Comparison of plasma and blood cell samples in metagenomic next-generation sequencing for identification of the causative pathogens of fever

Background Metagenomic next-generation sequencing (mNGS) of plasma DNA has become an attractive diagnostic method for infectious diseases; however, the rate of false-positive results is high. This study aims to evaluate the diagnostic accuracy of mNGS in plasma versus blood cell samples for immunocompromised children with febrile diseases. Methods The results of conventional microbiological test and mNGS using plasma and blood cells in 106 patients with 128 episodes of febrile diseases from the Department of Hematology/Oncology were analyzed and described. Results The positivity rates for conventional microbiological test (CMT) and mNGS of plasma and blood cells were 35.9%, 84.4% and 46.9%, respectively (P<0.001). Notably, mNGS identified multiple pathogens in a single specimen in 68.5% of plasma samples and 38.3% of blood cell samples (P<0.001). Furthermore, plasma and blood cell mNGS identified causative pathogens in 58 and 46 cases, accounting for 53.7% and 76.7% of the mNGS-positive cases for each sample type, respectively (P = 0.002). By integrating results from both plasma and blood cell samples, causative pathogens were identified in 77 cases (60.2%), enhancing sensitivity to 87.5% but reducing specificity to 15.0%, compared to plasma (65.9% sensitivity and 20.0% specificity) and blood cell samples (52.3% sensitivity and 80.0% specificity). Conclusions mNGS of plasma is sensitive but has a high false-positive rate, while mNGS of blood cells has low sensitivity but higher specificity.