Integrative bacteriome-resistome of U-BIOPRED metagenomes reveals severe asthma cluster of multidrug resistant H. influenzae

<bold>Introduction:</bold> Metagenomics may facilitate a novel stratification of severe asthma (SA). <bold>Methods:</bold> Bacteriome and resistome were extracted from U-BIOPRED metagenomes: N=23 healthy controls (HC), N=25 patients with mild/moderate asthma (MMA) and N=100 patients with SA (N=47 patients were followed up after 1 year). Integrative bacteriome-resistome using similarity network fusion followed by a spectral clustering was performed. Differences in clinical features across clusters were assessed. <bold>Results:</bold> Three clusters were identified. The first two are shared by HC, MMA and SA, dominated by <italic>Rothia</italic>, <italic>Prevotella</italic> and <italic>Veillonella</italic> species and a mix of tetracycline, macrolide and beta-lactam resistance genes, but differed in terms of their α-diversity. While HC shows no significant difference in clinical features, MMA and SA in less diverse cluster (C1) exhibit significantly lower lung function and sputum macrophages (but higher sputum neutrophils) compared to more diverse cluster (C2). Of interest, the third cluster (C3) is unique for SA, dominated by multidrug resistant <italic>H. influenzae</italic>, and associated with longer asthma and extremely low macrophages/high neutrophils in sputum. Longitudinal analysis indicates relative stability of C3 and reversibility between C1 and C2. Moreover, significant difference in clinical signals including exacerbation frequency and macrophage abundance across C1, C2 and C3 for SA is observed in nonsmokers but not ex/current-smokers who are mainly eosinophilic/pauci-granulocytic. <bold>Conclusion:</bold> Our metagenomics facilitates discovery of novel categories of SA that enhance understanding of immune dysregulation with an <italic>H. influenzae</italic> dominant phenotype.