the pathogen-positive rate of mNGS in BALF samples was higher than that of culture in patients despite prior antibiotic use, and the results also showed that mNGS of BALF was a potentially useful tool for testing mixed pathogens in severe pneumonia.…”

Section: Introductionmentioning

confidence: 99%

Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing for Lower Respiratory Tract Infections and Human Tumor Screening

Huang,

Weng,

et al. 2023

IJGM

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Background To evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in screening of lower respiratory tract infections (LRTIs) and human tumors. Methods Human samples included bronchoalveolar lavage fluid (BALF), sputum, lung biopsy tissue, and peripheral blood from 188 patients who were admitted to our hospital between January 2020 and September 2022 were analyzed using mNGS for simultaneous pathogen and chromosome copy number variation (CNV) detection. Traditional microbial culture and comprehensive microbial test (CMT) were also conducted. The diagnostic efficiencies of the three methods (mNGS, traditional culture, and CMT groups) were compared. Results Among the 188 patients, 149 (79.3%) were in the LRTIs group and 39 (20.7%) were in the non-LRTIs group. The diagnostic sensitivity and accuracy of the mNGS group were higher than those of the traditional culture and CMT groups ( P < 0.001; P < 0.001; P < 0.001; P < 0.001), and the specificity was higher than that of the CMT group ( P = 0.039) but lower than that of the traditional culture group ( P = 0.006). The positive predictive values of the mNGS and traditional culture groups were higher than that of the CMT group ( P = 0.004; P = 0.011). The negative predictive value of the mNGS group was higher than that of the CMT group ( P = 0.003). In addition, all samples were subjected to simultaneous chromosome CNV detection, and 8% (15/188) were positive for CNV. Of the 15 patients, 10 were initially misdiagnosed as non-neoplastic diseases, with a misdiagnosis rate of 66.7% (10/15). The BALF CNV test was performed on 13 patients diagnosed with primary or metastatic lung cancer, with a positivity rate of 38.5%. Conclusion The sensitivity and accuracy of pathogen diagnosis using mNGS were better than those of traditional culture and CMT. CNV detection is an important auxiliary diagnostic tool for cancer, particularly for screening occult tumors.

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Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid

Zou,

Yan,

Wang

et al. 2024

Advanced Science

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Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non‐LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non‐LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non‐LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.

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Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid on Antimicrobial Stewardship in Patients With Lower Respiratory Tract Infections: A Retrospective Cohort Study

Cited by 5 publications

References 31 publications

Optimizing treatment administration strategies using negative mNGS results in corticosteroid-sensitive diffuse parenchymal lung diseases

Optimizing treatment administration strategies using negative mNGS results in corticosteroid-sensitive diffuse parenchymal lung diseases

Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing for Lower Respiratory Tract Infections and Human Tumor Screening

Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid

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