Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (bulkRNA-seq)

We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found. Tracheal aspirate samples were processed for either bulk or single-cell RNA sequencing: 1) Bulk RNA-sequencing from 7 patients with severe COVID-19 patients who developed VAP, 10 COVID-19 patients who did not develop VAP, and 8 patients intubated but COVID-19 negative; 2) Single cell RNA-sequencing from 7 COVID-19 patients who developed VAP and 8 COVID-19 patients who did not develop VAP. Differential gene expression was analyzed for COVID-19 patients who developed VAP versus those who did not at: a) "early" time-point (median 2 days post intubation), 2) "late" time-point (median 2 days before VAP diagnosis), and when available c) differential gene expression also analyzed in those who developed VAP comparing the "early" and "late" time-points. Lastly, differential gene expression was done in the bulk RNA-sequencing in COVID-19 positive versus control patients at the "early" time-point. *** Raw data is not included in this GEO submission due to patient privacy concerns ***