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

While prior metagenomic sequencing assays for human biospecimens have demonstrated excellent detection of viral and bacterial nucleic acid, they have lacked sensitivity for detecting fastidious organisms such as filamentous mold (12, 13) . This study confirms the need for aggressive mechanical homogenization in stabilizing media in order to detect molds such as Aspergillus while simultaneously preserving the detection of bacteria and viruses (25) . Despite this, transcripts aligning to fungi remained significantly less ubiquitous than transcripts aligning to bacteria, perhaps due to relative organism abundance. Although the majority of commercial sequencing assays use DNA, our data demonstrate that RNA sequencing is >10 times as sensitive as DNA sequencing for the detection of such fastidious organisms, which we speculate may be due to high transcriptional activity of regions such as rRNA genes in active organisms (26) .