Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.
- Feigelman R Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
- Kahlert CR Infectious Diseases and Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland.
- Baty F Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
- Rassouli F Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
- Kleiner RL Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
- Kohler P Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
- Brutsche MH Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
- von Mering C Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. mering@imls.uzh.ch.
- 2017-02-12
Published in:
- Microbiome. - 2017
COPD
Cystic fibrosis
Lung metagenome
Sputum
WGS metagenomic sequencing
Bacteria
Cystic Fibrosis
Drug Resistance, Bacterial
Genetic Variation
Genomic Islands
High-Throughput Nucleotide Sequencing
Humans
Lung
Metagenome
Metagenomics
Microbiota
Multilocus Sequence Typing
Respiratory Tract Infections
Sputum
English
BACKGROUND
Cystic 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.
RESULTS
Here, 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.
CONCLUSIONS
Unbiased 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.
Cystic 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.
RESULTS
Here, 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.
CONCLUSIONS
Unbiased 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.
- Language
-
- English
- Open access status
- gold
- Identifiers
-
- DOI 10.1186/s40168-017-0234-1
- PMID 28187782
- Persistent URL
- https://sonar.ch/global/documents/296962
Statistics
Document views: 44
File downloads:
- Full-text: 0