A Pilot Study on Single-Cell Raman Spectroscopy Combined with Machine Learning for Phenotypic Characterization of Staphylococcus aureus

Rapid and accurate identification of pathogenic bacteria phenotypic traits, including virulence, drug resistance, and metabolic activity, is essential for clinical diagnosis and infectious disease control. Traditional methods are time-consuming, highlighting the need for more efficient approaches. This study develops a single-cell Raman spectroscopy approach to detect multiple phenotypic traits of Staphylococcus aureus (S. aureus) as a proof of concept. We constructed a single-cell Raman spectral database encompassing 6240 spectra from 10 strains of S. aureus with diverse phenotypic traits and developed a convolutional neural network (CNN) to predict these phenotypes from the Raman spectra. The CNN model achieved 93.90%, 98.73%, and 98.66% accuracy in identifying enterotoxin-producing strains, methicillin-resistant S. aureus (MRSA), and growth stages, respectively. Characteristic Raman peaks for enterotoxin producers mainly appeared at 781, 939, 1161, 1337, 1451, and 1524 cm−1, whereas MRSA primarily exhibited peaks at 723, 780, 939, 1095, 1162, 1340, 1451, 1523, and 1660 cm−1. During culture, nucleic acid-related peaks weakened, lipid peaks increased, and protein peaks initially increased and subsequently decreased. This integration of Raman spectroscopy and machine learning demonstrates considerable potential for rapid bacterial phenotyping. Future research should expand to a wider range of bacterial species and phenotypes to enhance the diagnosis, prevention, and management of infectious diseases.