Abstract
BACKGROUND: Bacterial and viral infections are difficult to clinically distinguish, leading to antibiotic overuse and resistance. Host response signatures are an alternative to traditional pathogen-detection methods to differentiate these etiologies. Several gene expression signatures have been described although performance in ambiguous clinical phenotypes is unknown. Here, we validate a host response signature and explore its performance in microbiology-negative and co-infection cases. METHODS: RT-PCR taqman low-density array (TLDA) was used to measure 87 gene targets in a training cohort of 151 samples from patients with microbiologically confirmed and clinically adjudicated phenotypes (48 bacterial; 54 viral; 49 non-infectious illness [NI]). This data were used to construct three distinct classifiers: bacterial vs. nonbacterial; viral vs. nonviral; and non-infectious vs. infectious. This model was then applied to 75 subjects with co-infection and 40 suspected bacterial cases without microbiological confirmation. RESULTS: Leave-one-out cross validation on the training cohort demonstrated AUC values of 0.85, 0.89, and 0.88 for bacterial, viral, and NI, respectively. In 40 subjects with microbiology-negative bacterial infections, a bacterial or co-infection signature was present in 72%. Of 75 subjects with co-infection, 53 included a bacterial infection following recent viral infection and 22 were bacterial infections in patients with chronic viral infection (e.g., HCV, HIV). Bacterial infection and co-infection were successfully identified in these varied scenarios. CONCLUSION: This gene expression signature distinguished bacterial, viral, and noninfectious causes of illness. The host response was able to confirm the majority of suspected bacterial infection without confirmatory microbiology but also highlighted a viral response in many. Furthermore, the use of distinct viral and bacterial signatures was capable of identifying co-infection. Such a host gene expression strategy, when translated to a clinically useful platform, can offer new insights into the etiology of both simple and complex cases that are not currently available. DISCLOSURES: G. S. Ginsburg, Host Response Inc.: Board Member, Founder, Scientific Advisor and Shareholder, Stock (currently worth <$100). C. W. Woods, Host Response: Founder, Licensing agreement or royalty; Qvella: Collaborator, Research support; BioFire: Collaborator, none. E. L. Tsalik, Host Response, Inc..: Founder, Equity.