Surface-Enhanced Raman Scattering-Based Surface Chemotaxonomy: Combining Bacteria Extracellular Matrices and Machine Learning for Rapid and Universal Species Identification

Rapid, universal, and accurate identification of bacteria in their natural states is necessary for on-site environmental monitoring and fundamental microbial research. Surface-enhanced Raman scattering (SERS) spectroscopy emerges as an attractive tool due to its molecule-specific spectral fingerprinting and multiplexing capabilities, as well as portability and speed of readout. Here, we develop a SERS-based surface chemotaxonomy that uses bacterial extracellular matrices (ECMs) as proxy biosignatures to hierarchically classify bacteria based on their shared surface biochemical characteristics to eventually identify six distinct bacterial species at >98% classification accuracy. Corroborating with in silico simulations, we establish a three-way inter-relation between the bacteria identity, their ECM surface characteristics, and their SERS spectral fingerprints. The SERS spectra effectively capture multitiered surface biochemical insights including ensemble surface characteristics, e.g., charge and biochemical profiles, and molecular-level information, e.g., types and numbers of functional groups. Our surface chemotaxonomy thus offers an orthogonal taxonomic definition to traditional classification methods and is achieved without gene amplification, biochemical testing, or specific biomarker recognition, which holds great promise for point-of-need applications and microbial research.

Machine Learning Assisted Real-Time Label-Free SERS Diagnoses of Malignant Pleural Effusion due to Lung Cancer

More than half of all pleural effusions are due to malignancy of which lung cancer is the main cause. Pleural effusions can complicate the course of pneumonia, pulmonary tuberculosis, or underlying systemic disease. We explore the application of label-free surface-enhanced Raman spectroscopy (SERS) as a point of care (POC) diagnostic tool to identify if pleural effusions are due to lung cancer or to other causes (controls). Lung cancer samples showed specific SERS spectral signatures such as the position and intensity of the Raman band in different wave number region using a novel silver coated silicon nanopillar (SCSNP) as a SERS substrate. We report a classification accuracy of 85% along with a sensitivity and specificity of 87% and 83%, respectively, for the detection of lung cancer over control pleural fluid samples with a receiver operating characteristics (ROC) area under curve value of 0.93 using a PLS-DA binary classifier to distinguish between lung cancer over control subjects. We have also evaluated discriminative wavenumber bands responsible for the distinction between the two classes with the help of a variable importance in projection (VIP) score. We found that our label-free SERS platform was able to distinguish lung cancer from pleural effusions due to other causes (controls) with higher diagnostic accuracy.

Recent Advances in Agglomeration Detection and Dual-Function Application of Surface-Enhanced Raman Scattering (SERS)

Surface-enhanced Raman scattering (SERS) has been widely utilized in early detection of disease biomarkers, cell imaging, and trace contamination detection, owing to its ultra-high sensitivity. However, it is also subject to certain application restrictions in virtue of its expensive detection equipment and long-term stability of SERS-active substrate. Recently, great progress has been made in SERS technology, represented by agglomeration method. Dual readout signal detection methods are combined with SERS, including electrochemical detection, fluorescence detection, etc., establishing a new fantastic viewpoint for application of SERS. In this review, we have made a comprehensive report on development of agglomeration detection and dual-function detection methods based on SERS. The synthesis methods for plasmonic materials and mainstream SERS enhancement mechanism are also summarized. Finally, the key facing challenges are discussed and prospects are addressed.

Novel Cellulose Fibre-Based Flexible Plasmonic Membrane for Point-of-Care SERS Biomarker Detection in Chronic Wound Healing

Background

Wound management is stretching the limits of health systems globally, challenging clinicians to evaluate the effectiveness of their treatments and deliver appropriate care to their patients. Visual inspection and manual measurement of wound size are subjective, often inaccurate and inconsistent. Growth factors, such as pro-inflammatory cytokines and proteases, play important roles in cutaneous wound healing. However, little is known about the point-of-care monitoring of the changes in such markers during the healing process. Here, we explore the capability of surface-enhanced Raman spectroscopy (SERS) as a viable point-of-care platform to monitor the changes of these surrogate indicators of healing status in chronic wounds.

Methods

We developed a biofunctionalized flexible, cost-effective, scalable and easy-to-fabricate plasmonic SERS substrate using cellulose fibre (CF), which is used for sensing of wound markers based on a modified immunoassay method.

Results

We evaluated and selected the reliable silver nano-island thickness that will be sputtered onto the CF-based substrate for the highest SERS enhancement. Using this biofunctionalized SERS substrate, we detected varying concentrations of MMP-9 (10–5000 ng/mL) and TNF-α (5–100 ng/mL) proteins to model the wound exudates. This SERS detection method demonstrates a linear response within biologically relevant concentrations, ranging from 10 to 500 ng/mL for MMP-9 and 5 to 25 ng/mL for TNF-α for these surrogate indicators.

Conclusion

Our SERS sensing platform achieved detection limits in the µM to sub-nM range and displayed high sensitivity and selectivity. This could result in a cheap, point-of-care device that provides a non-invasive measure of cutaneous wound healing in real time. We envision that these flexible substrates after activation may be incorporated into wound dressings in future for routine monitoring of wound healing status.

Frequency Shift Surface-Enhanced Raman Spectroscopy Sensing: An Ultrasensitive Multiplex Assay for Biomarkers in Human Health

The sensitive and selective detection of biomarkers for human health remains one of the grand challenges of the analytical sciences. Compared to established methods (colorimetric, (chemi) luminescent), surface-enhanced Raman spectroscopy (SERS) is an emerging alternative with enormous potential for ultrasensitive biological detection. Indeed even attomolar (10^-18 M) detection limits are possible for SERS due to an orders-of-magnitude boosting of Raman signals at the surface of metallic nanostructures by surface plasmons. However, challenges remain for SERS assays of large biomolecules, as the largest enhancements require the biomarker to enter a "hot spot" nanogap between metal nanostructures. The frequency-shift SERS method has gained popularity in recent years as an alternative assay that overcomes this drawback. It measures frequency shifts in intense SERS peaks of a Raman reporter during binding events on biomolecules (protein coupling, DNA hybridization, etc.) driven by mechanical transduction, charge transfer, or local electric field effects. As such, it retains the excellent multiplexing capability of SERS, with multiple analytes being identifiable by a spectral fingerprint in a single read-out. Meanwhile, like refractive index surface plasmon resonance methods, frequency-shift SERS measures the shift of an intense signal rather than resolving a peak above noise, easing spectroscopic resolution requirements. SERS frequency-shift assays have proved particularly suitable for sensing large, highly charged biomolecules that alter hydrogen-bonding networks upon specific binding. Herein we discuss the frequency-shift SERS method and promising applications in (multiplex) biomarker sensing as well as extensions to ion and gas sensing and much more.

Bifunctional Fluorescent/Raman Nanoprobe for the Early Detection of Amyloid

One of the pathological hallmarks of Alzheimer's disease (AD) is the abnormal aggregation of amyloid beta (Aβ) peptides. Therefore the detection of Aβ peptides and imaging of amyloid plaques are considered as promising diagnostic methods for AD. Here we report a bifunctional nanoprobe prepared by conjugating gold nanoparticles (AuNPs) with Rose Bengal (RB) dye. RB is chosen due to its unique Raman fingerprints and affinity with Aβ peptides. After the conjugation, Raman signals of RB were significantly enhanced due to the surface-enhanced Raman scattering (SERS) effect. Upon binding with Aβ42 peptides, a spectrum change was detected, and the magnitude of the spectrum changes can be correlated with the concentration of target peptides. The peptide/probe interaction also induced a remarkable enhancement in the probes' fluorescence emission. This fluorescence enhancement was further utilized to image amyloid plaques in the brain slices from transgenic mice. In this study, the RB-AuNPs were used for both SERS-based detection of Aβ42 peptides and fluorescence-based imaging of amyloid plaques. Compared to monofunctional probes, the multifunctional probe is capable to provide more comprehensive pathophysiological information, and therefore, the implementation of such multifunctional amyloid probes is expected to help the investigation of amyloid aggregation and the early diagnosis of AD.

Revisiting semicontinuous silver films as surface-enhanced Raman spectroscopy substrates

Surface-enhanced Raman spectroscopy (SERS) is a very promising analytical technique for the detection and identification of trace amounts of analytes. Among the many substrates used in SERS of great interest are nanostructures fabricated using physical methods, such as semicontinuous metal films obtained via electron beam physical vapor deposition. In these studies, we investigate the influence of morphology of semicontinuous silver films on their SERS properties. The morphologies studied ranged from isolated particles through percolated films to almost continuous films. We found that films below the percolation threshold (transition from dielectric-like to metal-like) made of isolated silver structures provided the largest SERS enhancement of 4-aminothiophenol (4-ATP) analyte signals. The substrate closest to the percolation threshold has the SERS signal about four times lower than the highest signal sample.

APTES Duality and Nanopore Seed Regulation in Homogeneous and Nanoscale-Controlled Reduction of Ag Shell on SiO2 Microparticle for Quantifiable Single Particle SERS

Noble-metal nanoparticles size and packing density are critical for sensitive surface-enhanced Raman scattering (SERS) and controlled preparation of such films required to achieve reproducibility. Provided that they are made reliable, Ag shell on SiO₂ microscopic particles (Ag/SiO₂) are promising candidates for lab-on-a-bead analytical measurements of low analyte concentration in liquid specimen. Here, we selected nanoporous silica microparticles as a substrate for reduction of AgNO₃ with 3-aminopropyltriethoxysilane (APTES). In a single preparation step, homogeneous and continuous films of Ag nanoparticles are formed on SiO₂ surfaces with equimolar concentration of APTES and silver nitrate in ethanol. It is discussed that amine and silane moieties in APTES contribute first to an efficient reduction on the silica and second to capping the Ag nanoparticles. The high density and homogeneity of nanoparticle nucleation is further regulated by the nanoporosity of the silica. The Ag/SiO₂ microparticles were tested for SERS using self-assembled 4-aminothiophenol monolayers, and an enhancement factor of ca. 2 × 10⁶ is measured. Importantly, the SERS relative standard deviation is 36% when a single microparticle is considered and drops to 11% when sets of 10 microparticles are considered. As prepared, the microparticles are highly suitable for state-of-the-art quantitative lab-on-a-bead interrogation of specimens.

Optical reconfiguration and polarization control in semi-continuous gold films close to the percolation threshold

Controlling and confining light by exciting plasmons in resonant metallic nanostructures is an essential aspect of many new emerging optical technologies. Here we explore the possibility of controllably reconfiguring the intrinsic optical properties of semi-continuous gold films, by inducing permanent morphological changes with a femtosecond (fs)-pulsed laser above a critical power. Optical transmission spectroscopy measurements show a correlation between the spectra of the morphologically modified films and the wavelength, polarization, and the intensity of the laser used for alteration. In order to understand the modifications induced by the laser writing, we explore the near-field properties of these films with electron energy-loss spectroscopy (EELS). A comparison between our experimental data and full-wave simulations on the exact film morphologies hints toward a restructuring of the intrinsic plasmonic eigenmodes of the metallic film by photothermal effects. We explain these optical changes with a simple model and demonstrate experimentally that laser writing can be used to controllably modify the optical properties of these semi-continuous films. These metal films offer an easy-to-fabricate and scalable platform for technological applications such as molecular sensing and ultra-dense data storage.

Uniaxially Stretched Flexible Surface Plasmon Resonance Film for Versatile Surface Enhanced Raman Scattering Diagnostics

Surface-enhanced Raman scattering (SERS) spectroscopy affords a rapid, highly sensitive, and nondestructive approach for label-free and fingerprint diagnosis of a wide range of chemicals. It is of great significance to develop large-area, uniform, and environmentally friendly SERS substrates for in situ identification of analytes on complex topological surfaces. In this work, we demonstrate a biodegradable flexible SERS film via irreversibly and longitudinally stretching metal deposited biocompatible poly(ε-caprolactone) film. This composite film after stretching shows surprising phenomena: three-dimensional and periodic wave-shaped microribbons array embedded with a high density of nanogaps functioning as hot-spots at an average gap size of 20 nm and nanogrooves array along the stretching direction. The stretched polymer surface plasmon resonance film gives rise to more than 10 times signal enhancement in comparison with that of the unstretched composite film. Furthermore, the SERS signals with high uniformity exhibit good temperature stability. The polymer SPR film with excellent flexibility and transparency can be conformally attached onto arbitrary nonplanar surfaces for in situ detection of various chemicals. Our results pave a new way for next-generation flexible SERS detection means, as well as enabling its huge potentials toward green wearable devices for point-of-care diagnostics.

Plasmonic tooth-multilayer structure with high enhancement field for surface enhanced Raman spectroscopy

The significant enhancement seen in surface-enhanced Raman scattering (SERS) heavily relies on the ability of plasmonic structures to strongly confine light. Current techniques used to fabricate plasmonic nanostructures have been limited in their reproducibility for bottom-up techniques or their feature size for top-down techniques. Here, we propose a tooth multilayer structure that can be fabricated by using physical vapor deposition and selective wet etching, achieving extremely small feature sizes and high reproducibility. A multilayer structure composed of two alternating materials whose thicknesses can be controlled accurately in the nanometer range is deposited on a flat substrate using ion-beam sputtering. Subsequent selective wet etching is used to form nanogaps in one of the materials constituting the multilayer, with the depth of the nanogaps being controlled by the wet etching time. Combining both techniques can allow the nanogap dimensions to be controlled at sub 10 nm length scale, thus achieving a tooth multilayer structure with high enhancement and tunability of the resonance mode over a broad range, ideal for SERS applications.

Label-free biosensors based on in situ formed and functionalized microwires in microfluidic devices

Label-free biosensors based on in situ formed and functionalized TTF-Au wires were developed using an integrated microfluidic system. By applying different modification protocols, TTF-Au wires were successfully used for sensitive label-free detection of catecholamines and human IgG by Raman spectroscopy.

Simulated Raman correlation spectroscopy for quantifying nucleic acid-silver composites

Plasmonic devices are of great interest due to their ability to confine light to the nanoscale level and dramatically increase the intensity of the electromagnetic field, functioning as high performance platforms for Raman signal enhancement. While Raman spectroscopy has been proposed as a tool to identify the preferential binding sites and adsorption configurations of molecules to nanoparticles, the results have been limited by the assumption that a single binding site is responsible for molecular adsorption. Here, we develop the simulated Raman correlation spectroscopy (SRCS) process to determine which binding sites of a molecule preferentially bind to a plasmonic material and in what capacity. We apply the method to the case of nucleic acids binding to silver, discovering that multiple atoms are responsible for adsorption kinetics. This method can be applied to future systems, such as to study the molecular orientation of adsorbates to films or protein conformation upon adsorption.

Ultrasensitive, Multiplex Raman Frequency Shift Immunoassay of Liver Cancer Biomarkers in Physiological Media

Highly sensitive multiplex biomarker detection is critical for the early diagnosis of liver cancer. Here, a surface-enhanced Raman scattering (SERS) frequency-shift immunoassay is developed for detection of liver cancer biomarkers α-fetoprotein and Glypican-3 down to subpicomolar concentrations in saline solution. A high temperature modification of the Tollen's method affords silver nanoparticle films with excellent SERS response upon which ordered domains of Raman reporters are chemisorbed by microcontact printing. Shifts in the reporters SERS spectrum in response to a bound antibody's biomarker recognition constitutes the frequency shift assay, exhibiting here exceptional sensitivity and specificity and shown to function in fetal calf serum and in the serum of a patient with hepatocellular carcinoma.

Texture orientation of silver thin films grown via gas-timing radio frequency magnetron sputtering and their SERS activity

Here we have demonstrated the special technique so called gas-timing (GT) rf magnetron sputtering which allow us to control a texture orientation of Ag thin films without applying any additional energy sources.

Hollow silver alginate microspheres for drug delivery and surface enhanced Raman scattering detection

Multifunctional silver alginate hydrogel microspheres are assembled via a template assisted approach using calcium carbonate cores.

New post-processing method of preparing nanofibrous SERS substrates with a high density of silver nanoparticles

The protocol to control density of AgNP on surfaces of nanofibers, and thus electromagnetic hotspots by variation of Tollens' reagent is established. Nanofiber films enable SERS either of solutes or macromolecular structures such as bacterial cells.

Sensing of p53 and EGFR Biomarkers Using High Efficiency SERS Substrates

In this paper we describe a method for the determination of protein concentration using Surface Enhanced Raman Resonance Scattering (SERRS) immunoassays. We use two different Raman active linkers, 4-aminothiophenol and 6-mercaptopurine, to bind to a high sensitivity SERS substrate and investigate the influence of varying concentrations of p53 and EGFR on the Raman spectra. Perturbations in the spectra are due to the influence of protein-antibody binding on Raman linker molecules and are attributed to small changes in localised mechanical stress, which are enhanced by SERRS. These influences are greatest for peaks due to the C-S functional group and the Full Width Half Maximum (FWHM) was found to be inversely proportional to protein concentration.

Thickness of a metallic film, in addition to its roughness, plays a significant role in SERS activity

In this paper we evaluate the effect of roughness and thickness of silver film substrates, fabricated on glass and polydimethylsiloxane (PDMS) templates, on surface-enhanced Raman Spectroscopy (SERS) activity. While the silver substrates obtained on glass templates exhibit nm-scale roughness, the silver substrates on PDMS templates show larger roughness, on the order of 10 s of nm. These roughness values do not change significantly with the thickness of the silver film. The SERS intensities of 4-aminothiophenol (ATP) deposited on these substrates strongly depend on both roughness and thickness, with more significant contribution from the roughness on thinner films. FEM simulations of the electric field intensities on surfaces of different thicknesses for rough and flat surfaces suggest higher localized plamons on thinner, rough surfaces. This study indicates that, besides roughness, the thickness of the metallic layer plays a significant role in the SERS activity.

SERS Detection of Amyloid Oligomers on Metallorganic-Decorated Plasmonic Beads

Protein misfolded proteins are among the most toxic endogenous species of macromolecules. These chemical entities are responsible for neurodegenerative disorders such as Alzheimer's, Parkinson's, Creutzfeldt-Jakob's and different non-neurophatic amyloidosis. Notably, these oligomers show a combination of marked heterogeneity and low abundance in body fluids, which have prevented a reliable detection by immunological methods so far. Herein we exploit the selectivity of proteins to react with metallic ions and the sensitivity of surface-enhanced Raman spectroscopy (SERS) toward small electronic changes in coordination compounds to design and engineer a reliable optical sensor for protein misfolded oligomers. Our strategy relies on the functionalization of Au nanoparticle-decorated polystyrene beads with an effective metallorganic Raman chemoreceptor, composed by Al(3+) ions coordinated to 4-mercaptobenzoic acid (MBA) with high Raman cross-section, that selectively binds aberrant protein oligomers. The mechanical deformations of the MBA phenyl ring upon complexation with the oligomeric species are registered in its SERS spectrum and can be quantitatively correlated with the concentration of the target biomolecule. The SERS platform used here appears promising for future implementation of diagnostic tools of aberrant species associated with protein deposition diseases, including those with a strong social and economic impact, such as Alzheimer's and Parkinson's diseases.

High performance SERS active substrates fabricated by directly growing graphene on Ag nanoparticles

An efficient surface enhanced Raman scattering (SERS) substrate of graphene-isolated Ag nanoparticle (G/AgNP) has been developed by using excimer laser to ablate the ordered pyrolytic graphite in high vacuum onto Ag nanoparticles.

Gold-decorated titania nanotube arrays as dual-functional platform for surface-enhanced Raman spectroscopy and surface-assisted laser desorption/ionization mass spectrometry

In this report, we demonstrate gold-decorated titania nanotube arrays (Au-TNA substrate) as a dual-functional platform for surface-enhanced Raman spectroscopy (SERS) and surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS). The Au nanoparticles are grown on the substrate using vapor deposition of Au. The resulting substrates perform better than Au colloids in terms of the reproducibility of the SERS measurements, long-term stability of the fabricated structures, and clean surface of the Au. The nanostructure of the Au-TNA substrate was designed to optimize the SALDI-MS and SERS performance. Excellent reproducibility of the SERS measurements using the Au-TNA substrate was obtained, with a standard error less than 6 %. SALDI activity was also demonstrated for the same Au-TNA substrates. Finally, the Au-TNA substrate was used for combined SERS and SALDI-MS analysis (i) to discriminate the structural isomers of pyridine compounds (para-, meta-, and ortho-pyridinecarboxylic acid) and (ii) to detect polycarbamate, a dithiocarbamate fungicide. These results are difficult to obtain using either approach alone.

Synthesis and characterization of an AgI/Ag hybrid nanocomposite with surface-enhanced Raman scattering performance and photocatalytic activity

Novel AgI/Ag hybrid nanocomposites with good SERS performance and excellent photocatalytic activity were prepared.