Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
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Abstract
Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.
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SciScore for 10.1101/2021.03.23.21253487: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Both studies were approved by the UCSF Institutional Review Board under protocols 17-24056 and 20-30497, respectively, which granted a waiver of initial consent for tracheal aspirate and blood sampling.
Consent: Informed consent was subsequently obtained from patients or their surrogates for continued study participation, as previously described(11).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Identification and mitigation of environmental contaminants: To minimize inaccurate taxonomic … SciScore for 10.1101/2021.03.23.21253487: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Both studies were approved by the UCSF Institutional Review Board under protocols 17-24056 and 20-30497, respectively, which granted a waiver of initial consent for tracheal aspirate and blood sampling.
Consent: Informed consent was subsequently obtained from patients or their surrogates for continued study participation, as previously described(11).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Identification and mitigation of environmental contaminants: To minimize inaccurate taxonomic assignments due to environmental and reagent derived contaminants, non-templated “water only” and HeLa cell RNA controls were processed with each group of samples that underwent nucleic acid extraction. HeLasuggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)Software and Algorithms Sentences Resources Bulk RNA sequencing and host transcriptome analysis: Pathway analysis: Gene set enrichment analyses (GSEA) were performed using the fgseaMultilevel function in the R package fgsea(32) and REACTOME pathways(33) with a minimum size of 10 genes and a maximum size of 1,500 genes. Gene set enrichment analysessuggested: NoneREACTOMEsuggested: (Reactome, RRID:SCR_003485)Significant pathways were defined as those with a Benjamini-Hochberg adjusted p-value < 0.05. Ingenuity Pathway Analysis (IPA) Canonical Pathway and Upstream Regulator Analysis(34) was employed on genes with p<0.1 and ranked by the test statistic to identify cytokine regulators. Ingenuity Pathway Analysissuggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)Statistical significance of pathway expression over time between VAP and No-VAP groups was calculated using a two-way analysis of variance (ANOVA) in GraphPad PRISM. GraphPad PRISMsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Sample size is a limitation of this study; however, the reproducibility of our observations across both bulk and scRNA-seq analyses and the significant number of differentially expressed genes among the comparator groups support the validity of our conclusions. Because this study was limited to critically ill, intubated patients, we were unable to assess early stages of COVID-19, which may provide additional insight regarding determinants of secondary bacterial infection. Additionally, we were unable to assess whether epithelial cells contributed to VAP risk due to enrichment for immune cells prior to scRNA-seq. With larger cohorts, the early detection of specific immune pathway suppression and microbiome collapse could be leveraged to develop clinically useful models for identifying COVID-19 patients with increased susceptibility to secondary bacterial pneumonia.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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