Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study

<h4>Background</h4>The European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC) registry shows considerable variation in culturable microbes in sputum between different European countries. The additive role of next-generation metagenomic sequencing remains unexplored and the association with antimicrobial resistomes unknown.<h4>Methods</h4>We used next-generation shotgun metagenomic sequencing to prospectively assess sputum from 349 individuals recruited into the EMBARC Bronchiectasis Research Involving Databases, Genomics and Endotyping (BRIDGE) study from three European regions: Northern and Western Europe, Southern Europe and the UK. Samples were included from eight European countries. Microbiome and resistome profiles were assessed in relation to clinical outcomes.<h4>Results</h4>Next-generation metagenomic sequencing reproduced differences between countries in microbial profiles that were previously shown by culture in the EMBARC study. Metagenomics provided enhanced detection for some bronchiectasis pathogens, including <i>Pseudomonas aeruginosa</i>, <i>Haemophilus influenzae</i> and <i>Streptococcus pneumoniae</i>. Three metagenomic microbial clusters dominated by the genera <i>Pseudomonas</i>, <i>Streptococcus</i> and <i>Haemophilus</i> demonstrated pan-European but variable distribution. 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 multidrug-resistant profiles. The EMBARC-BRIDGE cohort validated established bronchiectasis resistotypes RT1 and RT2, which occur at varying frequency across regions. Despite geographic variation in microbiome and resistome profiles in bronchiectasis across Europe, analogous antimicrobial resistance gene profiles associated with the key bronchiectasis genera <i>Pseudomonas</i>, <i>Streptococcus</i> and <i>Haemophilus</i>, independent of country or region.<h4>Conclusion</h4>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.