FilmArray® Measurement of Host Response Signatures Rapidly Discriminates Viral, Bacterial, and Non-Infectious Etiologies of Illness

Background: The inability to reliably discriminate bacterial, viral, and non-infectious illness has led to an epidemic of antibiotic overuse and rising rates of antimicrobial resistance. Host gene expression provides a powerful approach to distinguish infection etiologies and guide appropriate therapy. However, existing platforms for transcriptomic analysis are not amenable for clinical application. The FilmArray platform is a sample-to-answer multiplex RT-PCR system that automates transcriptomic analysis including sample preparation and data analysis. Here we report the validation of a host gene expression FilmArray test to discriminate bacterial, viral, and non-infectious etiologies of illness.

Methods: Research use only (RUO) FilmArray pouches were manufactured with 45 host response assays previously shown to discriminate bacterial, viral, and non-infectious illness. These pouches were tested on whole blood samples from 226 patients with acute respiratory illness (ARI). Using clinical adjudication as the reference standard, there were 52 bacterial, 100 viral, and 75 non-infectious cases. Quantification cycles were recorded for each assay and normalized to an internal control. A logistic regression model generated probabilities of each condition, which were used to classify subjects.

Results: Beginning with 100ul of blood, the FilmArray host response panel provided results in ~45 minutes from sample to answer. Overall accuracy for bacterial ARI relative to clinical adjudication was 85% with an area under the receiver operating characteristic curve (AUC) of 0.92. Accuracy and AUC for viral infection were 85% and 0.91, respectively. Ill patients without infection were correctly identified 86% of the time with an AUC of 0.88.

Conclusion: These results show that the FilmArray system can rapidly measure host gene expression to accurately discriminate bacterial, viral, and non-infectious illness. The development of such a system creates a new option to mitigate inappropriate antibiotic use. It also presents opportunities to use host gene expression as a diagnostic modality for a variety of disease states.