Tsalik EL, Henao R, Montgomery JL, Nawrocki JW, Aydin M, Lydon EC, Ko ER, Petzold E, Nicholson BP, Cairns CB, Glickman SW, Quackenbush E, Kingsmore SF, Jaehne AK, Rivers EP, Langley RJ, Fowler VG, McClain MT, Crisp RJ, Ginsburg GS, Burke TW, Hemmert AC, and Woods CW
Objectives: Host gene expression signatures discriminate bacterial and viral infection but have not been translated to a clinical test platform. This study enrolled an independent cohort of patients to describe and validate a first-in-class host response bacterial/viral test., Design: Subjects were recruited from 2006 to 2016. Enrollment blood samples were collected in an RNA preservative and banked for later testing. The reference standard was an expert panel clinical adjudication, which was blinded to gene expression and procalcitonin results., Setting: Four U.S. emergency departments., Patients: Six-hundred twenty-three subjects with acute respiratory illness or suspected sepsis., Interventions: Forty-five-transcript signature measured on the BioFire FilmArray System (BioFire Diagnostics, Salt Lake City, UT) in ~45 minutes., Measurements and Main Results: Host response bacterial/viral test performance characteristics were evaluated in 623 participants (mean age 46 yr; 45% male) with bacterial infection, viral infection, coinfection, or noninfectious illness. Performance of the host response bacterial/viral test was compared with procalcitonin. The test provided independent probabilities of bacterial and viral infection in ~45 minutes. In the 213-subject training cohort, the host response bacterial/viral test had an area under the curve for bacterial infection of 0.90 (95% CI, 0.84-0.94) and 0.92 (95% CI, 0.87-0.95) for viral infection. Independent validation in 209 subjects revealed similar performance with an area under the curve of 0.85 (95% CI, 0.78-0.90) for bacterial infection and 0.91 (95% CI, 0.85-0.94) for viral infection. The test had 80.1% (95% CI, 73.7-85.4%) average weighted accuracy for bacterial infection and 86.8% (95% CI, 81.8-90.8%) for viral infection in this validation cohort. This was significantly better than 68.7% (95% CI, 62.4-75.4%) observed for procalcitonin (p < 0.001). An additional cohort of 201 subjects with indeterminate phenotypes (coinfection or microbiology-negative infections) revealed similar performance., Conclusions: The host response bacterial/viral measured using the BioFire System rapidly and accurately discriminated bacterial and viral infection better than procalcitonin, which can help support more appropriate antibiotic use., Competing Interests: Dr. Tsalik received in-kind support from BioFire Diagnostics by way of consumables and test instruments; received funding from Predigen, Inc.. BioFire, Inc. provided in-kind support for test development reagents used in this study. Drs. Tsalik, Henao, McClain, Ginsburg, Burke, and Woods disclosed filing for a patent pertaining to the signatures discussed in this study (WO 2017/004390 A1). Dr. Montgomery was an employee of BioFire Diagnostics, LLC. Dr. Nawrocki disclosed he has shares in BioMérieux. Dr. Lydon was supported by the Eugene A. Stead Scholarship from Duke University School of Medicine and the Infectious Diseases Society of America Medical Scholars Program. Drs. Tsalik, Ginsburg, and Woods disclosed that they are cofounders of Predigen, Inc. Drs. Tsalik, Ko, Petzold, Cairns, Kingsmore, Fowler, Ginsburg, Burke, and Woods received support for article research from the National Institutes of Health (NIH). Drs. Nawrocki and Hemmert received funding from BioFire Diagnostics, LLC.; and disclosed that they are employees of BioFire Diagnostics, LLC. Dr. Cairns is a consultant for BioMérieux, Inc. Dr. Ko’s institution received funding from the Antibiotic Resistance Leadership Group; disclosed the off-label product use of diagnostic tests. Dr. Petzold received support for article research from the Defense Advanced Research Projects Agency (DARPA) (NIH National Institute of Allergy and Infectious Diseases (NIAID) U01AI066569 and UM1AI104681 U.S. DARPA contract—N66001-09-C2082). Dr. Cairns’ institution received funding from the NIH (NIAID) and the DARPA; and received funding from BioMérieux. Dr. Kingsmore’s institution received funding from the NIH. Dr. Fowler received funding from the NIH, MedImmune, Allergan, Pfizer, Advanced Liquid Logics, Theravance, Novartis, Merck; Medical Biosurfaces; Locus; Affinergy; Contrafect; Karius; Genentech, Regeneron, Basilea, and Janssen; received funding from Basilea, Affinergy, Janssen, Basilea, Integrated Biotherapeutics; C3J, Armata, Valanbio; Akagera, Aridis, Novartis, Novadigm, Durata, Debiopharm, Genentech, Achaogen, Affinium, Medicines Co., Cerexa, Tetraphase, Trius, MedImmune, Bayer, Theravance, Basilea, Affinergy, Janssen, xBiotech, Contrafect, Regeneron, Destiny, UpToDate; Stock options Valanbio; a patent for sepsis diagnosis (US9850539B2). Dr. McClain disclosed he has patents pending on diagnostic signatures for respiratory infections. Dr. Crisp was an employee of BioFire Diagnostics and is currently an employee of BioMérieux, Inc. Dr. Ginsburg’s institution received funding from DARPA; received support for article research from the Bill & Melinda Gates Foundation. Dr. Burke is a consultant for and holds equity in Predigen, Inc. Dr. Burke’s institution received funding from the NIH; received funding from Predigen, Inc.; disclosed he is a coinventor on patents pending on Molecular Methods to Diagnose and Treat Respiratory Infections. Dr. Hemmert disclosed the off-label product use of BioFire FilmArray System. The remaining authors have disclosed that they do not have any potential conflicts of interest., (Copyright © 2021 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.)