Abstract
Abstract
Raman optical spectroscopy promises label-free bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving clinically relevant speeds and accuracies remains challenging due to weak Raman signal from bacterial cells and numerous bacterial species and phenotypes. Here we generate an extensive dataset of bacterial Raman spectra and apply deep learning approaches to accurately identify 30 common bacterial pathogens. Even on low signal-to-noise spectra, we achieve average isolate-level accuracies exceeding 82% and antibiotic treatment identification accuracies of 97.0±0.3%. We also show that this approach distinguishes between methicillin-resistant and -susceptible isolates of Staphylococcus aureus (MRSA and MSSA) with 89±0.1% accuracy. We validate our results on clinical isolates from 50 patients. Using just 10 bacterial spectra from each patient isolate, we achieve treatment identification accuracies of 99.7%. Our approach has potential for culture-free pathogen identification and antibiotic susceptibility testing, and could be readily extended for diagnostics on blood, urine, and sputum.
Funder
Bill and Melinda Gates Foundation
Stanford Catalyst for Collaborative Solutions
U.S. Department of Defense
Alfred P. Sloan Foundation
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry
Reference52 articles.
1. Fleischmann, C. et al. Assessment of global incidence and mortality of hospital-treated sepsis. current estimates and limitations. Am. J. Respir. Crit. Care Med. 193, 259–272 (2016).
2. DeAntonio, R., Yarzabal, J.-P., Cruz, J. P., Schmidt, J. E. & Kleijnen, J. Epidemiology of community-acquired pneumonia and implications for vaccination of children living in developing and newly industrialized countries: A systematic literature review. Hum. Vaccin. Immunother. 12, 2422–2440 (2016).
3. Torio, C.M. & Moore, B.J. National inpatient hospital costs: The most expensive conditions by payer, 2013. Tech. Rep. HCUP Statistical Brief #204., Agency for Healthcare Research and Quality (2016).
4. Dellinger, R. P. et al. Surviving sepsis campaign: international guidelines for management of severe sepsis and septic shock: 2012.
5. Chaudhuri, A. et al. EFNS guideline on the management of community-acquired bacterial meningitis: report of an EFNS task force on acute bacterial meningitis in older children and adults. Eur. J. Neurol. 15, 649–659 (2008).
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