ArticleMicrobiome2017
Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.
Article in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 2 of them syntheses that pooled it.
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Who cites it
75 citing papers in PubMed, 2 syntheses or guidelines pooled it, 127 citations in OpenAlex.
- The alterations of oral, airway and intestine microbiota in chronic obstructive pulmonary disease: a systematic review and meta-analysis.Frontiers in immunology · 2024Pooled it
- The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis.Respiratory research · 2022Pooled it
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Relationship between airway stents and airway microorganisms: a literature review.Journal of thoracic disease · 2026Review
- Comparative analysis of the lung microbiota in patients with lung cancer, chronic obstructive pulmonary disease, and community-acquired pneumonia.Microbiology spectrum · 2026Article
- SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.BMC microbiology · 2026Article
- Characterization of pulmonary tuberculosis in high-altitude region using nanopore targeted sequencing.BMC microbiology · 2026Article
- Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.medRxiv : the preprint server for health sciences · 2026Article
- Strain-level characterization of bacterial pathogens using metagenomic sequencing for patients with pneumonia.Journal of translational medicine · 2025Article
- Shallow metagenomic shotgun sequencing improves detection of pathogenic species in cystic fibrosis respiratory samples.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2025Article
- Dysglycemia and the airway microbiome in cystic fibrosis.PloS one · 2025Article
- Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.Frontiers in cellular and infection microbiology · 2025Article
- Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum.mSystems · 2024Article
- Microbiome-Mucosal Immunity Nexus: Driving Forces in Respiratory Disease Progression.Journal of microbiology (Seoul, Korea) · 2024Review
- Clinical characteristics and microbial signatures in the lower airways of diabetic and nondiabetic patients with pneumonia.Journal of thoracic disease · 2024Article
- Article
- Genomic and Metagenomic Insights into the Distribution of Nicotine-degrading Enzymes in Human Microbiota.Current genomics · 2024Article
- Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.International journal of molecular sciences · 2024Article
- Genomic attributes of airway commensal bacteria and mucosa.Communications biology · 2024Article
- Lung microbiome: new insights into the pathogenesis of respiratory diseases.Signal transduction and targeted therapy · 2024Review
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typically involves regular respiratory-tract cultures in order to identify pathogens and to guide treatment. However, culture-based methods can miss atypical or slow-growing microbes. Furthermore, the isolated microbes are often not classified at the strain level due to limited taxonomic resolution.
resultsHere, we show that untargeted metagenomic sequencing of sputum DNA can provide valuable information beyond the possibilities of culture-based diagnosis. We sequenced the sputum of six CF patients and eleven control samples (including healthy subjects and chronic obstructive pulmonary disease patients) without prior depletion of human DNA or cell size selection, thus obtaining the most unbiased and comprehensive characterization of CF respiratory tract microbes to date. We present detailed descriptions of the CF and healthy lung microbiome, reconstruct near complete pathogen genomes, and confirm that the CF lungs consistently exhibit reduced microbial diversity. Crucially, the obtained genomic sequences enabled a detailed identification of the exact pathogen strain types, when analyzed in conjunction with existing multi-locus sequence typing databases. We also detected putative pathogenicity islands and indicators of antibiotic resistance, in good agreement with independent clinical tests.
conclusionsUnbiased sputum metagenomics provides an in-depth profile of the lung pathogen microbiome, which is complementary to and more detailed than standard culture-based reporting. Furthermore, functional and taxonomic features of the dominant pathogens, including antibiotics resistances, can be deduced-supporting accurate and non-invasive clinical diagnosis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.