High Individuality of Respiratory Bacterial Communities in a Large Cohort of Adult Cystic Fibrosis Patients under Continuous Antibiotic Treatment

A large cohort of 56 adults with continuous antibiotic treatment was studied and different microbial diagnostic methods were compared, including culture-independent and culture-based bacterial diagnostics. A total of 72 sputum samples including longitudinal observations were analysed by targeting marker gene 16S rRNA gene, using Illumina Genome AnalyzerIIx. PCR amplification of parts of the 16S rRNA gene. Amplicons were pooled and identified by 'barcode' sequence integrated by forward primers. Afterwarss, specific Illumina multiplexing sequencing primers were used to integrate 'index' sequence in a second perfomed PCR reaction.Prevalence of known pathogens was highly similar among all methods but the vast spectrum of bacteria associated with CF was only revealed by culture-independent techniques. The sequence comparison enabled confident determination of the bacterial community composition and revealed a high diversity and individuality in the communities across the cohort.