Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Pediatric Transplant Patients

Metagenomic next-generation sequencing (mNGS) is a significant advancement in the diagnostic evaluation of infectious diseases, especially in immunocompromised patients at risk for complex, atypical, and opportunistic infections. In pediatric solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients, mNGS can augment a diagnostic evaluation when conventional microbiological testing (CMT) fails to identify the infectious etiology. Current evidence supports the use of mNGS for specific syndromes, including complicated pneumonia, central nervous system infections, and febrile neutropenia, due to greater sensitivity. While it is considered a second-line test, early application for high-risk infections, such as diagnosis of invasive fungal disease, has been shown to be impactful. Furthermore, mNGS can detect donor-derived infections (DDIs), where the breadth of the assay can identify unexpected pathogens transmitted via the graft that are often omitted from routine screening protocols. Despite the potential, interpretation remains challenging due to the detection of DNA from commensal organisms, latent viral reactivation, and low-level detection of pathogens that do not correlate with disease. Establishing diagnostic stewardship is key to directing testing to maximize diagnostic yield and improve clinical outcomes.