Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients

C Langelier; MS Zinter; K Kalantar; GA Yanik; S Christenson; B Odonovan; C White; M Wilson; A Sapru; CC Dvorak; S Miller; CY Chiu; JL DeRisi

An average of 49 million paired-end sequencing reads were generated from each BAL sample, of which <1% were microbial. Sequencing statistics and pipeline output for each patient are described in Table E3 . mNGS identified all seven microbes found by standard clinical diagnostics, demonstrating 100% sensitivity for pathogen detection. In total, RNAseq identified 10 RNA viruses, all of which have established pathogenicity in the lungs, and the RNA intermediates of five DNA viruses that have uncertain pulmonary pathogenicity. DNAseq identified the genomes of these same five DNA viruses as well as five others including CMV and HHV-6, which have been associated with pneumonitis. mNGS captured entire viral genomes for five patients at an average read depth of 3500-fold, as shown in Figure E1 . Bacteria known to exist contextually as either pathogens or commensals, including Stenotrophomonas maltophilia, Streptococcus mitis, and Corynebacterium propinquum were identified, as were genera not typically considered pathogenic (30) (31) (32) . Specificity of mNGS could not be assessed because this cohort lacked patients with proven non-infectious respiratory illnesses.