A Pilot Study of RNA Sequencing to Improve the Diagnostic Yield of Bronchoalveolar Lavage Specimens in Pediatric Allogeneic Hematopoietic Stem Cell Transplant Recipients

Respiration. 2021;100(4):356-363. doi: 10.1159/000513250. Epub 2021 Mar 16.


Background: Pulmonary complications often cause morbidity and mortality in pediatric allogeneic hematopoietic stem cell transplant (HSCT) recipients. While detection of infection and initiation of appropriate antimicrobial therapy improves survival, present techniques oftentimes do not detect infections in bronchoalveolar lavage (BAL) samples because of pretreatment with antimicrobial therapies and the need for a priori knowledge of likely viral pathogens, decreasing the yield of BAL.

Objective: We evaluated whether RNA-based massively parallel sequencing (MPS) would improve detection of infections in BAL fluid in pediatric allogeneic HSCT recipients.

Results: Nine patients underwent 10 BAL (1 patient underwent 2 BAL) and had sufficient BAL fluid for inclusion in this study. Clinical microbiological testing identified infections in 7 patients, and MPS identified infections in 5 patients, although some of these detected organisms were not detected by clinical testing. Results were fully concordant in 5 patients, fully discordant in 3 patients, and partially discordant in 2 patients. Bacterial, viral, and fungal infections were detected via both techniques.

Conclusion: This suggests that MPS in conjunction with routine clinical testing increases the yield of detection of infectious organisms in the BAL fluid.

Keywords: Allogeneic hematopoietic stem cell transplant; Bronchoalveolar lavage; Massively parallel sequencing; Pediatrics; Posttransplant complications.

MeSH terms

  • Adolescent
  • Anti-Infective Agents / administration & dosage*
  • Anti-Infective Agents / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bronchoalveolar Lavage / methods
  • Bronchoalveolar Lavage Fluid / microbiology*
  • Female
  • Fungi / genetics
  • Fungi / isolation & purification
  • Hematopoietic Stem Cell Transplantation* / adverse effects
  • Hematopoietic Stem Cell Transplantation* / methods
  • Humans
  • Male
  • Patient Selection
  • Pediatrics / methods
  • Pilot Projects
  • Pneumonia* / diagnosis
  • Pneumonia* / drug therapy
  • Pneumonia* / microbiology
  • Quality Improvement
  • Sequence Analysis, RNA / methods*
  • Viruses / genetics
  • Viruses / isolation & purification


  • Anti-Infective Agents