Rapid and sensitive discrimination among carbapenem resistant and susceptible E. coli strains using Surface Enhanced Raman Spectroscopy combined with chemometric tools

Background: Raman spectroscopy is a powerful technique for the robust, reliable and rapid detection and discrimination of bacteria. Objectives: To develop a rapid and sensitive technique based on surface-enhanced Raman spectroscopy (SERS) with multivariate data analysis tools for discrimination among carbapenem resistant and susceptible E. coli strains. Methods: SERS was employed to differentiate different strains of carbapenem resistant and susceptible E. coli by using silver nanoparticles (Ag NPs) as a SERS substrate. For this purpose, four strains of carbapenem resistant and three strains of carbapenem susceptible E. coli were analyzed by comparing their SERS spectral signatures. Furthermore, multivariate data analysis techniques including Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were performed over the spectral range of 400-1800 cm-1 (fingerprint region) for the identification and differentiation of different E. coli strains. Results: The SERS spectral features associated with resistant development against carbapenem antibiotics were separated by comparing each spectrum of susceptible strains with each resistant strain. PCA and HCA were found effective for the qualitative differentiation of all the strains analysed. PLS-DA successfully discriminated the carbapenem resistant and susceptible E. coli pellets on the strain level with 99.8 % sensitivity, 100 % specificity, 100 % accuracy and 86 % area under receiver operating characteristic (AUROC) curve. Conclusion: SERS can be employed for the rapid discrimination among carbapenem resistant and susceptible strains of E. coil.