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Open AccessArticle

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

1
Centre for Interventions in Infection, Inflammation and Immunity (4i) and Graduate Entry Medical School, University of Limerick, Limerick V94 T9PX, Ireland
2
National Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin D12 N512, Ireland
3
Teagasc Food Research Centre, Moorepark, Fermoy, Co Cork P61 C996, Ireland
4
APC Microbiome Ireland, University College Cork, Cork T12 YN60, Ireland
5
Pathology Department, Our Lady’s Children’s Hospital, Crumlin, Dublin D12 N512, Ireland
6
Department of Clinical Microbiology, Trinity College Dublin, Trinity Centre for Health Science, Tallaght University Hospital, Dublin 24, Ireland
7
Department of Paediatrics, Royal College of Surgeons in Ireland, Our Lady’s Children’s Hospital Crumlin, Dublin D12 N512, Ireland
*
Author to whom correspondence should be addressed.
These senior authors contributed equally to this work.
Academic Editor: Giovanni Di Bonaventura
Microorganisms 2021, 9(3), 492; https://doi.org/10.3390/microorganisms9030492
Received: 20 January 2021 / Revised: 20 February 2021 / Accepted: 24 February 2021 / Published: 26 February 2021
(This article belongs to the Section Medical Microbiology)
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. View Full-Text
Keywords: infection; inflammation; microbiota; microbiome; lung; cystic fibrosis; children; paediatrics; bronchoscopy; bronchoalveolar lavage infection; inflammation; microbiota; microbiome; lung; cystic fibrosis; children; paediatrics; bronchoscopy; bronchoalveolar lavage
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MDPI and ACS Style

Linnane, B.; Walsh, A.M.; Walsh, C.J.; Crispie, F.; O’Sullivan, O.; Cotter, P.D.; McDermott, M.; Renwick, J.; McNally, P. The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study. Microorganisms 2021, 9, 492. https://doi.org/10.3390/microorganisms9030492

AMA Style

Linnane B, Walsh AM, Walsh CJ, Crispie F, O’Sullivan O, Cotter PD, McDermott M, Renwick J, McNally P. The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study. Microorganisms. 2021; 9(3):492. https://doi.org/10.3390/microorganisms9030492

Chicago/Turabian Style

Linnane, Barry; Walsh, Aaron M.; Walsh, Calum J.; Crispie, Fiona; O’Sullivan, Orla; Cotter, Paul D.; McDermott, Michael; Renwick, Julie; McNally, Paul. 2021. "The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study" Microorganisms 9, no. 3: 492. https://doi.org/10.3390/microorganisms9030492

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