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

Abstract

BACKGROUND The 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 association with antimicrobial resistomes unknown. METHODS 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. Microbiome and resistome profiles were assessed in relation to clinical outcomes. RESULTS 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. Three metagenomic microbial clusters dominated by the genera Pseudomonas, Streptococcus and Haemophilus 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 multi-drug-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 associate with the key bronchiectasis genera Pseudomonas, Streptococcus and Haemophilus, independent of country or region. CONCLUSION 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.