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The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study

The cystic fibrosis (CF) lung harbours a diverse microbiome and reduced diversity in the CF lung has been associated with advancing age, increased inflammation and poorer lung function. Data suggest that the window for intervention is early in CF, yet there is a paucity of studies on the lung microb...

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Autores principales: Linnane, Barry, Walsh, Aaron M., Walsh, Calum J., Crispie, Fiona, O’Sullivan, Orla, Cotter, Paul D., McDermott, Michael, Renwick, Julie, McNally, Paul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7996874/
https://www.ncbi.nlm.nih.gov/pubmed/33652802
http://dx.doi.org/10.3390/microorganisms9030492
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author Linnane, Barry
Walsh, Aaron M.
Walsh, Calum J.
Crispie, Fiona
O’Sullivan, Orla
Cotter, Paul D.
McDermott, Michael
Renwick, Julie
McNally, Paul
author_facet Linnane, Barry
Walsh, Aaron M.
Walsh, Calum J.
Crispie, Fiona
O’Sullivan, Orla
Cotter, Paul D.
McDermott, Michael
Renwick, Julie
McNally, Paul
author_sort Linnane, Barry
collection PubMed
description The cystic fibrosis (CF) lung harbours a diverse microbiome and reduced diversity in the CF lung has been associated with advancing age, increased inflammation and poorer lung function. Data suggest that the window for intervention is early in CF, yet there is a paucity of studies on the lung microbiome in children with CF. The objective of this study was to thoroughly characterise the lower airway microbiome in pre-school children with CF. Bronchoalveolar lavage (BAL) samples were collected annually from children attending the three clinical centres. Clinical and demographic data were collated on all subjects alongside BAL inflammatory markers. 16S rRNA gene sequencing was performed on the Illumina MiSeq platform. Bioinformatics and data analysis were performed using Qiime and R project software. Data on 292 sequenced BALs from 101 children with CF and 51 without CF show the CF lung microbiome, while broadly similar to that in non-CF children, is distinct. Alpha diversity between the two cohorts was indistinguishable at this early age. The CF diagnosis explained only 1.1% of the variation between the cohort microbiomes. However, several key genera were significantly differentially abundant between the groups. While the non-CF lung microbiome diversity increased with age, diversity reduced in CF with age. Pseudomonas and Staphylococcus were more abundant with age, while genera such as Streptococcus, Porphyromonas and Veillonella were less abundant with age. There was a negative correlation between alpha diversity and interleukin-8 and neutrophil elastase in the CF population. Neither current flucloxacillin or azithromycin prophylaxis, nor previous oral or IV antibiotic exposure, was correlated with microbiome diversity. Consecutive annual BAL samples over 5 years from a subgroup of children demonstrated diverse patterns of development in the first years of life.
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spelling pubmed-79968742021-03-27 The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study Linnane, Barry Walsh, Aaron M. Walsh, Calum J. Crispie, Fiona O’Sullivan, Orla Cotter, Paul D. McDermott, Michael Renwick, Julie McNally, Paul Microorganisms Article The cystic fibrosis (CF) lung harbours a diverse microbiome and reduced diversity in the CF lung has been associated with advancing age, increased inflammation and poorer lung function. Data suggest that the window for intervention is early in CF, yet there is a paucity of studies on the lung microbiome in children with CF. The objective of this study was to thoroughly characterise the lower airway microbiome in pre-school children with CF. Bronchoalveolar lavage (BAL) samples were collected annually from children attending the three clinical centres. Clinical and demographic data were collated on all subjects alongside BAL inflammatory markers. 16S rRNA gene sequencing was performed on the Illumina MiSeq platform. Bioinformatics and data analysis were performed using Qiime and R project software. Data on 292 sequenced BALs from 101 children with CF and 51 without CF show the CF lung microbiome, while broadly similar to that in non-CF children, is distinct. Alpha diversity between the two cohorts was indistinguishable at this early age. The CF diagnosis explained only 1.1% of the variation between the cohort microbiomes. However, several key genera were significantly differentially abundant between the groups. While the non-CF lung microbiome diversity increased with age, diversity reduced in CF with age. Pseudomonas and Staphylococcus were more abundant with age, while genera such as Streptococcus, Porphyromonas and Veillonella were less abundant with age. There was a negative correlation between alpha diversity and interleukin-8 and neutrophil elastase in the CF population. Neither current flucloxacillin or azithromycin prophylaxis, nor previous oral or IV antibiotic exposure, was correlated with microbiome diversity. Consecutive annual BAL samples over 5 years from a subgroup of children demonstrated diverse patterns of development in the first years of life. MDPI 2021-02-26 /pmc/articles/PMC7996874/ /pubmed/33652802 http://dx.doi.org/10.3390/microorganisms9030492 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Linnane, Barry
Walsh, Aaron M.
Walsh, Calum J.
Crispie, Fiona
O’Sullivan, Orla
Cotter, Paul D.
McDermott, Michael
Renwick, Julie
McNally, Paul
The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
title The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
title_full The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
title_fullStr The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
title_full_unstemmed The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
title_short The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study
title_sort lung microbiome in young children with cystic fibrosis: a prospective cohort study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7996874/
https://www.ncbi.nlm.nih.gov/pubmed/33652802
http://dx.doi.org/10.3390/microorganisms9030492
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