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.
Highlights
Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways
CF is caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene, whose protein product is involved in the transport of chloride ions across the apical membrane of epithelial and
The CF lungs are colonized by a number of pathogenic bacteria, commonly including Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae, and Burkholderia cepacia [5]
Summary
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. Culture-based methods can miss atypical or slow-growing microbes. Cystic fibrosis (CF) is one of the most prevalent genetic disorders in the Caucasian population, affecting about one in 2500 newborns [1]. This autosomal recessive condition affects mostly secretory organs, such as the pancreas, liver, and lungs. The culture conditions and procedures are necessarily biased towards known, previously encountered pathogens—whereas novel, slow-growing or rare microbes might potentially be missed (e.g. atypical mycobacteria). The “background” community—opportunistic or accidental members of the lung microbiome—is not routinely studied for clinical use [9, 10], despite its potential to harbor antibiotic resistance genes and to elicit or modulate immune responses
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