Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study

Hayoung Choi; Hollian Richardson; Chandani Hennayake; Morven Shuttleworth; Erin Cant; Mathieu Bottier; Arietta Spinou; Kara Robertson; Merete B. Long; Anthony De Soyza; Felix C. Ringshausen; Pieter Goeminne; Natalie Lorent; Charles Haworth; Josje Altenburg; Michael R. Loebinger; Daniela Alferes de Lima Headley; Alison J. Dicker; Francesco Blasi; Michal Shteinberg; Stefano Aliberti; Eva Polverino; Oriol Sibila; Amelia Shoemark; James D. Chalmers

doi:10.1164/rccm.202504-0875OC

Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study

Hayoung Choi
, Hollian Richardson
, Chandani Hennayake
, Morven Shuttleworth
, Erin Cant
, Mathieu Bottier
, Arietta Spinou
, Kara Robertson
, Merete B. Long
, Anthony De Soyza
, Felix C. Ringshausen
, Pieter Goeminne
, Natalie Lorent
, Charles Haworth
, Josje Altenburg
, Michael R. Loebinger
, Daniela Alferes de Lima Headley
, Alison J. Dicker
, Francesco Blasi
, Michal Shteinberg

Stefano Aliberti, Eva Polverino, Oriol Sibila, Amelia Shoemark, James D. Chalmers (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

Abstract

Rationale: Infection is a key disease driver in bronchiectasis, and the upper-airway microbiome has been known to shape the lower-airway microbiome. Objective: To evaluate the relationship between the upper-airway microbiome, mucociliary function, and clinical outcomes in bronchiectasis. Methods: Nasopharyngeal swabs were collected from 344 patients with bronchiectasis enrolled across five European centers. A total of 104 patients had nasopharyngeal samples obtained at the 1-year follow-up. Microbiome composition was assessed according to Bronchiectasis Severity Index and severe exacerbations. The α- and β-diversity were measured using the Chao1 and Bray-Curtis indices, respectively. Random forest analysis was performed. Dysbiosis was defined as >10% relative abundance of pathogenic taxa comprising Pseudomonas, Haemophilus, and Staphylococcus. Measurements and Main Results: Of the 344 patients, 200 (58.1%) were female (median age, 68 yr; IQR, 59-75 yr). α-Diversity significantly differed according to disease severity (P = 0.002), and β-diversity analysis revealed distinct microbiome profiles associated with disease severity and severe exacerbation (permutational multivariate ANOVA, P = 0.021 and P = 0.001, respectively). Random forest analysis identified Pseudomonas as being associated with severe bronchiectasis (Bronchiectasis Severity Index ⩾9) and severe exacerbations. The genus-level relative taxon abundance of Pseudomonas was well correlated with Pseudomonas aeruginosa growth in the sputum culture. Patients with nasopharyngeal dysbiosis had more severe respiratory symptoms, showed epithelial disruption on nasal epithelial biopsy, and experienced more severe exacerbation over a 1-year follow-up period than those in the nondysbiosis group. The microbiome profiles were relatively stable between baseline and 1-year follow-up (P = 0.95). Conclusions: The upper-airway microbiome is associated with disease severity and severe exacerbation of bronchiectasis.

Original language	English
Pages (from-to)	2296-2306
Number of pages	11
Journal	American Journal of Respiratory and Critical Care Medicine
Volume	211
Issue number	12
DOIs	https://doi.org/10.1164/rccm.202504-0875OC
Publication status	Published - 1 Dec 2025

Keywords

bronchiectasis
infection
microbiome
dysbiosis
precision medicine

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10.1164/rccm.202504-0875OC

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Choi, H., Richardson, H., Hennayake, C., Shuttleworth, M., Cant, E., Bottier, M., Spinou, A., Robertson, K., Long, M. B., De Soyza, A., Ringshausen, F. C., Goeminne, P., Lorent, N., Haworth, C., Altenburg, J., Loebinger, M. R., Alferes de Lima Headley, D., Dicker, A. J., Blasi, F., ... Chalmers, J. D. (2025). Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study. American Journal of Respiratory and Critical Care Medicine, 211(12), 2296-2306. https://doi.org/10.1164/rccm.202504-0875OC

@article{7c1a257682fe494da27e6b177f202d7e,

title = "Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study",

abstract = "Rationale: Infection is a key disease driver in bronchiectasis, and the upper-airway microbiome has been known to shape the lower-airway microbiome. Objective: To evaluate the relationship between the upper-airway microbiome, mucociliary function, and clinical outcomes in bronchiectasis. Methods: Nasopharyngeal swabs were collected from 344 patients with bronchiectasis enrolled across five European centers. A total of 104 patients had nasopharyngeal samples obtained at the 1-year follow-up. Microbiome composition was assessed according to Bronchiectasis Severity Index and severe exacerbations. The α- and β-diversity were measured using the Chao1 and Bray-Curtis indices, respectively. Random forest analysis was performed. Dysbiosis was defined as >10\% relative abundance of pathogenic taxa comprising Pseudomonas, Haemophilus, and Staphylococcus. Measurements and Main Results: Of the 344 patients, 200 (58.1\%) were female (median age, 68 yr; IQR, 59-75 yr). α-Diversity significantly differed according to disease severity (P = 0.002), and β-diversity analysis revealed distinct microbiome profiles associated with disease severity and severe exacerbation (permutational multivariate ANOVA, P = 0.021 and P = 0.001, respectively). Random forest analysis identified Pseudomonas as being associated with severe bronchiectasis (Bronchiectasis Severity Index ⩾9) and severe exacerbations. The genus-level relative taxon abundance of Pseudomonas was well correlated with Pseudomonas aeruginosa growth in the sputum culture. Patients with nasopharyngeal dysbiosis had more severe respiratory symptoms, showed epithelial disruption on nasal epithelial biopsy, and experienced more severe exacerbation over a 1-year follow-up period than those in the nondysbiosis group. The microbiome profiles were relatively stable between baseline and 1-year follow-up (P = 0.95). Conclusions: The upper-airway microbiome is associated with disease severity and severe exacerbation of bronchiectasis.",

keywords = "bronchiectasis, infection, microbiome, dysbiosis, precision medicine",

author = "Hayoung Choi and Hollian Richardson and Chandani Hennayake and Morven Shuttleworth and Erin Cant and Mathieu Bottier and Arietta Spinou and Kara Robertson and Long, \{Merete B.\} and \{De Soyza\}, Anthony and Ringshausen, \{Felix C.\} and Pieter Goeminne and Natalie Lorent and Charles Haworth and Josje Altenburg and Loebinger, \{Michael R.\} and \{Alferes de Lima Headley\}, Daniela and Dicker, \{Alison J.\} and Francesco Blasi and Michal Shteinberg and Stefano Aliberti and Eva Polverino and Oriol Sibila and Amelia Shoemark and Chalmers, \{James D.\}",

note = "Copyright: {\textcopyright} 2025 by the American Thoracic Society ",

year = "2025",

month = dec,

day = "1",

doi = "10.1164/rccm.202504-0875OC",

language = "English",

volume = "211",

pages = "2296--2306",

journal = "American Journal of Respiratory and Critical Care Medicine",

issn = "1073-449X",

publisher = "American Thoracic Society",

number = "12",

}

Choi, H, Richardson, H, Hennayake, C, Shuttleworth, M, Cant, E, Bottier, M, Spinou, A, Robertson, K , Long, MB, De Soyza, A, Ringshausen, FC, Goeminne, P, Lorent, N, Haworth, C, Altenburg, J, Loebinger, MR, Alferes de Lima Headley, D , Dicker, AJ, Blasi, F, Shteinberg, M, Aliberti, S, Polverino, E, Sibila, O, Shoemark, A & Chalmers, JD 2025, 'Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study', American Journal of Respiratory and Critical Care Medicine, vol. 211, no. 12, pp. 2296-2306. https://doi.org/10.1164/rccm.202504-0875OC

TY - JOUR

T1 - Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis

T2 - Data from the EMBARC-BRIDGE Study

AU - Choi, Hayoung

AU - Richardson, Hollian

AU - Hennayake, Chandani

AU - Shuttleworth, Morven

AU - Cant, Erin

AU - Bottier, Mathieu

AU - Spinou, Arietta

AU - Robertson, Kara

AU - Long, Merete B.

AU - De Soyza, Anthony

AU - Ringshausen, Felix C.

AU - Goeminne, Pieter

AU - Lorent, Natalie

AU - Haworth, Charles

AU - Altenburg, Josje

AU - Loebinger, Michael R.

AU - Alferes de Lima Headley, Daniela

AU - Dicker, Alison J.

AU - Blasi, Francesco

AU - Shteinberg, Michal

AU - Aliberti, Stefano

AU - Polverino, Eva

AU - Sibila, Oriol

AU - Shoemark, Amelia

AU - Chalmers, James D.

PY - 2025/12/1

Y1 - 2025/12/1

N2 - Rationale: Infection is a key disease driver in bronchiectasis, and the upper-airway microbiome has been known to shape the lower-airway microbiome. Objective: To evaluate the relationship between the upper-airway microbiome, mucociliary function, and clinical outcomes in bronchiectasis. Methods: Nasopharyngeal swabs were collected from 344 patients with bronchiectasis enrolled across five European centers. A total of 104 patients had nasopharyngeal samples obtained at the 1-year follow-up. Microbiome composition was assessed according to Bronchiectasis Severity Index and severe exacerbations. The α- and β-diversity were measured using the Chao1 and Bray-Curtis indices, respectively. Random forest analysis was performed. Dysbiosis was defined as >10% relative abundance of pathogenic taxa comprising Pseudomonas, Haemophilus, and Staphylococcus. Measurements and Main Results: Of the 344 patients, 200 (58.1%) were female (median age, 68 yr; IQR, 59-75 yr). α-Diversity significantly differed according to disease severity (P = 0.002), and β-diversity analysis revealed distinct microbiome profiles associated with disease severity and severe exacerbation (permutational multivariate ANOVA, P = 0.021 and P = 0.001, respectively). Random forest analysis identified Pseudomonas as being associated with severe bronchiectasis (Bronchiectasis Severity Index ⩾9) and severe exacerbations. The genus-level relative taxon abundance of Pseudomonas was well correlated with Pseudomonas aeruginosa growth in the sputum culture. Patients with nasopharyngeal dysbiosis had more severe respiratory symptoms, showed epithelial disruption on nasal epithelial biopsy, and experienced more severe exacerbation over a 1-year follow-up period than those in the nondysbiosis group. The microbiome profiles were relatively stable between baseline and 1-year follow-up (P = 0.95). Conclusions: The upper-airway microbiome is associated with disease severity and severe exacerbation of bronchiectasis.

AB - Rationale: Infection is a key disease driver in bronchiectasis, and the upper-airway microbiome has been known to shape the lower-airway microbiome. Objective: To evaluate the relationship between the upper-airway microbiome, mucociliary function, and clinical outcomes in bronchiectasis. Methods: Nasopharyngeal swabs were collected from 344 patients with bronchiectasis enrolled across five European centers. A total of 104 patients had nasopharyngeal samples obtained at the 1-year follow-up. Microbiome composition was assessed according to Bronchiectasis Severity Index and severe exacerbations. The α- and β-diversity were measured using the Chao1 and Bray-Curtis indices, respectively. Random forest analysis was performed. Dysbiosis was defined as >10% relative abundance of pathogenic taxa comprising Pseudomonas, Haemophilus, and Staphylococcus. Measurements and Main Results: Of the 344 patients, 200 (58.1%) were female (median age, 68 yr; IQR, 59-75 yr). α-Diversity significantly differed according to disease severity (P = 0.002), and β-diversity analysis revealed distinct microbiome profiles associated with disease severity and severe exacerbation (permutational multivariate ANOVA, P = 0.021 and P = 0.001, respectively). Random forest analysis identified Pseudomonas as being associated with severe bronchiectasis (Bronchiectasis Severity Index ⩾9) and severe exacerbations. The genus-level relative taxon abundance of Pseudomonas was well correlated with Pseudomonas aeruginosa growth in the sputum culture. Patients with nasopharyngeal dysbiosis had more severe respiratory symptoms, showed epithelial disruption on nasal epithelial biopsy, and experienced more severe exacerbation over a 1-year follow-up period than those in the nondysbiosis group. The microbiome profiles were relatively stable between baseline and 1-year follow-up (P = 0.95). Conclusions: The upper-airway microbiome is associated with disease severity and severe exacerbation of bronchiectasis.

KW - bronchiectasis

KW - infection

KW - microbiome

KW - dysbiosis

KW - precision medicine

U2 - 10.1164/rccm.202504-0875OC

DO - 10.1164/rccm.202504-0875OC

M3 - Article

C2 - 40938736

SN - 1073-449X

VL - 211

SP - 2296

EP - 2306

JO - American Journal of Respiratory and Critical Care Medicine

JF - American Journal of Respiratory and Critical Care Medicine

IS - 12

ER -

Upper-Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study

Abstract

Keywords

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