Cargando…
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...
Autores principales: | , , , , , , , , |
---|---|
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 |
_version_ | 1783670200115134464 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7996874 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT linnanebarry thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT walshaaronm thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT walshcalumj thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT crispiefiona thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT osullivanorla thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT cotterpauld thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT mcdermottmichael thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT renwickjulie thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT mcnallypaul thelungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT linnanebarry lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT walshaaronm lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT walshcalumj lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT crispiefiona lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT osullivanorla lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT cotterpauld lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT mcdermottmichael lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT renwickjulie lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy AT mcnallypaul lungmicrobiomeinyoungchildrenwithcysticfibrosisaprospectivecohortstudy |