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

Next, to contextualize the burden of Aspergillus in each sample, we estimated the number of Aspergillus CFU according to the linear regression associating Aspergillus CFU with RNA transcripts derived from our spike-in experiments. Aspergillus RNA levels correlated with ≥1 CFU in 14/41 samples, suggesting that the lower airways of immunocompromised children are frequently exposed to quantities of Aspergillus RNA consistent with low numbers of CFUs. Of these 14 samples, one patient sample was positive for IPA by both culture and galactomannan assay (Figure 2b, labeled) . Although the remaining 13 were all culturenegative, 12/13 had received fungicidal or fungistatic anti-Aspergillus pharmacotherapy within 48 hours of sample collection, suggesting that empiric antifungal pharmacotherapy significantly confounds the association between Aspergillus RNA and growth in culture. While Aspergillus RNA sequencing reads did not correlate with growth in culture (T-test p=0.148), they did correlate with BAL galactomannan The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 +0.92 and +1.78. Additionally, two patients had viral co-infections (Parainfluenza-3 and Influenza-C;