ArticleRespiratory research2022
Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing.
Article in Respiratory research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.BMC infectious diseases · 2026Article
- Review
- Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection.Frontiers in cellular and infection microbiology · 2026Article
- Lower respiratory tract microbiota characteristics in patients withFrontiers in cellular and infection microbiology · 2026Article
- Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.Frontiers in cellular and infection microbiology · 2026Article
- ChronicInfection and drug resistance · 2026Article
- Admission-time immunologic patterns in hospitalized children withFrontiers in pediatrics · 2026Article
- RTTAP: Empowering metatranscriptomic data analysis with a read-based total-infectome taxonomic solution.iMetaOmics · 2025Article
- Performance of metagenomic next-generation sequencing, Xpert MTB/RIF and acid-fast staining for diagnosing tuberculous pleurisy and empyema.Journal of thoracic disease · 2025Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.Scientific reports · 2025Article
- Comparison of molecular testing methods for diagnosing non-tuberculous mycobacterial infections.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- The application prospect of metagenomic next-generation sequencing technology in diagnosing suspected lower respiratory tract infections.Frontiers in cellular and infection microbiology · 2025Article
- Value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in acute exacerbation of fibrosing interstitial lung disease: an individualized treatment protocol based on microbiological evidence.BMC pulmonary medicine · 2024Observational
- Duplex recombinase aided amplification-lateral flow dipstick assay for rapid distinction ofFrontiers in cellular and infection microbiology · 2024Article
- Characteristics of the pulmonary microbiota in patients with mild and severe pulmonary infection.Frontiers in cellular and infection microbiology · 2023Article
- BALF metagenomic next-generation sequencing analysis in hematological malignancy patients with suspected pulmonary infection: clinical significance of negative results.Frontiers in medicine · 2023Article
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21 authors.
Funding
Abstract
backgroundThe application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.
methodsStrategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.
resultsThe positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.
conclusionsTo achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.
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