EBioMedicine (Oct 2023)
A multicenter prospective study of comprehensive metagenomic and transcriptomic signatures for predicting outcomes of patients with severe community-acquired pneumoniaResearch in context
- Jingya Zhao,
- Xiangyan He,
- Jiumeng Min,
- Rosary Sin Yu Yao,
- Yu Chen,
- Zhonglin Chen,
- Yi Huang,
- Zhongyi Zhu,
- Yanping Gong,
- Yusang Xie,
- Yuping Li,
- Weiwei Luo,
- Dongwei Shi,
- Jinfu Xu,
- Ao Shen,
- Qiuyue Wang,
- Ruixue Sun,
- Bei He,
- Yang Lin,
- Ning Shen,
- Bin Cao,
- Lingling Yang,
- Danyang She,
- Yi Shi,
- Jiali Zhou,
- Xin Su,
- Hua Zhou,
- Zhenzi Ma,
- Hong Fan,
- Yongquan Lin,
- Feng Ye,
- Xifang Nie,
- Qiao Zhang,
- Xinlun Tian,
- Guoxiang Lai,
- Min Zhou,
- Jinmin Ma,
- Jing Zhang,
- Jieming Qu
Affiliations
- Jingya Zhao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
- Xiangyan He
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Jiumeng Min
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Rosary Sin Yu Yao
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Yu Chen
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Zhonglin Chen
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Yi Huang
- Department of Pulmonary and Critical Care Medicine, Changhai Hospital, Shanghai, China
- Zhongyi Zhu
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Yanping Gong
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Yusang Xie
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
- Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital Wenzhou Medical College, Zhejiang, China
- Weiwei Luo
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Dongwei Shi
- Department of Emergency Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Jinfu Xu
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
- Ao Shen
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Qiuyue Wang
- Department of Pulmonary and Critical Care Medicine, The First Hospital of China Medical University, Shenyang, China
- Ruixue Sun
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Bei He
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Yang Lin
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Bin Cao
- Department of Pulmonary and Critical Care Medicine, China–Japan Friendship Hospital, Beijing, China
- Lingling Yang
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Danyang She
- Department of Pulmonary and Critical Care Medicine, The General Hospital of the People’s Liberation Army, Beijing, China
- Yi Shi
- Department of Pulmonary and Critical Care Medicine, Jinling Hospital, Nanjing, China
- Jiali Zhou
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Xin Su
- Department of Pulmonary and Critical Care Medicine, Jinling Hospital, Nanjing, China
- Hua Zhou
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital Zhejiang University, Hangzhou, China
- Zhenzi Ma
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Hong Fan
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Sichuan, China
- Yongquan Lin
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Feng Ye
- Department of Pulmonary and Critical Care Medicine, The First Affiliate Hospital of Guangzhou Medical University, Guangzhou, China
- Xifang Nie
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
- Qiao Zhang
- Department of Pulmonary and Critical Care Medicine, Xinqiao Hospital of Army Medical University, Chongqing, China
- Xinlun Tian
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
- Guoxiang Lai
- Department of Pulmonary and Critical Care Medicine, Fuzhou General Hospital, Fuzhou, China
- Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China; Corresponding author. Ruijin Hospital, Shanghai Jiao Tong University, No. 197 Ruijin’er Road, Shanghai 200025, China.
- Jinmin Ma
- Clin Lab, BGI Genomics, Shenzhen 518083, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China; Corresponding author. BGI-ShenzhenDabaihui Health Industry Park, No. 2028 Shenyan Road, Yantian District, Shenzhen, Guangdong 518083, China.
- Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Corresponding author. Zhongshan Hospital, Shanghai Medical College, Fudan University, No. 180 Fenglin Road, Shanghai 200032, China.
- Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China; Corresponding author. Ruijin Hospital, Shanghai Jiao Tong University, No. 197 Ruijin’er Road, Shanghai 200025, China.
- Journal volume & issue
-
Vol. 96
p. 104790
Abstract
Summary: Background: Severe community-acquired pneumonia (SCAP) results in high mortality as well as massive economic burden worldwide, yet limited knowledge of the bio-signatures related to prognosis has hindered the improvement of clinical outcomes. Pathogen, microbes and host are three vital elements in inflammations and infections. This study aims to discover the specific and sensitive biomarkers to predict outcomes of SCAP patients. Methods: In this study, we applied a combined metagenomic and transcriptomic screening approach to clinical specimens gathered from 275 SCAP patients of a multicentre, prospective study. Findings: We found that 30-day mortality might be independent of pathogen category or microbial diversity, while significant difference in host gene expression pattern presented between 30-day mortality group and the survival group. Twelve outcome–related clinical characteristics were identified in our study. The underlying host response was evaluated and enrichment of genes related to cell activation, immune modulation, inflammatory and metabolism were identified. Notably, omics data, clinical features and parameters were integrated to develop a model with six signatures for predicting 30-day mortality, showing an AUC of 0.953 (95% CI: 0.92–0.98). Interpretation: In summary, our study linked clinical characteristics and underlying multi-omics bio-signatures to the differential outcomes of patients with SCAP. The establishment of a comprehensive predictive model will be helpful for future improvement of treatment strategies and prognosis with SCAP. Funding: National Natural Science Foundation of China (No. 82161138018), Shanghai Municipal Key Clinical Specialty (shslczdzk02202), Shanghai Top-Priority Clinical Key Disciplines Construction Project (2017ZZ02014), Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100).
