Conversely, a greater representation of T-helper cell-tagging genes was found in the top 100 upregulated genes for H1N1 influenza A pneumonia (P = 2.1E-11). In addition, B-cell genes were significantly overrepresented in the H1N1 influenza A pneumonia group compared with the bacterial group 17-AAG HSP (P = 0.0062). These findings are consistent with the known biology of infection, in which bacterial infection is driven by a neutrophil-dominant response, and viral infection is driven by a lymphocyte-dominant response. Across the 5 days of patient follow-up, the expression level of T-helper cell-tagging genes is consistently higher in H1N1 influenza A, whereas the expression level of the neutrophil-tagging genes is consistently higher in the bacterial group, as shown in Figure Figure55.

Figure 4Immune 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 …Figure 5Expression 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. …A group of genes well known to be associated with viral infection, referred to as interferon-stimulated genes, were highly represented in the H1N1 influenza A gene signature. With Gene Set Enrichment Analysis, the interferon-stimulated genes were shown to be significantly enriched in the genes overexpressed in H1N1 influenza A pneumonia, compared with healthy controls (FDR = 0.

0010). In contrast, even at a 5% FDR, no significance was observed for interferon-stimulated genes among genes overexpressed in bacterial pneumonia, compared with healthy controls (FDR = 0.080). We repeated the analysis by directly comparing the bacterial and H1N1 influenza A groups. Again, a highly significant enrichment of the interferon-stimulated genes was noted in genes overexpressed in the H1N1 influenza A group (FDR = 0.0010) but not for genes overexpressed in the bacterial group (FDR = 0.97).Because the H1N1 influenza A infection group displayed a gene-expression profile distinctively different from that of bacterial infection, we explored the potential of using the gene-expression profile to diagnose H1N1 influenza A infection. By using an SVM algorithm, we found a 29-gene class predictor Anacetrapib to be highly accurate in discriminating H1N1 influenza A infection from bacterial pneumonia (Figure (Figure6).6). This ability to discriminate between bacterial and viral infection was consistent across the 5 days of patient follow-up (see Additional file 1, Figures S1 and S2).