Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients

作者：Lin Wang, Jia-Bao Cao, Binbin Xia, Yuejuan Li, Xuan Zhang, Guoxin Mo, Ruijuan Wang, Siqi Guo, Yuqing Zhang, Kun Xiao, Guangfa Zhu, Pengfei Liu, Li‐Cheng Song, Xi-Hui Ma, Pingchao Xiang, Jiang Wang, Jiang Wang, Yu-Hong Liu, Fei Xie, Xudong Zhang, Xiangxin Li, Wanlu Sun, Yan Cao, Kai-Fei Wang, Weichao Zhao, Wei-Chao Zhao, Peng Yan, Jichao Chen, Yuwei Yang, Zhong-Kuo Yu, Jing-Si Tang, Li Xiao, Jiemin Zhou, Lixin Xie, Jun Wang, Jun Wang · 发表于：Signal Transduction and Targeted Therapy · 年份：2023 · DOI：10.1038/s41392-023-01684-1 · 被引用次数：20 · 研究领域：Gut microbiota and health、Respiratory viral infections research、Antifungal resistance and susceptibility

The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infected a substantial proportion of Chinese population, and understanding the factors underlying the severity of the disease and fatality is valuable for future prevention and clinical treatment. We recruited 64 patients with invasive ventilation for COVID-19 and performed metatranscriptomic sequencing to profile host transcriptomic profiles, plus viral, bacterial, and fungal content, as well as virulence factors and examined their relationships to 28-day mortality were examined. In addition, the bronchoalveolar lavage fluid (BALF) samples from invasive ventilated hospital/community-acquired pneumonia patients (HAP/CAP) sampled in 2019 were included for comparison. Genomic analysis revealed that all Omicron strains belong to BA.5 and BF.7 sub-lineages, with no difference in 28-day mortality between them. Compared to HAP/CAP cohort, invasive ventilated COVID-19 patients have distinct host transcriptomic and microbial signatures in the lower respiratory tract; and in the COVID-19 non-survivors, we found significantly lower gene expressions in pathways related viral processes and positive regulation of protein localization to plasma membrane, higher abundance of opportunistic pathogens including bacterial Alloprevotella, Caulobacter, Escherichia-Shigella, Ralstonia and fungal Aspergillus sydowii and Penicillium rubens. Correlational analysis further revealed significant associations between ...