Rapid detection and discrimination of bacteria for biomedical and food safety applications remain a considerable challenge. We report a label-free near infrared surface-enhanced Raman scattering (NIR-SERS) method for the discrimination of pathogenic bacteria from drinking water. The approach relies on the in situ synthesis of silver nanoparticles (Ag NPs) within the bacterial cell suspensions. Pre-treatment of cells with Triton X-100 significantly improved the sensitivity of the assay. Using this method, we were able to discriminate several common pathogenic bacteria such as Escherichia coli, Pseudomonas aeruginosa, Methicillin-resistant Staphylococcus aureus (MRSA) and Listeria spp. A comparison of the SERS spectra allowed for the discrimination of two Listeria species, namely L. monocytogenes and L. innocua. We further report the application of the method to discriminate two MRSA strains from clinical isolates. The complete assay was completed in a span of 5 min. The proposed analytical method proves to be a rapid tool for selective and label-free identification of pathogenic bacterium. Pre-treatment of bacterial cells with Triton X-100 resulted in new features on the SERS spectra, allowing for a successful discrimination of common disease related bacteria including E. coli, P. aeruginosa, Listeria and MRSA. We also demonstrate that the spectral features obtained using in situ synthesis of nanoparticles could be could be used to differentiate two species of listeria. By using L. innocua as a model sample, we found the limit of detection of our assay to be 10(3) CFU/mL. The method can selectively discriminate different bacterial species, and has a potential to be used in the development of point-of-care diagnostics with biomedical and food safety applications.