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

Approximately half of viral genera were detected below 1 read per million sequencing reads (50.9%). These The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 Mycoplasma-specific PCR, and 16S bacterial and 28/ITS fungal amplicon sequencing (Supplemental Text 5). All validation tests were concordant with mNGS with one exception: 28S/ITS amplicon DNA sequencing failed to identify C.glabrata in Sample 37. For this sample, we confirmed the presence of this organism with 3 separate species-specific RT-PCR primer sets followed by Sanger sequencing in-house, confirming the initial mNGS report of C.glabrata. As there are numerous complementary bioinformatics approaches for analyzing metagenomic datasets, we tested the reproducibility of our approach by reanalyzing our data using a parallel method developed in-house that weights organisms by both abundance and concordance of paired RNA and DNA sequencing reads without Z-scores (Supplemental Table 1 ).