Abstract
Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.
Highlights
Cystic fibrosis (CF) is the most common lethal autosomal recessively inherited disorder of Europids
We have applied the parallel technologies of ribosomal tag sequencing based on DNA and RNA and metabolomics to sputum samples taken from separate cohorts of CF and non-CF subjects as an approach to characterise the ‘active’ bacterial community and environment in the CF airway
Patients and those presenting with CF pulmonary exacerbation, (ii) that the population size of all dominant orders of bacteria as measured by DNA- and RNA-based methods are close, greater discrepancies are seen with less prevalent organisms, some of which we associate with CF for the first time, and (iii) that a strong relationship exists between the abundance of specific strict anaerobes and fluctuations in the level of several metabolites during CF pulmonary exacerbation
Summary
Cystic fibrosis (CF) is the most common lethal autosomal recessively inherited disorder of Europids It is caused by a mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene that makes those diagnosed extremely susceptible to pulmonary infections. A range of these techniques has been deployed: generation of 16S rRNA clone libraries [4,5], terminal restriction fragment length polymorphism analysis [2,6], microarray hybridisation [7], phylochip analysis [8] and pyrosequencing [9] These studies demonstrate that a number of previously unrecognised aerobic and anaerobic species are present in CF airways, some of which represent new potential pathogens
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