Andrei Novikov
Gubkin University
Andrei Novikov graduated in 2007 from Perm State University with M.Sc. in Organic Chemistry. He acquired Ph.D. degree in Gubkin University in 2010 with thesis dedicated to isolation and description of novel species of bacteria Carboxydothermus islandicus, and the studying of biocatalysis of water-gas shift reaction in bubble columns. Since 2010, his research group provides lipid analysis for the description of new species of microbes (published in IJSEM). Interests: synthesis of metal nanoparticles, surface-enhanced Raman scattering, its application for detection and identification of microbes. He's assistant professor now, teaching classes "Physical Chemistry", "Kinetics and Catalysis", and others.
Introduction
Detection of microorganisms is an important task in the fields of clinical diagnostics, food safety, and water quality control. The severity of this problem is due to the emergence of clinical infections by multidrug-resistant biofilm-forming bacteria. Traditional methods based on cultivation or PCR are effective, but usually require some preliminary information about the nature of pathogens, take a lot of time and are quite costly, which in most cases makes such studies not applicable. Thus, the problem of a broad-spectrum, feasible and fast way of detecting and identifying microorganisms remains relevant today.
Surface enhanced Raman scattering (SERS) spectroscopy can be efficiently employed for the label-free detection and discrimination of different bacteria. The fingerprint-quality bacterial spectra allow identification of bacteria at the genus, the species, and even at the intraspecies level.
Methods
SERS spectra were acquired with BWS415 spectrometer (BWTEC, Germany). The specimen was put on the XYZ-stage, while the position of laser focus was controlled by USB microscope Mikmed-2000R (Micromed, Russia). For maximum enhancement, SERS substrates were prepared by multilayer deposition of gold nanoparticles without any additional coagulants.
Results
SERS spectra were obtained for the active Gram(+) and Gram(-) bacteria cells and for spores, such as Escherichia coli, Staphylococcus aureus, Micrococcus luteus, Bacillus mycoides, Bacillus thuringiensis var. cereus, Desulfovibrio sp. Spectra of bacteria grown on 15N isotope containing substrate were also registered. Fluorescence background subtraction, filtering, normalizing and automated peak recognition were performed by means of GNU/Octave subroutines developed by us for the processing of spectral data.
Discussion
SERS spectra of bacteria were collected with cheap portable Raman spectrometer. All spectra have distinct differences, including those between spectra of cells and spores of the same strain. Stable isotope labeling revealed the relation between major SERS peaks and N-X bonds oscillations (presumably, in adenine and guanine cycles) – these peaks shifted towards lower Raman shifts. The PCA dimensionality reduction revealed the correlation between certain peaks in bacterial spectra and provided an opportunity to study the changes in cell surface chemistry in the biofilms formation by clinically relevant bacterial species.
This work was funded by the Russian Science Foundation (project 17-79-10489).
Biological & medical nanodevices and biosensors , Nano-Imaging for diagnosis, therapy and delivery
