Metagenomic Sequencing Detects Respiratory Pathogens in Hematopoietic Cellular Transplant Patients

[...]of the clear need for enhanced LRTI diagnostics in HCT recipients, we sequentially enrolled 22 adult HCT recipients hospitalized for acute respiratory illnesses who underwent bronchoscopy and BAL between January 25, 2012, and May 20, 2013, under University of Michigan protocol HUM00043287. Standard-of-care BAL microbiologic testing was uniformly performed on all patients and included semiquantitative cultures for bacteria, mycobacteria, fungi, and cytomegalovirus; Aspergillus galactomannan assay; silver stain for Pneumocystis jirovecii; multiplex polymerase chain reaction influenza A/B, respiratory syncytial virus and human metapneumovirus; and human herpesvirus-6 polymerase chain reaction, as detailed in the Methods in the online supplement (4). With respect to potential bacterial pathogens, mNGS identified Streptococcus mitis in patient 13, an oropharyngeal microbe known to cause bacteremia and acute respiratory distress in HCT recipients (6), and Corynebacterium proprinquum, one of the few virulent Corynebacterium species associated with LRTI (7). mNGS identified a diversity of DNA viruses including human herpesvirus-6, cytomegalovirus, herpes simplex virus, Epstein-Barr virus, human papilloma virus, and torque teno viruses; however, only five of these also had well-defined evidence of active replication marked by detectable RNA transcripts (Table 1). mNGS identified microbes of uncertain pathogenicity in nine patients (Table 1) who had coexisting clinical diagnoses of graft-versus-host disease (patients 11, 22, 23, 24, 25, 31, 34, 35, and 37) or bacteremia/sepsis (patient 3), which could have contributed to respiratory symptoms resulting from noninfectious pulmonary inflammation. Because asymptomatic carriage of respiratory pathogens is well described (8), establishing biomarkers of genuine infection is critical for determining the significance of a given microbiologic finding. [...]our limited sequencing depth did not yield the human transcriptome coverage that would be desired for optimal differential gene expression analyses, although we were able to rigorously evaluate a composite metric of immunity genes.