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

Due to inherent challenges in sampling the lower respiratory tract, the pulmonary microbiome was not one of the original sites sampled in the 2008 Human Microbiome Project and data regarding pulmonary microbial communities in health and disease have lagged decades behind similar analyses of human intestinal, cutaneous, and nasopharyngeal microbiomes (27) . In this study, we detected that many pathogenic bacteria such as Pseudomonas and Streptococcus are ubiquitous and hence their abundance The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/291864 doi: bioRxiv preprint needs to be contextualized by cohort-specific norms. By using cohort-specific Z-scores, we provide a template for discriminating normal from abnormal microbial burden in the lungs of immunocompromised children. For example, 100% of samples had detectable Pseudomonas RNA, but only Sample 29 had detectable Pseudomonas RNA more than 2 standard deviations above the cohort mean (Appendix 1).