Clinical Features of Microbial Reactivation in Early Onset of Severe Pneumonia by Metagenomic Next-Generation Sequencing in Intensive Care Units, a Multicenter, Retrospective Study

Abstract Purpose: This study aims to assess the clinical features of microorganism reactivation in the early onset of severe pneumonia in ICU patients.Methods: A total of 97 patients’ clinical data was collected retrospectively from intensive care units of five teaching hospitals in China from June 2018 to July 2021 followed by metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid (BALF) at the onset of severe pneumonia.Results: A total of 43 pathogenic microorganisms were detected in 97 patients with severe pneumonia by mNGS, where CMV (21.6%), HSV-1 (18.6%), and Pneumocystis (14.4%) were the most common reactivated microorganisms in the lungs of patients with severe pneumonia. In the present study, reactivation was considered when mNGS detected CMV, HSV-1, or Pneumocystisc DNA. A total of 11 patients (11.3%) had two or more reactivated microorganisms, and the overall rate of microbial reactivation was 40.2%. After adjusting for the risk of confounding and competition, one or more reactivations of CMV, HSV-1, and Pneumocystis resulted in an overall increase of 2.381 folds of mortality (95% CI: 1.198-4.733). Conclusion: This study showed that CMV, HSV-1, and Pneumocystis were the most common reactivated microorganisms in the lungs of patients in the ICU at the onset of severe pneumonia. Reactivation of two or three microorganisms is common and is associated with an increased risk of mortality.