Background The diagnosis of infections in stem-cell transplant (SCT) patients is challenging. There is a need for improved diagnostics that can quickly and accurately detect a broad range of viruses, bacteria, and fungi that can infect these patients to guide targeted therapy. Methods We enrolled 20 patients in a prospective study evaluating the Karius plasma next-generation sequencing (plasma NGS) test to detect infections in SCT patients. Patients had baseline plasma samples drawn prior to transplant followed by weekly collections during engraftment and at onset of febrile episodes. Samples were transferred to the Karius CLIA/CAP laboratory (Redwood City, CA) where cell-free DNA was extracted from plasma and NGS performed. Human sequences were removed and remaining reads were aligned against a curated pathogen database. Organisms present at a significance level above a predefined threshold were reported. Results Cytomegalovirus (CMV) was identified in 12/20 patients. Using a nearest-neighbor method, 61 pairs of observations were identified for a comparison of plasma NGS and CMV qPCR collected within 1 day of each other. Positive agreement (PPA) between plasma NGS and CMV qPCR was 84.1% (37/44). PPA was 100% (20/20) when values below the lower limit of quantitation (
