The diagnostic value of RNA-mNGS and DNA-mNGS in differentiating bacterial infection from colonization in the lower respiratory tract.

Background: Metagenomic next-generation sequencing(mNGS) has been widely used in the pathogenetic diagnosis of lower respiratory tract infections. However, the interpretation of pathogens detected by mNGS remains inconclusive. Objective: Our study aimed to compare the differential diagnostic value of sequencing reads and the relative abundance of bacteria detected by RNA-mNGS versus DNA-mNGS in distinguishing between bacterial infection and colonization in the lower respiratory tract. Methods: The hospitalized patients with suspected lower respiratory tract infections who had completed RNA-mNGS and DNA-mNGS testing at our hospital from June 2021 to December 2023 were reviewed and divided into two groups: the infected group and the colonized group, based on their final diagnoses. The Mann-Whitney U test was used to analyze differences in the number of bacterial sequencing reads and relative abundance between the two groups; the predictive capability of bacterial sequencing reads and relative abundance for identifying bacterial infections was evaluated using receiver operating characteristic (ROC) curves. Results: A total of 69 eligible patients were enrolled, with 85 detections of the four target bacterial species ( Conclusions: Bacterial relative abundance and sequencing reads can serve as indicators to distinguish between infection and colonization, and the relative abundance based on RNA-mNGS exhibits the best differential diagnostic performance; when DNA-mNGS results stand alone, the relative abundance of the detected bacteria and the ratio of relative abundance between the first-ranked and the second-ranked detected bacteria can be utilized for a comprehensive assessment of infection versus colonization.