Metagenomic/Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

Respiratory disease in immunocompromised children can include a broad array of microbiome perturbations and infections as well as inflammation and injury to the tissue. Here we describe RNA-based next generation sequencing (mNGS) of lower respiratory samples from immunocompromised children, including those with cancer, immunodeficiencies, and a history of solid organ or stem cell transplant. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Lower respiratory samples largely include bronchoalveolar lavage samples with some other sample types as well. A subset of patients have paired blood and/or nasal samples also sequenced for comparative analysis.