Antimicrobial resistance (AMR) is a major health threat
worldwide
and the culture-based bacterial detection methods are slow. Surface-enhanced
Raman spectroscopy (SERS) can be used to identify target analytes
in real time with sensitivity down to the single-molecule level, providing
a promising solution for the culture-free bacterial detection. We
report the fabrication of SERS substrates having tightly packed silver
(Ag) nanoparticles loaded onto long silicon nanowires (Si NWs) grown
by the metal-assisted chemical etching (MACE) method for the detection
of bacteria. The optimized SERS chips exhibited sensitivity down to
10–12 M concentration of R6G molecules and detected
reproducible Raman spectra of bacteria down to a concentration of
100 colony forming units (CFU)/mL, which is a thousand times lower
than the clinical threshold of bacterial infections like UTI (105 CFU/mL). A Siamese neural network model was used to classify
SERS spectra from bacteria specimens. The trained model identified
12 different bacterial species, including those which are causative
agents for tuberculosis and urinary tract infection (UTI). Next, the
SERS chips and another Siamese neural network model were used to differentiate
AMR strains from susceptible strains of Escherichia
coli (E. coli). The enhancement offered
by SERS chip-enabled acquisitions of Raman spectra of bacteria directly
in the synthetic urine by spiking the sample with only 103 CFU/mL E. coli. Thus, the present
study lays the ground for the identification and quantification of
bacteria on SERS chips, thereby offering a potential future use for
rapid, reproducible, label-free, and low limit detection of clinical
pathogens.