Lower airway dysbiosis in nontuberculous mycobacteria–positive bronchiectasis is associated with neutrophil extracellular trap–predominant severe phenotypes

RATIONALE: The discoveries of neutrophilic inflammation and Pseudomonas-dominant pulmonary dysbiosis have helped pave the way for host-directed therapy in bronchiectasis. Substantial knowledge gaps still remain about the interplay between neutrophilic signatures and microbes in nontuberculous mycobacterial lung disease (NTM-LD), a phenotypically diverse lung infection that is increasingly prevalent in the United States and other parts of the world. OBJECTIVES: To evaluate the lower airway microbiota and neutrophilic traits in NTM-negative (NTM-) and NTM-positive (NTM+) bronchiectasis. METHODS: 16S rRNA gene sequencing, cell counts, and neutrophil extracellular trap (NET) immunoassays were performed on bronchoscopic lower airway samples in 200 bronchiectasis subjects (108 NTM-, 92 NTM+). A preclinical model of oral commensal microaspiration and NTM infection was used to profile the murine lower airways with flow cytometry and a NET assay. MEASUREMENTS AND MAIN RESULTS: Lower airways of NTM+ bronchiectasis patients were enriched with Mycobacterium and oral commensals (eg, Veillonella, Prevotella, and Streptococcus). NET levels were higher in NTM+ BAL fluid. Mycobacterium and oral commensals co-occurred with NET and neutrophils in network studies. Distinct oral commensal taxa were associated with severe disease phenotypes such as cavitary disease and exacerbators. In a murine microaspiration model, the combination of oral commensals and Mycobacterium led to a sustained proinflammatory immune response marked by an increase in Th17 cells, γδT cells, and PD-1+ T lymphocytes as well as higher NET levels. CONCLUSIONS: Our analyses showed that distinct microbiome features beyond the primary pathogen can contribute to neutrophilic inflammation and severe disease phenotypes in bronchiectasis/NTM-LD.