Abstract
BackgroundInvasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway microbiota. Non-invasive upper airway sampling is an alternative method for monitoring airway microbiota; however, there are limited data describing the relationship of such results with lung microbiota in young children. In this study, we compared the upper and lower airway microbiota in young children to determine whether non-invasive upper airway sampling procedures provide a reliable measure of either lung microbiota or clinically defined differences.ResultsThe microbiota in oropharyngeal (OP) swabs, nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) from 78 children (median age 2.2 years) with and without lung disease were characterised using 16S rRNA gene sequencing. Permutational multivariate analysis of variance (PERMANOVA) detected significant differences between the microbiota in BAL and those in both OP swabs (p = 0.0001, Pseudo-F = 12.2, df = 1) and NP swabs (p = 0.0001; Pseudo-F = 21.9, df = 1) with the NP and BAL microbiota more different than the OP and BAL, as indicated by a higher Pseudo-F value. The microbiota in combined OP and NP data (upper airways) provided a more comprehensive representation of BAL microbiota, but significant differences between the upper airway and BAL microbiota remained, albeit with a considerably smaller Pseudo-F (PERMANOVA p = 0.0001; Pseudo-F = 4.9, df = 1). Despite this overall difference, paired BAL and upper airway (OP and NP) microbiota were >50 % similar among 69 % of children. Furthermore, canonical analysis of principal coordinates (CAP analysis) detected significant differences between the microbiota from clinically defined groups when analysing either BAL (eigenvalues >0.8; misclassification rate 26.5 %) or the combined OP and NP data (eigenvalues >0.8; misclassification rate 12.2 %).ConclusionsUpper airway sampling provided an imperfect, but reliable, representation of the BAL microbiota for most children in this study. We recommend inclusion of both OP and NP specimens when non-invasive upper airway sampling is needed to assess airway microbiota in young children who do not expectorate. The results of the CAP analysis suggest lower and upper airway microbiota profiles may differentiate children with chronic suppurative lung disease from those with persistent bacterial bronchitis; however, further research is needed to confirm this observation.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0182-1) contains supplementary material, which is available to authorized users.
Highlights
Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate
The PERMANOVA components of variation showed that differences in the microbiota among specimen types contributed 25.3, 17.9 and 13.0 % of variation between NP, OP and combined upper airway data, respectively, when compared to Lavage-1. These findings indicate that the combined OP and NP data provided a better representation of Lavage-1 microbiota than analysis of either upper airway site alone; significant differences remained
We have shown that the combined OP and NP microbiota provided a better representation of bronchoalveolar lavage (BAL) microbiota for most children in our study (67.3 %) than the analysis of the microbiota in either the upper airway site alone; low similarity between the paired upper and lower airway microbiota was detected for 32.7 % of the children
Summary
Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway microbiota. Studies in very young children who do not expectorate are more challenging as invasive procedures, such as bronchoalveolar lavage (BAL) collected via bronchoscopy, are required to sample the lower airway microbiota [3]. The invasive nature of BAL, including a requirement for general anaesthesia, renders it neither suitable nor ethically feasible for longitudinal studies [4] Reflecting this limitation, studies of lung microbiota in very young children have generally been cross-sectional [5]
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