Abstract
BackgroundAirway microbiota dynamics during lower respiratory infection (LRI) are still poorly understood due, in part, to insufficient longitudinal studies and lack of uncontaminated lower airways samples. Furthermore, the similarity between upper and lower airway microbiomes is still under debate. Here we compare the diversity and temporal dynamics of microbiotas directly sampled from the trachea via tracheostomy in patients with (YLRI) and without (NLRI) lower respiratory infections.MethodsWe prospectively collected 127 tracheal aspirates across four consecutive meteorological seasons (quarters) from 40 patients, of whom 20 developed LRIs and 20 remained healthy. All aspirates were collected when patients had no LRI. We generated 16S rRNA-based microbial profiles (~250 bp) in a MiSeq platform and analyzed them using Mothur and the SILVAv123 database. Differences in microbial diversity and taxon normalized (via negative binomial distribution) abundances were assessed using linear mixed effects models and multivariate analysis of variance.Results and discussionAlpha-diversity (ACE, Fisher and phylogenetic diversity) and beta-diversity (Bray-Curtis, Jaccard and Unifrac distances) indices varied significantly (P<0.05) between NLRI and YLRI microbiotas from tracheostomised patients. Additionally, Haemophilus was significantly (P = 0.009) more abundant in YLRI patients than in NLRI patients, while Acinetobacter, Corynebacterium and Pseudomonas (P<0.05) showed the inverse relationship. We did not detect significant differences in diversity and bacterial abundance among seasons. This result disagrees with previous evidence suggesting seasonal variation in airway microbiotas. Further study is needed to address the interaction between microbes and LRI during times of health and disease.
Highlights
The population of children with a tracheostomy is increasing [1] and these children are at high risk of developing lower respiratory infections (LRI) [2] that require intensive care [3]
Further study is needed to address the interaction between microbes and LRI during times of health and disease
Forty patients were enrolled in this study of whom 20 had at least one clinically-evident LRI (YLRI) and 20 had no LRI (NLRI)
Summary
The population of children with a tracheostomy is increasing [1] and these children are at high risk of developing lower respiratory infections (LRI) [2] that require intensive care [3]. A retrospective analysis of 917 children aged 0–18 years from 36 children’s hospitals who received a tracheostomy in 2002 demonstrated that in the 5-year follow-up period, the mean number of hospitalizations experienced per child was 3.8 (SD: 4.4; range: 0–34) and 46% of the hospitalizations were for “respiratory” diagnoses [2]. Despite this risk of LRI, there is no consensus about how providers should treat common acute respiratory infections in tracheostomised children [3, 4]. We compare the diversity and temporal dynamics of microbiotas directly sampled from the trachea via tracheostomy in patients with (YLRI) and without (NLRI) lower respiratory infections
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