Inconsistent intra-individual microbiota between upper and lower respiratory niches has been reported among infants with Cystic Fibrosis (CF). We aimed to investigate the concordance between the bacterial community composition of 20 oropharyngeal (OP) samples and 20 corresponding sputa, collected from children with CF above one year of age.
As part of the ‘’Cystic Fibrosis, respiratory viruses, intracellular bacteria and fastidious organisms’’ (MUCOVIB) project, all children under 18 years of age with diagnosed CF were recruited into a swiss multicentric study. Respiratory samples included OP swabs collected from all children in addition to sputa collected from those able to expectorate. Sequencing and data analysis of amplicons of the V3-V4 variable region of the 16S rRNA-encoding gene were performed. Paired-read were assembled with PANDAseq and clustered into operational taxonomic units (OTUs) using vsearch and assigned to taxonomical ranks using Qiime and the EzBioCloud database. Non-metric multidimensional scaling, ANOVA and PERMANOVA were used to analyze the bacterial diversity in upper and lower respiratory niches.
Fifty-eight children, of whom 29 (50%) provided 51 sputa samples. From these 29, 10 patients (40 samples) provided concomitant OP and sputa samples collected during the same visit. Equivalent species diversity (alpha-diversity; Shannon index) was documented from both upper and lower samples (P-value=0.26). In most cases, hierarchical clustering based on OTU presence/absence clustered upper and lower samples from the same patient and during the same visit, thus suggesting a signature microbiota in most patients. A similar variance of bacterial microbiota was observed in upper and lower respiratory niches (P-value=0.9422), with some differences in species composition.
Our preliminary findings conducted on a small subset of patients, suggested a good intra-individual concordance of the microbiota in upper and lower respiratory niches, thus suggesting that OP swabs could be used as proxy to measure bacterial biodiversity among children with CF unable to expectorate.
S. Asner, None