Concordance between upper and lower airway microbiota in infants with cystic fibrosis

Abstract

Nasopharyngeal and oropharyngeal samples are commonly used to direct therapy for lower respiratory tract infections in non-expectorating infants with cystic fibrosis (CF).We aimed to investigate the concordance between the bacterial community compositions of 25 sets of nasopharyngeal, oropharyngeal and bronchoalveolar lavage (BAL) samples from 17 infants with CF aged ∼5 months (n=13) and ∼12 months (n=12) using conventional culturing and 16S-rRNA sequencing.Clustering analyses demonstrated that BAL microbiota profiles were in general characterised by a mixture of oral and nasopharyngeal bacteria, including commensals like ,, and spp. and potential pathogens like , and spp. Within each individual, however, the degree of concordance differed between microbiota of both upper respiratory tract niches and the corresponding BAL.The inconsistent intra-individual concordance between microbiota of the upper and lower respiratory niches suggests that the lungs of infants with CF may have their own microbiome that seems seeded by, but is not identical to, the upper respiratory tract microbiome.

Do combined upper airway cultures identify lower airway infections in children with chronic cough?

“…11,23,24 Three of these studies compared nasopharyngeal, oropharyngeal and BAL, or bronchial fluid microbiota. 11,20,21 Although the microbiota in combined nasopharyngeal and orophar- analyses did not detect any significant between-group differences.…”

“…Recent studies have also used 16S rRNA gene sequencing to characterize the microbiota in upper and lower airway specimens from otherwise healthy older children undergoing elective surgery, infants with CF or young children with various chronic lung diseases . Three of these studies compared nasopharyngeal, oropharyngeal and BAL, or bronchial fluid microbiota .…”

“…Recent studies have also used 16S rRNA gene sequencing to characterize the microbiota in upper and lower airway specimens from otherwise healthy older children undergoing elective surgery, infants with CF or young children with various chronic lung diseases . Three of these studies compared nasopharyngeal, oropharyngeal and BAL, or bronchial fluid microbiota . Although the microbiota in combined nasopharyngeal and oropharyngeal cultures provided a more comprehensive representation of BAL microbiota, these studies consistently concluded that upper airway samples did not accurately reflect lower airway bacterial communities and were insufficiently reliable to guide clinical management.…”

“…18,19 The anatomy of the upper airway in children may facilitate recurrent microaspiration of heavily bacteria-laden nasal secretions, 8,11 while in adults repeated microaspiration of oropharyngeal secretions is thought to be important. 18,19 Recent studies have also used 16S rRNA gene sequencing to characterize the microbiota in upper and lower airway specimens from otherwise healthy older children undergoing elective surgery, 20 infants with CF 21,22 or young children with various chronic lung diseases. 11,23,24 Three of these studies compared nasopharyngeal, oropharyngeal and BAL, or bronchial fluid microbiota.…”

Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects

“…In our study, the prominent phyla in the lower airways was Firmicutes , followed by Bacteroidetes , Proteobacteria , Actinobacteria and Fusobacteria ; the prominent genera in the lower airways included Streptococcus , Prevotella , Haemophilus and Neisseria (see Table SI in the online supplement).These phyla or genera were also dominated in oral samples of patients with lung cancer, which presumably spread from the upper respiratory tract through dispersal by micro‐aspiration or inhalation . Since the respiratory tract are covered in a continuous mucosal layer, and all bathed in mucus and saliva, shifts in one anatomical location may be associated with changes in others .…”