Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study
Sputum metagenomics in bronchiectasis: European variation and resistome profiles
Microbial variation in bronchiectasis across Europe
The EMBARC registry shows considerable variation in culturable microbes in sputum between different European countries.
Study design and European cohort characteristics
We prospectively assessed sputum from N=349 individuals recruited into the EMBARC-BRIDGE study with next-generation shotgun metagenomic sequencing including three European regions: Northern and Western Europe, Southern Europe and the United Kingdom, including samples from ten European countries.
Enhanced detection of bronchiectasis pathogens through metagenomics
Next generation metagenomic sequencing reproduced differences between countries in microbial profiles previously shown by culture in the EMBARC study.
Metagenomics provided enhanced detection for some bronchiectasis pathogens including P. aeruginosa, H. influenzae and S. pneumoniae.
Pan-European microbial clusters in bronchiectasis
Three metagenomic microbial clusters dominated by the genera Pseudomonas, Streptococcus and Haemophilus demonstrated pan-European but variable distribution.
Diverse resistomes and regional multidrug resistance
Diverse resistomes, linked to underlying microbiomes, were identified across Europe, with significantly higher diversity of resistance gene determinants in Southern Europe. Resistome composition significantly differed between regions characterised by regionally contrasting multi-drug-resistant profiles.
Validation of bronchiectasis resistotypes across regions
The EMBARC-BRIDGE cohort validated established bronchiectasis resistotypes: RT1 and RT2, which occur at varying frequency across regions.
Implications for antimicrobial resistance in bronchiectasis
Despite geographic variation in microbiome and resistome profiles in bronchiectasis across Europe, analogous antimicrobial resistance gene profiles associate with the key bronchiectasis genera Pseudomonas, Streptococcus and Haemophilus, independent of country or region.
Conclusion: The value of sputum metagenomics in bronchiectasis
Sputum metagenomics confirms and extends prior observations of regional variation in bronchiectasis microbiology. Important variation in the distribution of pathogens and antimicrobial resistance genes has implications for antimicrobial practices across Europe.
Authors
Kai Xian Thng, Pei Yee Tiew, Micheál Mac Aogáin, Jayanth Kumar Narayana, Tavleen Kaur Jaggi, Fransiskus Xaverius Ivan, Morven Shuttleworth, Merete B Long, Hollian Richardson, Holly Lind, Daniela Alferes de Lima Headley, Kara Robertson, Jennifer Pollock, Pieter C Goeminne, Michal Shteinberg, Anthony De Soyza, Stefano Aliberti, Josje Altenburg, Charles S Haworth, Oriol Sibila, Eva Polverino, Michael R Loebinger, Felix C Ringshausen, Natalie Lorent, Katerina Dimakou, Amelia Shoemark, James D Chalmers, Sanjay H. Chotirmall
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Fecha de publicación
Published online 22 May 2025
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