Metatranscriptome of human lung microbial communities in a cohort of mechanically ventilated COVID-19 Omicron patients.
Lin WangJia-Bao CaoBin-Bin XiaYue-Juan LiXuan ZhangGuo-Xin MoRui-Juan WangSi-Qi GuoYu-Qing ZhangKun XiaoGuang-Fa ZhuPeng-Fei LiuLi-Cheng SongXi-Hui MaPing-Chao XiangJiang WangYu-Hong LiuFei XieXu-Dong ZhangXiang-Xin LiWan-Lu SunYan CaoKai-Fei WangWen-Hui ZhangWei-Chao ZhaoPeng YanJi-Chao ChenYu-Wei YangZhong-Kuo YuJing-Si TangLi XiaoJie-Min ZhouLi-Xin XieJun WangPublished in: Signal transduction and targeted therapy (2023)
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 host immune responses and microbial compositions, besides synergy within viral, bacterial, and fungal pathogens. Our study presents the relationships of lower respiratory tract microbiome and transcriptome in invasive ventilated COVID-19 patients, providing the basis for future clinical treatment and reduction of fatality.
Keyphrases
- sars cov
- respiratory syndrome coronavirus
- respiratory tract
- end stage renal disease
- single cell
- intensive care unit
- coronavirus disease
- acute respiratory distress syndrome
- chronic kidney disease
- newly diagnosed
- immune response
- ejection fraction
- genome wide
- escherichia coli
- peritoneal dialysis
- microbial community
- risk factors
- healthcare
- prognostic factors
- type diabetes
- cardiovascular events
- pseudomonas aeruginosa
- cardiovascular disease
- dna methylation
- mechanical ventilation
- inflammatory response
- community acquired pneumonia
- cystic fibrosis
- copy number
- transcription factor
- electronic health record
- current status
- wastewater treatment
- respiratory failure
- data analysis
- patient reported