NEXT-generation metagenomic sequencing has uncovered key differences in bronchiectasis pathogens and resistance genes across Europe, offering new insights for tailoring antimicrobial strategies.
The EMBARC registry has previously shown geographical variation in culturable sputum microbes in bronchiectasis, but the full role of next-generation sequencing and its ability to characterise the associated antimicrobial resistome remained unexamined. In the EMBARC-BRIDGE study, researchers prospectively analysed sputum samples from 349 patients across ten countries in Northern, Western, Southern Europe, and the UK using shotgun metagenomic sequencing. This approach enabled the identification of microbial and resistance gene patterns in relation to geography and clinical outcomes.
Metagenomic analysis confirmed previously observed regional microbial differences identified by culture, while also enhancing detection of important bronchiectasis pathogens such as Pseudomonas aeruginosa, Haemophilus influenzae, and Streptococcus pneumoniae. Three dominant microbial clusters, Pseudomonas, Streptococcus, and Haemophilus, were present throughout Europe but varied by region. Notably, Southern Europe exhibited a significantly more diverse resistome, with a broader range of resistance gene determinants and distinctive multidrug-resistant patterns. These regional differences aligned with variations in bronchiectasis resistotypes RT1 and RT2, though antimicrobial resistance gene profiles were found to associate with key genera independently of geographical location.
This study demonstrates that sputum metagenomics not only replicates known microbial trends but also reveals novel, clinically relevant resistance gene distributions. These findings reinforce the need for regionally informed antimicrobial stewardship while highlighting common resistome features across Europe.
Reference
Thng KX et al. Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study. Eur Respir J. 2025; DOI: 10.1183/13993003.00054-2025.
