A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections.

Journal: Nature communications
Published Date: Mar 4, 2020

Abstract

Improved identification of bacterial and viral infections would reduce morbidity from sepsis, reduce antibiotic overuse, and lower healthcare costs. Here, we develop a generalizable host-gene-expression-based classifier for acute bacterial and viral infections. We use training data (N = 1069) from 18 retrospective transcriptomic studies. Using only 29 preselected host mRNAs, we train a neural-network classifier with a bacterial-vs-other area under the receiver-operating characteristic curve (AUROC) 0.92 (95% CI 0.90-0.93) and a viral-vs-other AUROC 0.92 (95% CI 0.90-0.93). We then apply this classifier, inflammatix-bacterial-viral-noninfected-version 1 (IMX-BVN-1), without retraining, to an independent cohort (N = 163). In this cohort, IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.86 (95% CI 0.77-0.93), and viral-vs.-other 0.85 (95% CI 0.76-0.93). In patients enrolled within 36 h of hospital admission (N = 70), IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.92 (95% CI 0.83-0.99), and viral-vs.-other 0.91 (95% CI 0.82-0.98). With further study, IMX-BVN-1 could provide a tool for assessing patients with suspected infection and sepsis at hospital admission.

Authors

  • Michael B Mayhew
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • Ljubomir Buturovic
    Clinical Persona Inc., East Palo Alto, California. Electronic address: ljubomir@clinicalpersona.com.
  • Roland Luethy
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • Uros Midic
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • Andrew R Moore
    Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA.
  • Jonasel A Roque
    Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA.
  • Brian D Shaller
    Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA.
  • Tola Asuni
    Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA.
  • David Rawling
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • Melissa Remmel
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • Kirindi Choi
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • James Wacker
    Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
  • Purvesh Khatri
    Department of Radiation Oncology, Stanford University School of Medicine , Stanford, California 94305, United States.
  • Angela J Rogers
    Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
  • Timothy E Sweeney
    Biomedical Informatics Training Program, Stanford University, Stanford CA 94305-5479, USA.

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