A multi-platform approach to identify a blood-based host protein signature for distinguishing between bacterial and viral infections in febrile children (PERFORM): a multi-cohort machine learning study.

BACKGROUND

Differentiating between self-resolving viral infections and bacterial infections in children who are febrile is a common challenge, causing difficulties in identifying which individuals require antibiotics. Studying the host response to infection can provide useful insights and can lead to the identification of biomarkers of infection with diagnostic potential. This study aimed to identify host protein biomarkers for future development into an accurate, rapid point-of-care test that can distinguish between bacterial and viral infections, by recruiting children presenting to health-care settings with fever or a history of fever in the previous 72 h.

METHODS

In this multi-cohort machine learning study, patient data were taken from EUCLIDS, the Swiss Pediatric Sepsis study, the GENDRES study, and the PERFORM study, which were all based in Europe. We generated three high-dimensional proteomic datasets (SomaScan and two via liquid chromatography tandem mass spectrometry, referred to as MS-A and MS-B) using targeted and untargeted platforms (SomaScan and liquid chromatography mass spectrometry). Protein biomarkers were then shortlisted using differential abundance analysis, feature selection using forward selection-partial least squares (FS-PLS; 100 iterations), along with a literature search. Identified proteins were tested with Luminex and ELISA and iterative FS-PLS was done again (25 iterations) on the Luminex results alone, and the Luminex and ELISA results together. A sparse protein signature for distinguishing between bacterial and viral infections was identified from the selected proteins. The performance of this signature was finally tested using Luminex assays and by calculating disease risk scores.

FINDINGS

376 children provided serum or plasma samples for use in the discovery of protein biomarkers. 79 serum samples were collected for the generation of the SomaScan dataset, 147 plasma samples for the MS-A dataset, and 150 plasma samples for the MS-B dataset. Differential abundance analysis, and the first round of feature selection using FS-PLS identified 35 protein biomarker candidates, of which 13 had commercial ELISA or Luminex tests available. 16 proteins with ELISA or Luminex tests available were identified by literature review. Further evaluation via Luminex and ELISA and the second round of feature selection using FS-PLS revealed a six-protein signature: three of the included proteins are elevated in bacterial infections (SELE, NGAL, and IFN-γ), and three are elevated in viral infections (IL18, NCAM1, and LG3BP). Performance testing of the signature using Luminex assays revealed area under the receiver operating characteristic curve values between 89·4% and 93·6%.

INTERPRETATION

This study has led to the identification of a protein signature that could be ultimately developed into a blood-based point-of-care diagnostic test for rapidly diagnosing bacterial and viral infections in febrile children. Such a test has the potential to greatly improve care of children who are febrile, ensuring that the correct individuals receive antibiotics.

FUNDING

European Union's Horizon 2020 research and innovation programme, the European Union's Seventh Framework Programme (EUCLIDS), Imperial Biomedical Research Centre of the National Institute for Health Research, the Wellcome Trust and Medical Research Foundation, Instituto de Salud Carlos III, Consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Grupos de Refeencia Competitiva, Swiss State Secretariat for Education, Research and Innovation.

Informations de copyright

Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests AJP, AJC, MP, SM, MNT, ML, WZ, RdG, and UvB disclose payments made to institution through the PERFORM consortium from EU Horizon 2020 Programme (grant number 668303). AJC discloses funding from National Institute for Health and Care Research (NIHR; grant number NIHR134694), EPSRC (grant number EP/T029005/1), and EU Horizon Europe Programme (grant number 848196) in addition to support from the European Society for Paediatric Infectious Disease and Excellence in Paediatrics Institute for attending or travelling to meetings; a patent for a new diagnostic method for infection in children unrelated to the current study; and an unpaid role as Chair of Committee for Scientific Affairs and Awards, European Society for Paediatric Infectious Disease. AJP discloses funding from The Bill & Melinda Gates Foundation, the Wellcome Trust, Cepi, Medical Research Council, and NIHR to their institution, an Institutional (Oxford University) partnership with AstraZeneca for development of COVID-19 vaccines, consulting fees from Shionogi for a COVID-19 vaccine, and acting as unpaid chair of the UK's Department of Health and Social Care's Joint Committee on Vaccination and Immunisation and an unpaid member of WHO's SAGE until 2022. MWT discloses support from Janssen and Pfizer for attending or travelling to meetings, unpaid contributions to the National Committee on Immunization Practices, Greece and the Scientific Advisory Group of Experts for COVID-19, Greece, and acting as the President of the Hellenic Society for Paediatric Infectious Diseases. FM-T discloses consulting fees from Sanofi, MSD, Moderna, GSK, Biofabri, AstraZeneca, Novovax, Jansenn, and Pfizer as honoraria for lectures and presentations; support from Pfizer, MSD, GSK, and Sanofi for travel expenses and meeting fees; participation on a data safety monitoring board or advisory board for Pfizer and Biofabri; is a member of The European Technical Advisory Group of Experts (ETAGE) with WHO Europe, Coordinator of Spanish Pediatric Critical Trials Network, and Coordinator of WHO Collaborating Centre for Vaccine Safety of Santiago de Compostela; and is principal investigator in randomised controlled trials of Ablynx, Abbot, Seqirus, Sanofi, MSD, Merck, Pfizer, Roche, Regeneron, Jansen, Medimmune, Novavax, Novartis, and GSK. PKAA discloses Sanofi Nirsevimab payment to institution. HRJ, JZ, ML, MK, TWK and MIdJ have filed a patent application for the six-protein signature described here. CF is co-founder and Medical Director of Micropathology. All other authors declare no competing interests.