Plasma metagenomic sequencing testing for diagnosis of invasive fungal infection in children and young adults.

Invasive fungal infection (IFI) is challenging to diagnose, often involving invasive sampling. Plasma cell-free metagenomic next-generation sequencing (mNGS) has shown promise in diagnosing infections, but data are limited on specific clinical scenarios in which this test is most helpful. We conducted a retrospective single-center study of children and young adults with high-risk conditions evaluated for IFI between December 2016 and November 2024. Clinical concern for IFI was indicated by (i) evaluation with both serum β-D-glucan and galactomannan testing, (ii) either or both of CT scans of sinuses and chest, and (iii) antifungal treatment either started or broadened. Episodes in which mNGS testing was sent within 30 days of initiation or broadening of antifungal coverage were evaluated to determine the diagnostic performance of mNGS testing, using EORTC-MSG criteria for proven or probable IFI as the comparator. We identified 227 episodes in 180 high-risk patients consistent with clinical concern for IFI. Of these, 45 episodes met EORTC-MSG criteria for proven/probable IFI. Plasma mNGS testing was sent in 36 episodes and identified the causative organism in 28. Positive and negative percent agreement for diagnosis of proven/probable IFI in this population was 77.8% and 90.4%, respectively. Among proven/probable cases with mNGS testing, IMPORTANCE: Performance of plasma mNGS testing for diagnosis of invasive fungal infection in high-risk pediatric and young adult patients was comparable to the combination of fungal culture and targeted PCR from invasively acquired samples, suggesting that it might allow earlier diagnosis for some patients.