Strain-level typing and identification of bacteria – a novel approach for SERS active plasmonic nanostructures

Abstract

One of the potential applications of surface-enhanced Raman spectroscopy (SERS) is the detection of biological compounds and microorganisms. Here we demonstrate that SERS coupled with principal component analysis (PCA) serves as a perfect method for determining the taxonomic affiliation of bacteria at the strain level. We demonstrate for the first time that it is possible to distinguish different genoserogroups within a single species, Listeria monocytogenes, which is one of the most virulent foodborne pathogens and in some cases contact with which may be fatal. We also postulate that it is possible to detect additional proteins in the L. monocytogenes cell envelope, which provide resistance to benzalkonium chloride and cadmium. A better understanding of this infectious agent could help in selecting the appropriate pharmaceutical product for enhanced treatment. Graphical abstractᅟ Electronic supplementary materialThe online version of this article (10.1007/s00216-018-1153-0) contains supplementary material, which is available to authorized users.

Label-Free SERS Discrimination and In Situ Analysis of Life Cycle in Escherichia coli and Staphylococcus epidermidis

“…Moreover, the presence of nucleic acids is pointed out by the signal related to the vibration of guanine, located at around 1319 cm −1 (Band 24) [19,29]. Even though this region does not show big differences compared to the literature, it is worth noting that a comprehensive and detailed characterization of the spectra is provided showing an enhanced sensitivity, with respect to previous works [19,29,31,48].…”

“…Additional bands in Zone I are related to the twisting mode of phenylalanine at 621 cm −1 [19] (only in E. coli ), and to the vibrational modes of the nitrogenous bases of nucleic acids, located at ~650 cm −1 , 660 cm −1 (Band 3; only in S. epidermidis ) [17,19], 725 cm −1 (Band 6) [4,17,31,32], 780 cm −1 (Band 9) [17,27,29,31], 800 cm −1 (Band 10; only in S. epidermidis ) [27,29], and ~850 cm −1 (Band 12) [17,19]. In particular, Band 6 at 725 cm −1 belongs to the ring breathing of adenine [4,19,31,32], which can be ascribed to the presence of extracellular DNA (eDNA), or to other common adenine-containing molecules, such as RNA, FAD, NAD, AMP, ADP, or ATP, which are critical molecules for the biochemical processes of cells [33]. From the comparison between the two spectra, it can be noticed that the DNA related bands (Band 6–9) are less intense in the S. epidermidis spectrum.…”

“…Comparing the results obtained in this work with those shown in other studies [19,32,35], the explanation involving the eDNA is seen as the most plausible, taking into account that the eDNA could better interact, rather than the intracellular DNA, with the Ag NP on the surface of the substrates. It is worth noting that the majority of previous works take advantage of metal NPs (Au and Ag) dispersed in water as a colloidal solution, applying a treatment protocol of the bacteria samples that aims to remove the extracellular components of the biofilm matrix [19,31,32,36]. For this reason, the SERS characterization of E. coli , carried out by Lemma et al, revealed that this band is completely missing [19], whereas in the results displayed by Witkowska et al, it has a really low intensity [31].…”

“…It is worth noting that the majority of previous works take advantage of metal NPs (Au and Ag) dispersed in water as a colloidal solution, applying a treatment protocol of the bacteria samples that aims to remove the extracellular components of the biofilm matrix [19,31,32,36]. For this reason, the SERS characterization of E. coli , carried out by Lemma et al, revealed that this band is completely missing [19], whereas in the results displayed by Witkowska et al, it has a really low intensity [31]. The lack of this vibrational feature could be due to the removal of the biofilm matrix, supporting the eDNA hypothesis.…”

“…The sharp character of this band makes it suitable to normalize the overall spectrum. Additional bands related to the presence of phenylalanine are located at around 1030 cm −1 and 1204 cm −1 (Bands 15 and 20, respectively) [19,27,29,31,37]. The characteristic features of the proteins are displayed by the amide I, II, and III bands, which arise from the bond vibrations in the peptide units.…”