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

In this study, we developed an optimized mNGS assay with adequate sensitivity to identify bacteria, fungi, and both RNA and DNA viruses within the lower respiratory tract of immunocompromised children. In doing so, we identified a rich molecular portrait of the pulmonary microbiome in this vulnerable patient population. Further, by comparing the quantity of microbial nucleic acid to other microbes within a sample and to other samples within the cohort, we were able to identify outlying potential pathogens in approximately half of previously-negative samples.