AUTHOR=Lu Weilai , Li Haifei , Qiu Haoning , Wang Lu , Feng Jie , Fu Yu Vincent TITLE=Identification of pathogens and detection of antibiotic susceptibility at single-cell resolution by Raman spectroscopy combined with machine learning JOURNAL=Frontiers in Microbiology VOLUME=13 YEAR=2023 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.1076965 DOI=10.3389/fmicb.2022.1076965 ISSN=1664-302X ABSTRACT=

Rapid, accurate, and label-free detection of pathogenic bacteria and antibiotic resistance at single-cell resolution is a technological challenge for clinical diagnosis. Overcoming the cumbersome culture process of pathogenic bacteria and time-consuming antibiotic susceptibility assays will significantly benefit early diagnosis and optimize the use of antibiotics in clinics. Raman spectroscopy can collect molecular fingerprints of pathogenic bacteria in a label-free and culture-independent manner, which is suitable for pathogen diagnosis at single-cell resolution. Here, we report a method based on Raman spectroscopy combined with machine learning to rapidly and accurately identify pathogenic bacteria and detect antibiotic resistance at single-cell resolution. Our results show that the average accuracy of identification of 12 species of common pathogenic bacteria by the machine learning method is 90.73 ± 9.72%. Antibiotic-sensitive and antibiotic-resistant strains of Acinetobacter baumannii isolated from hospital patients were distinguished with 99.92 ± 0.06% accuracy using the machine learning model. Meanwhile, we found that sensitive strains had a higher nucleic acid/protein ratio and antibiotic-resistant strains possessed abundant amide II structures in proteins. This study suggests that Raman spectroscopy is a promising method for rapidly identifying pathogens and detecting their antibiotic susceptibility.