Metagenomic NGS and Targeted NGS Driven Precision Therapy in Pediatric Chemotherapy-Associated Infections: A Single-Center Retrospective Study

Background Infections in immunocompromised pediatric hematology-oncology patients present a major challenge. This study utilized pathogen NGS (metagenomic next generation sequencing (mNGS) / targeted next generation sequencing (tNGS)) to characterize the microbial spectrum in this population, thereby enhancing detection and enabling targeted antimicrobial therapy. Methods This retrospective study enrolled pediatric patients with hematologic malignancies. The analysis employed descriptive statistics for pathogen profiles and comparative statistics to assess variations by clinical stage and outcome, and to evaluate NGS against traditional pathogen detection (TPD). Results This study included 72 children with a median age of 8 years. A total of 83 NGS tests were performed. Microbial organisms were detected by NGS in 70 samples, yielding 26 bacterial, 14 viral, and 12 fungal species. No statistically significant difference in NGS positivity was observed between the non-agranulocytosis (A1) and agranulocytosis (A2) groups ( P  = 0.374). Escherichia coli (n  = 5), Candida albicans (n  = 5), and Human beta herpesvirus 5 (CMV, n  = 21) were the most prevalent bacterial, fungal, and viral pathogens, respectively. Analysis of blood samples revealed that Escherichia coli, Aspergillus flavus , and Human gamma herpesvirus 4 (EBV) were the predominant bacterial, fungal, and viral pathogens, respectively. Statistical comparison revealed comparable rates of viremia between groups A1 and A2 ( P >0.999), whereas group A2 had a greater risk of bloodstream infection ( P  = 0.023). Among the 61 blood samples, 49 (80.3%) were positive by mNGS, whereas only 7 were positive by TPD)(all of which were also mNGS-positive). All 11 pulmonary samples tested by tNGS were positive, while TPD was positive in only 1 specimen. tNGS identified Pneumocystis jirovecii in 3 samples, all of which were missed by TPD. NGS-guided antibiotic adjustment in 53.5% of patients with bacterial/fungal infections led to a favorable outcome, with an 88.4% cure rate after a median treatment of 12.1 days. Conclusions This study identified predominant pathogens ( Escherichia coli . Candida albicans s, CMV) and demonstrated that NGS, which is agranulocytosis, enhances detection of bacterial/fungal infections, enabling precision antimicrobial therapy in pediatric chemotherapy patients. Clinical trial number: not applicable. Trial registration: not applicable.