Rapid identification of pathogenic bacteria using Raman spectroscopy and deep learning
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Oct 30, 2019
- Source ID
- 10.1038/s41467-019-12898-9
Entities
People
- Amr A E Saleh
- Catherine A. Hogan
- Chi-Sing Ho
- Jennifer Dionne
- Lena Blackmon
- Mark Holodniy
- Neal Jean
- Niaz Banaei
- Stefanie S Jeffrey
- Stefano Ermon
Organizations
- Alfred P. Sloan Foundation
- Gates Foundation
- United States Department of Defense