Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infections after Allogeneic Hematopoietic Stem Cell Transplantation

Abstract

Early and accurate identification of pathogens is still challenging in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The clinical usefulness of metagenomic next-generation sequencing (mNGS) remains under discussion in diagnosis of pulmonary infections after allo-HSCT. This multi-center retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in investigating the pathogens of pulmonary infections in allo-HSCT recipients. A hundred and forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs were performed in BALF. Among 140 allo-HSCT recipients with suspected pulmonary infections, the positive rate of mNGS was 71.4% whereas the positive rate of CMTs was 55.0%. mNGS identified 182 pathogens included bacteria (n = 88), fungi (n = 35) and viruses (n = 59) while 106 pathogens were detected by CMTs included bacteria (n = 31), fungi (n = 24) and viruses (n = 51). Ninety-eight patients were finally diagnosed as pulmonary infections, including 22 bacterial infections, 7 fungal,18 viral, 48 mixed infections, and 3 with unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections were 88.8% and 69.4%, respectively (P=0.001) while the specificity were 81.0% and 85.7%, respectively (P = 0.688). mNGS might be a promising technology for diagnosis of pulmonary infections in the recipients of allo-HSCT.