Diagnostic Performance and Clinical Impacts of Metagenomic Sequencing after Allogeneic Hematopoietic Stem Cell Transplantation

Metagenomic Next-Generation Sequencing (mNGS) is a rapid, non-culture-based, high-throughput technique for pathogen diagnosis. Despite its numerous advantages, only a few studies have investigated its use in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). We conducted a retrospective analysis of 404 mNGS tests performed on 264 patients after allo-HSCT. The tests were divided into three groups (Phase A, B, C) based on the time spent hospitalized post-transplantation, and we evaluated the analytical performance of mNGS in comparison with conventional microbiological tests (CMT), while also analyzing its clinical utility for clinical impacts. Metagenomic sequencing demonstrated a significantly higher rate of positive microbiological findings as compared to CMT (334/404 (82.7%) vs. 159/404 (39.4%), respectively, P < 0.001). The detection rates by both mNGS and CMT varied across the three-phase (mNGS: A-60/89 (67.4%), B-147/158 (93.0%), C-125/157 (79.6%), respectively, P<0.001; CMT: A-21/89 (23.6%), B-79/158 (50.0%), C-59/157 (37.6%), respectively, P < 0.001). The infection sites and types of pathogens were also different across the three phases. Compared to non-GVHD cases, mNGS detected more Aspergillus spp. and Mucorales in GVHD patients (Aspergillus: 12/102 (11.8%) vs. 8/158 (5.1%), respectively, P = 0.048; Mucorales: 6/102 (5.9%) vs. 2/158 (1.3%), respectively, P = 0.035). Forty-five (181/404) percent of mNGS tests yielded a positive impact on the clinical diagnosis, while 24.3% (98/404) of tests benefited the patients in antimicrobial treatment. Conclusion: mNGS is an indispensable diagnostic tool in identifying pathogens and optimizing antibiotic therapy for hematological patients receiving allo-HSCT.