The host response in different aetiologies of community-acquired pneumonia

Abstract

Background: Community-acquired pneumonia (CAP) can be caused by a variety of pathogens, of which Streptococcus pneumoniae, Influenza and currently SARS-CoV-2 are the most common. We sought to identify shared and pathogen-specific host response features by directly comparing different aetiologies of CAP.

Methods: We measured 72 plasma biomarkers in a cohort of 265 patients hospitalized for CAP, all sampled within 48 hours of admission, and 28 age-and sex matched non-infectious controls. We stratified the biomarkers into several pathophysiological domains- antiviral response, vascular response and function, coagulation, systemic inflammation, and immune checkpoint markers. We directly compared CAP caused by SARS-CoV-2 (COVID-19, n=39), Streptococcus pneumoniae (CAP-strep, n=27), Influenza (CAP-flu, n=22) and other or unknown pathogens (CAP-other, n=177). We adjusted the comparisons for age, sex and disease severity scores.

Findings: Biomarkers reflective of a stronger cell-mediated antiviral response clearly separated COVID-19 from other CAPs (most notably granzyme B). Biomarkers reflecting activation and function of the vasculature showed endothelial barrier integrity was least affected in COVID-19, while glycocalyx degradation and angiogenesis were enhanced relative to other CAPs. Notably, markers of coagulation activation, including D-dimer, were not different between the CAP groups. Ferritin was most increased in COVID-19, while other systemic inflammation biomarkers such as IL-6 and procalcitonin were highest in CAP-strep. Immune checkpoint markers showed distinctive patterns in viral and non-viral CAP, with highly elevated levels of Galectin-9 in COVID-19.

Interpretation: Our investigation provides insight into shared and distinct pathophysiological mechanisms in different aetiologies of CAP, which may help guide new pathogen-specific therapeutic strategies.

Funding: This study was financially supported by the Dutch Research Council, the European Commission and the Netherlands Organization for Health Research and Development.

Keywords: Aetiology; COVID-19; Community-acquired pneumonia; Host response; Influenza; Streptococcus pneumoniae.

Figure 1

Common and distinct host response biomarkers in patients with community-acquired pneumonia with different microbial aetiologies. a) Volcano plot comparing plasma biomarkers between patients with non-COVID-19 CAP (n=226) and patients with COVID-19 (n=39). X-axis depicts the fold change of Box-Cox transformed values between groups, Y-axis depicts the Benjamini-Hochberg adjusted P-value. b) Venn-Euler plot showing the number of biomarkers that are significantly different from the non-infectious control group, either specific for COVID-19, specific for non-COVID-19 CAP or common between the two disease groups. c) Heatmap depicting the Hedges’ g, a measure of effect size, between the disease groups and controls for all biomarkers in the common response. d) Volcano plots showing plasma biomarkers for CAP-strep (n=27) versus COVID-19 (n=39), CAP-flu (n=22) versus COVID-19 (n=39), and CAP-flu (n=22) versus CAP-strep (n=27). X-axis depicts the fold change of Box-Cox transformed values between groups, Y-axis depicts the Benjamini-Hochberg adjusted p-value.

Figure 2

Biomarker levels reflective of cell-mediated antiviral responses in patients with community-acquired pneumonia with different microbial aetiologies. a) Boxplots comparing cell-mediated antiviral response markers between the CAP groups. The Y-axis depicts biomarker concentrations in pg/ml (prior to Box-Cox transformation). The median value for control subjects is shown as a dashed line. The p-value listed in each boxplot is obtained from the White-adjusted ANOVA, the adjusted (adj.) P-value was obtained from the White-adjusted ANCOVA model including age, sex, and disease severity scores as covariates. The stars depict the significance of the post-hoc pairwise Games-Howell tests performed after a significant ANOVA. *P<0·05, **P<0·01, ***P<0·001, ****P<0·0001. b) Heatmap depicting the Hedges’ g between the disease groups and controls for all antiviral response markers. c) Principal component analysis (PCA) of all viral response markers. X-axis label shows the percentage of explained variance on principal component 1, Y-axis label shows the percentage of explained variance on principal component 2. The ellipse indicates the central 10% of the groups. The arrows indicate the direction (arrow orientation) and strength (arrow length) of the correlation between each marker and the principal components.

Figure 3

Biomarker levels reflective of vascular responses and function in patients with community-acquired pneumonia with different microbial aetiologies. a) Boxplots comparing markers of the endothelial response between the CAP groups. The Y-axis depicts biomarker concentrations in pg/ml (prior to Box-Cox transformation). The median value for control subjects is shown as a dashed line. The P-value listed in each boxplot is obtained from the White-adjusted ANOVA, the adjusted (adj.) P-value was obtained from the White-adjusted ANCOVA model including age, sex, and disease severity scores as covariates. The stars depict the significance of the post-hoc pairwise Games-Howell tests performed after a significant ANOVA. *P<0·05, **P<0·01, ***P<0·001, ****P<0·0001. Pairwise Tukey's post-hoc tests using the adjusted means from the ANCOVA for VEGF did not result significantly different groups. b) Heatmap depicting the Hedges’ g between the disease groups and controls for all biomarkers of the endothelial response. c) Principal component analysis of all biomarkers of the endothelial response. X-axis label shows the percentage of explained variance on principal component 1, Y-axis label shows the percentage of explained variance on principal component 2. The ellipse indicates the central 10% of the groups. The arrows indicate the direction (arrow orientation) and strength (arrow length) of the correlation between each marker and the principal components.

Figure 4

Biomarker levels reflective of coagulation in patients with community-acquired pneumonia with different microbial aetiologies. a) Boxplots comparing markers of coagulation between the CAP groups. The Y-axis depicts biomarker concentrations in pg/ml (prior to Box-Cox transformation). The median value for control subjects is shown as a dashed line. The P-value listed in each boxplot is obtained from the White-adjusted ANOVA, the adjusted (adj.) P-value was obtained from the White-adjusted ANCOVA model including age, sex, and disease severity scores as covariates. The stars depict the significance of the post-hoc pairwise Games-Howell tests performed after a significant ANOVA. *P<0·05, **P<0·01. b) Heatmap depicting the Hedges’ g between the disease groups and controls for all markers of coagulation. c) Principal component analysis of all markers of coagulation. X-axis label shows the percentage of explained variance on principal component 1, Y-axis label shows the percentage of explained variance on principal component 2. The ellipse indicates the central 10% of the groups. The arrows indicate the direction (arrow orientation) and strength (arrow length) of the correlation between each marker and the principal components.

Figure 5

Biomarker levels reflective of systemic inflammation in patients with community-acquired pneumonia with different microbial aetiologies. a) Boxplots comparing markers of systemic inflammation between the CAP groups. The Y-axis depicts biomarker concentrations (prior to Box-Cox transformation) in pg/ml for all markers except for ferritin, procalcitonin, CD163 (ng/ml) and CRP (mg/L). The median value for control subjects is shown as a dashed line. The P-value listed in each boxplot is obtained from the White-adjusted ANOVA, the adjusted (adj.) P-value was obtained from the White-adjusted ANCOVA model including age, sex, and disease severity scores as covariates. The stars depict the significance of the post-hoc pairwise Games-Howell tests performed after a significant ANOVA. *P<0·05, **P<0·01, ***P<0·001, ****P<0·0001. b) Heatmap depicting the Hedges’ g between the disease groups and controls for all markers of systemic inflammation. c) Principal component analysis of all markers of systemic inflammation. X-axis label shows the percentage of explained variance on principal component 1, Y-axis label shows the percentage of explained variance on principal component 2. The ellipse indicates the central 10% of the groups. The arrows indicate the direction (arrow orientation) and strength (arrow length) of the correlation between each marker and the principal components.

Figure 6

Immune checkpoint markers in patients with community-acquired pneumonia with different microbial aetiologies. a) Boxplots comparing immune checkpoint markers between the CAP groups. The Y-axis depicts biomarker concentrations in pg/ml (prior to Box-Cox transformation). The median value for control subjects is shown as a dashed line. The P-value listed in each boxplot is obtained from the White-adjusted ANOVA, the adjusted (adj.) P-value was obtained from the White-adjusted ANCOVA model including age, sex, and disease severity scores as covariates. The stars depict the significance of the post-hoc pairwise Games-Howell tests performed after a significant ANOVA. *P<0·05, **P<0·01, ***P<0·001, ****P<0·0001. b) Heatmap depicting the Hedges’ g between the disease groups and controls for all checkpoint markers. c) Principal component analysis of all immune checkpoint markers. X-axis label shows the percentage of explained variance on principal component 1, Y-axis label shows the percentage of explained variance on principal component 2. The ellipse indicates the central 10% of the groups. The arrows indicate the direction (arrow orientation) and strength (arrow length) of the correlation between each marker and the principal components.