Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

MS Zinter; CC Dvorak; MY Mayday; K Iwanaga; NP Ly; ME McGarry; GD Church; LE Faricy; CM Rowan; JR Hume; ME Steiner; ED Crawford; C Langelier; K Kalantar; ED Chow; S Miller; K Shimano; A Melton; GA Yanik; A Sapru; JL DeRisi

Recent advances in metagenomic next generation sequencing (mNGS) have shown promising results in diagnosing neurologic, ocular, and other infections (9) (10) (11) . However, the identification of fastidious pathogens such as Aspergillus and other filamentous molds remain difficult due to thick extracellular matrices and the relatively small inoculum required to induce disease (12) (13) (14) (15) . Unfortunately, off-the-shelf assays for respiratory biospecimens have proven inadequate to survey the variety of organisms present in thick and mucoid respiratory secretions. As such, unlike the better-characterized microbiomes of the human gastrointestinal tract and nasopharynx, data describing the composition of the pulmonary microbiome are sparse and insufficient to reliably discriminate between health and disease (16) . Therefore, we conducted a pilot study aimed to (1) develop and optimize a highly sensitive mNGS assay capable of detecting pulmonary bacterial, fungal, and viral pathogens clinically relevant to immunocompromised children, and (2) test this mNGS assay on a cohort of immunocompromised children undergoing lower respiratory tract sampling as evaluation for suspected pulmonary infection. We hypothesized that an optimized mNGS assay could improve characterization of the pulmonary microbiome and aid in the identification of potential pulmonary pathogens in this high-risk population.