Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details
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...
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| Vydáno v: | Microbiome Ročník 5; číslo 1; s. 20 |
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| Hlavní autoři: | , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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London
BioMed Central
10.02.2017
Springer Nature B.V |
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| ISSN: | 2049-2618, 2049-2618 |
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| Abstract | 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. |
|---|---|
| AbstractList | 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. 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. 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. 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. 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. |
| ArticleNumber | 20 |
| Author | Rassouli, Frank Baty, Florent Kahlert, Christian R. Kleiner, Rebekka L. Brutsche, Martin H. von Mering, Christian Feigelman, Rounak Kohler, Philipp |
| Author_xml | – sequence: 1 givenname: Rounak surname: Feigelman fullname: Feigelman, Rounak organization: Institute of Molecular Life Sciences, University of Zurich, Swiss Institute of Bioinformatics – sequence: 2 givenname: Christian R. surname: Kahlert fullname: Kahlert, Christian R. organization: Infectious Diseases and Hospital Epidemiology, Children’s Hospital of Eastern Switzerland, Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen – sequence: 3 givenname: Florent surname: Baty fullname: Baty, Florent organization: Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen – sequence: 4 givenname: Frank surname: Rassouli fullname: Rassouli, Frank organization: Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen – sequence: 5 givenname: Rebekka L. surname: Kleiner fullname: Kleiner, Rebekka L. organization: Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen – sequence: 6 givenname: Philipp surname: Kohler fullname: Kohler, Philipp organization: Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen, Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen – sequence: 7 givenname: Martin H. surname: Brutsche fullname: Brutsche, Martin H. organization: Pneumology and Sleep Medicine, Cantonal Hospital St. Gallen – sequence: 8 givenname: Christian orcidid: 0000-0001-7734-9102 surname: von Mering fullname: von Mering, Christian email: mering@imls.uzh.ch organization: Institute of Molecular Life Sciences, University of Zurich, Swiss Institute of Bioinformatics |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28187782$$D View this record in MEDLINE/PubMed |
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| Keywords | WGS metagenomic sequencing Cystic fibrosis Sputum Lung metagenome COPD |
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| Snippet | Background
Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus... Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions... Background Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus... BACKGROUNDCystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus... |
| SourceID | pubmedcentral proquest pubmed crossref springer |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
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| SubjectTerms | Bacteria - genetics Bacteria - isolation & purification Bacteria - pathogenicity Bioinformatics Biomedical and Life Sciences Biomedicine Cystic Fibrosis - microbiology Drug Resistance, Bacterial - genetics Genetic Variation Genomic Islands High-Throughput Nucleotide Sequencing Humans Lung - microbiology Medical Microbiology Metagenome Metagenomics Microbial Ecology Microbial Genetics and Genomics Microbiology Microbiota - genetics Multilocus Sequence Typing Respiratory Tract Infections - microbiology Sputum - microbiology Virology |
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| Title | Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details |
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