Lower respiratory microbiota from pediatric BAL samples

This study investigates the clinical utility of 16S rRNA gene-based sequencing of pediatric bronchoalveolar lavage (BAL) samples. Samples were taken from cystic fibrosis (CF), immunocompromised (IC) and non-immunocompromised (nIC) patients, and culture-independent results were compared to routine cultures of the same samples. Based on 16S rRNA gene sequencing results, we investigated the influence of diagnosis group and recent antibiotic exposure on sample diversity.While the vast majority of cultured organisms were also identified by culture-independent methods, many additional taxa, including a number of potential pathogens, were identified by 16S rRNA gene-based sequencing that were not detected by routine culture. We found that CF samples had lower alpha diversity than those from IC and nIC patients. We also saw reduced abundances of Escherichia and Corynebacterium in the CF group, and lower Streptococcus, Veillonella and Haemophilus abundance in samples from patients exposed to antibiotics. Lastly, we identified a core group of 15 taxa present in all diagnosis groups.