A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia

Abstract

Introduction: Diagnosis of severe influenza pneumonia remains challenging because of a lack of correlation between the presence of influenza virus and clinical status. We conducted gene-expression profiling in the whole blood of critically ill patients to identify a gene signature that would allow clinicians to distinguish influenza infection from other causes of severe respiratory failure, such as bacterial pneumonia, and noninfective systemic inflammatory response syndrome.

Methods: Whole-blood samples were collected from critically ill individuals and assayed on Illumina HT-12 gene-expression beadarrays. Differentially expressed genes were determined by linear mixed-model analysis and overrepresented biological pathways determined by using GeneGo MetaCore.

Results: The gene-expression profile of H1N1 influenza A pneumonia was distinctly different from those of bacterial pneumonia and systemic inflammatory response syndrome. The influenza gene-expression profile is characterized by upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways. In contrast, no distinctive gene-expression signature was found in patients with bacterial pneumonia or systemic inflammatory response syndrome. The gene-expression profile of influenza infection persisted through 5 days of follow-up. Furthermore, in patients with primary H1N1 influenza A infection in whom bacterial co-infection subsequently developed, the influenza gene-expression signature remained unaltered, despite the presence of a superimposed bacterial infection.

Conclusions: The whole-blood expression-profiling data indicate that the host response to influenza pneumonia is distinctly different from that caused by bacterial pathogens. This information may speed the identification of the cause of infection in patients presenting with severe respiratory failure, allowing appropriate patient care to be undertaken more rapidly.

Figure 1

Overlap of differentially expressed genes in H1N1 influenza A pneumonia, bacterial pneumonia, and noninfective systemic inflammatory response syndrome. Venn diagrams for genes upregulated (A) and genes downregulated (B) compared with healthy controls, at 5% false-discovery rate. H1N1 influenza A pneumonia (H1N1), bacterial pneumonia (Bacteria), noninfective systemic inflammatory response syndrome (SIRS).

Figure 2

The top-ranking biological pathways in genes upregulated in H1N1 influenza A infection, ordered by statistical significance (with cell cycle being the most significant among the top 10 pathways).

Figure 3

Representation of biological pathway ontologies in the downregulated genes at 5% false discovery rate (FDR) for H1N1 influenza A, bacterial pneumonia, and systemic inflammatory response syndrome (SIRS), compared with healthy controls.

Figure 4

Immune cell deconvolution of the top 100 upregulated genes for bacterial pneumonia and H1N1 influenza A pneumonia, compared with healthy controls. Fisher Exact test two-tailed P values are given for cell types with significantly different proportions between the two groups.

Figure 5

Expression of neutrophil and T-helper cell-specific genes across 5 days for H1N1 influenza A pneumonia and bacterial pneumonia patients. Intensity of red corresponds to level of upregulation, whereas intensity of green refers to level of downregulation.

Figure 6

The Support Vector Machines (SVM) class-prediction integer in training and validation datasets. The x-axis corresponds to the threshold of 36.03, with all samples falling above the line predicted as belonging to an individual with influenza infection. Correctly predicted samples are shaded blue; incorrectly predicted samples are shaded red.

Figure 7

Dendrogram for clustering bacterial (CAP), H1N1 influenza A (H1N1), systemic inflammatory response syndrome (SIRS), and concurrent bacterial and H1N1 influenza A infection (CAP+H1N1) patients for the 29-gene signature by using Euclidean distance and average linkage (all samples were obtained on day 1).