Label-Free in Situ Discrimination of Live and Dead Bacteria by Surface-Enhanced Raman Scattering

Characterization and Discrimination of Gram-Positive Bacteria Using Raman Spectroscopy with the Aid of Principal Component Analysis

Raman scattering and its particular effect, surface-enhanced Raman scattering (SERS), are whole-organism fingerprinting spectroscopic techniques that gain more and more popularity in bacterial detection. In this work, two relevant Gram-positive bacteria species, Lactobacillus casei (L. casei) and Listeria monocytogenes (L. monocytogenes) were characterized based on their Raman and SERS spectral fingerprints. The SERS spectra were used to identify the biochemical structures of the bacterial cell wall. Two synthesis methods of the SERS-active nanomaterials were used and the recorded spectra were analyzed. L. casei and L. monocytogenes were successfully discriminated by applying Principal Component Analysis (PCA) to their specific spectral data.

Intuitive Label-Free SERS Detection of Bacteria Using Aptamer-Based in Situ Silver Nanoparticles Synthesis

The characteristic of an ideal bacteria-detection method should have high sensitivity and specificity, be easy to operate, and not have a time-consuming culture process. In this study, we report a new bacteria-detection strategy that can recognize bacteria quickly and directly by surface-enhanced Raman scattering (SERS) with the formation of well-defined bacteria-aptamer@AgNPs. SERS signals generated by bacteria-aptamer@AgNPs exhibited a linear dependence on bacteria (R² = 0.9671) concentration ranging from 10¹ to 10⁷ cfu/mL. The detection limit is sensitive down to 1.5 cfu/mL. Meanwhile, the bacteria SERS signal was dramatically enhanced by its specifically recognized aptamer, and the bacteria could be identified directly and visually through the SERS spectrum. This strategy eliminates the puzzling data analysis of previous studies and offers significant advantages over existing approaches, getting a critical step toward the creation of SERS-based biochips for rapid in situ bacteria detection in mixture samples.

Chemically imaging bacteria with super-resolution SERS on ultra-thin silver substrates

Plasmonic hotspots generate a blinking Surface Enhanced Raman Spectroscopy (SERS) effect that can be processed using Stochastic Optical Reconstruction Microscopy (STORM) algorithms for super-resolved imaging. Furthermore, by imaging through a diffraction grating, STORM algorithms can be modified to extract a full SERS spectrum, thereby capturing spectral as well as spatial content simultaneously. Here we demonstrate SERS and STORM combined in this way for super-resolved chemical imaging using an ultra-thin silver substrate. Images of gram-positive and gram-negative bacteria taken with this technique show excellent agreement with scanning electron microscope images, high spatial resolution at <50 nm, and spectral SERS content that can be correlated to different regions. This may be used to identify unique chemical signatures of various cells. Finally, because we image through as-deposited, ultra-thin silver films, this technique requires no nanofabrication beyond a single deposition and looks at the cell samples from below. This allows direct imaging of the cell/substrate interface of thick specimens or imaging samples in turbid or opaque liquids since the optical path doesn’t pass through the sample. These results show promise that super-resolution chemical imaging may be used to differentiate chemical signatures from cells and could be applied to other biological structures of interest.

Detection of molecular changes induced by antibiotics in Escherichia coli using vibrational spectroscopy

This study aimed to test Raman (400-1800cm^-1) and Infra-red (1900-500cm^-1) spectroscopies followed by statistical analysis (principal component analysis) to detect molecular changes induced by antibiotics (ampicillin, cefotaxime - cell wall synthesis inhibitors, tetracycline - protein synthesis inhibitor, ciprofloxacin - DNA synthesis inhibitor) against Escherichia coli TOP10. In case of ampicillin and cefotaxime, a decrease in protein bands in both Raman (1240, 1660cm^-1), and IR spectra (1230, 1530, 1630cm^-1), and an increase in carbohydrate bands (1150, 1020cm^-1) in IR spectra were observed. Tetracycline addition caused an increase in nucleic acid bands (775, 1478, 1578cm^-1), a sharp decrease in phenylalanine (995cm^-1) in Raman spectra and the amide I and amide II bands (1630, 1530cm^-1) in IR spectra, an increase in DNA in both Raman (1083cm^-1) and IR spectra (1080cm^-1). Regarding ciprofloxacin, an increase in nucleic acids (775, 1478, 1578cm^-1) in Raman spectra and in protein bands (1230, 1520, 1630cm^-1), in DNA (1080cm^-1) in IR spectra were detected. Clear discrimination of antibiotic-treated samples compared to the control was recorded, showing that Raman and IR spectroscopies, coupled to principal component analysis for data, could be used to detect molecular modifications in bacteria exposed to different classes of antibiotics. These findings contribute to the understanding of the mechanisms of action of antibiotics in bacteria.

Review: Microbial analysis in dielectrophoretic microfluidic systems

Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques.

Discrimination of Nosiheptide Sources with Plasmonic Filters

Bacteria identification plays a vital role in the field of clinical diagnosis, food industry, and environmental monitoring, which is in great demand of point of care detection methods. In this paper, in order to discriminate the source of nosiheptide product, a plasmonic filter was fabricated to filtrate, capture and identify Streptomycete spores with Surface enhanced Raman Scattering (SERS). Since the plasmonic filter was derived from self-assembled photonic crystal coated with silver, the plasmonic "hot spots" on the filter surface was distributed evenly in a fare good density and the SERS enhancement factor was 7.49 × 10⁷. With this filter, a stain- and PCR-free detection was realized with only 5 μL sample solution and 5 min in a manner of "filtration and measure". Comparison to traditional Gram stain method and silver-plated nylon filter membrane, the plasmonic filter showed good sensitivity and efficiency in the discrimination of nosiheptide prepared with chemical and biological methods. It is anticipated that this simple SERS detection method with plasmonic filter has promising potentials in food safety, environmental, or clinical applications.

Bacteria-derived fluorescent carbon dots for microbial live/dead differentiation

Microbial viability assessment plays a key role in many areas such as pathogen detection, infectious disease treatment and antimicrobial drug development. Many conventional viability dyes (such as propidium iodide, PI) used for differentiating live/dead microbes suffer from notable cytotoxicity, poor photostability and are of high cost. Thus their applications for accurate microbial viability determination are limited. Herein, for the first time we report the successful synthesis of fluorescent carbon dots (CDs) from bacteria via one-step hydrothermal carbonization. Benefiting from their highly negative surface charge (the zeta potential is as high as around -42 mV) and suitable size, the CDs can selectively stain dead microbial cells (bacteria and fungi) but not live ones. Importantly, compared to the widely used commercial dye PI, the developed CDs possess many great advantages including low cytotoxicity, multicolor imaging ability, excellent photostability and high selectivity. Moreover, because the synthetic method is simple, inexpensive and eco-friendly, this type of CD is suitable for large-scale production, making it an excellent candidate for microbial live/dead differentiation and viability assessment. The present work explores the feasibility of using bacteria to fabricate novel CDs and broadens the applications of CDs for biomedical applications.

Rapid single-cell detection and identification of pathogens by using surface-enhanced Raman spectroscopy

For the successful treatment of infections, real-time analysis and enhanced multiplex capacity, sensitivity and cost-effectiveness of the developed detection method are critical.

Fluorescent carbon dots with highly negative charges as a sensitive probe for real-time monitoring of bacterial viability

Doped carbon dots from a yeast extract were first applied in real-time monitoring of bacterial viability as a nano-thermometer.

Enhanced Self-Organized Dewetting of Ultrathin Polymer Blend Film for Large-Area Fabrication of SERS Substrate

We study the enhanced dewetting of ultrathin Polystyrene (PS)/Poly (methyl methacrylate) (PMMA) blend films in a mixed solution, and reveal the dewetting can act as a simple and effective method to fabricate large-area surface-enhanced Raman scattering (SERS) substrate. A bilayer structure consisting of under PMMA layer and upper PS layer forms due to vertical phase separation of immiscible PS/PMMA during the spin-coating process. The thicker layer of the bilayer structure dominates the dewetting structures of PS/PMMA blend films. The diameter and diameter distribution of droplets, and the average separation spacing between the droplets can be precisely controlled via the change of blend ratio and film thickness. The dewetting structure of 8 nm PS/PMMA (1:1 wt%) blend film is proved to successfully fabricate large-area (3.5 cm × 3.5 cm) universal SERS substrate via deposited a silver layer on the dewetting structure. The SERS substrate shows good SERS-signal reproducibility (RSD < 7.2%) and high enhancement factor (2.5 × 10⁷). The enhanced dewetting of polymer blend films broadens the application of dewetting of polymer films, especially in the nanotechnology, and may open a new approach for the fabrication of large-area SERS substrate to promote the application of SERS substrate in the rapid sensitive detection of trace molecules.

Three-dimensional (3D) plasmonic hot spots for label-free sensing and effective photothermal killing of multiple drug resistant superbugs

Drug resistant superbug infection is one of the foremost threats to human health. Plasmonic nanoparticles can be used for ultrasensitive bio-imaging and photothermal killing by amplification of electromagnetic fields at nanoscale "hot spots". One of the main challenges to plasmonic imaging and photothermal killing is design of a plasmonic substrate with a large number of "hot spots". Driven by this need, this article reports design of a three-dimensional (3D) plasmonic "hot spot"-based substrate using gold nanoparticle attached hybrid graphene oxide (GO), free from the traditional 2D limitations. Experimental results show that the 3D substrate has capability for highly sensitive label-free sensing and generates high photothermal heat. Reported data using p-aminothiophenol conjugated 3D substrate show that the surface enhanced Raman spectroscopy (SERS) enhancement factor for the 3D "hot spot"-based substrate is more than two orders of magnitude greater than that for the two-dimensional (2D) substrate and five orders of magnitude greater than that for the zero-dimensional (0D) p-aminothiophenol conjugated gold nanoparticle. 3D-Finite-Difference Time-Domain (3D-FDTD) simulation calculations indicate that the SERS enhancement factor can be greater than 10⁴ because of the bent assembly structure in the 3D substrate. Results demonstrate that the 3D-substrate-based SERS can be used for fingerprint identification of several multi-drug resistant superbugs with detection limits of 5 colony forming units per mL. Experimental data show that 785 nm near infrared (NIR) light generates around two times more photothermal heat for the 3D substrate with respect to the 2D substrate, and allows rapid and effective killing of 100% of the multi-drug resistant superbugs within 5 minutes.

Nanomaterials-based biosensors for detection of microorganisms and microbial toxins

Detection of microorganisms and microbial toxins is important for health and safety. Due to their unique physical and chemical properties, nanomaterials have been extensively used to develop biosensors for rapid detection of microorganisms with microbial cells and toxins as target analytes. In this paper, the design principles of nanomaterials-based biosensors for four selected analyte categories (bacteria cells, toxins, mycotoxins, and protozoa cells), closely associated with the target analytes' properties is reviewed. Five signal transducing methods that are less equipment intensive (colorimetric, fluorimetric, surface enhanced Raman scattering, electrochemical, and magnetic relaxometry methods) is described and compared for their sensory performance (in term oflimit of detection, dynamic range, and response time) for all analyte categories. In the end, the suitability of these five sensing principles for on-site or field applications is discussed. With a comprehensive coverage of nanomaterials, design principles, sensing principles, and assessment on the sensory performance and suitability for on-site application, this review offers valuable insight and perspective for designing suitable nanomaterials-based microorganism biosensors for a given application.

Single-cell level methods for studying the effect of antibiotics on bacteria during infection

Considerable evidence about phenotypic heterogeneity among bacteria during infection has accumulated during recent years. This heterogeneity has to be considered if the mechanisms of infection and antibiotic action are to be understood, so we need to implement existing and find novel methods to monitor the effects of antibiotics on bacteria at the single-cell level. This review provides an overview of methods by which this aim can be achieved. Fluorescence label-based methods and Raman scattering as a label-free approach are discussed in particular detail. Other label-free methods that can provide single-cell level information, such as impedance spectroscopy and surface plasmon resonance, are briefly summarized. The advantages and disadvantages of these different methods are discussed in light of a challenging in vivo environment.

Surface-enhanced resonance Raman scattering (SERRS) simulates PCR for sensitive DNA detection

This paper describes a novel double-stranded DNA detection method through resonance between SYBR Green I and DNA with the surface-enhanced resonance Raman scattering (SERRS) assay, which opens an avenue to the quantitative and reliable application of SERRS in DNA detection.

Highly Sensitive Detection of Hormone Estradiol E2 Using Surface-Enhanced Raman Scattering Based Immunoassays for the Clinical Diagnosis of Precocious Puberty

The hormone estradiol (17β-estradiol, E2) plays an important role in sexual development and serves as an important diagnostic biomarker of various clinical conditions. Particularly, the serum E2 concentration is very low (<10 pg/mL) in prepubertal girls. Accordingly, many efforts to develop a sensitive method of detection and quantification of E2 in human serum have been made. Nonetheless, current clinical detection methods are insufficient for accurate assessment of E2 at low concentrations (<10 pg/mL). Thus, there is an urgent need for new technologies with efficient and sensitive detection of E2 for use in routine clinical diagnostics. In this study, we introduce a new E2 assay technique using a surface-enhanced Raman scattering (SERS)-based detection method. The SERS-based assay was performed with 30 blood samples to assess its clinical feasibility, and the results were compared with data obtained using the ARCHITECT chemiluminescence immunoassay. Whereas the commercial assay system was unable to quantify serum levels of E2 lower than 10 pg/mL, the limit of detection of E2 using the novel SERS-based assay described in this study was 0.65 pg/mL. Thus, the proposed SERS-based assay has a strong potential to be a valuable tool in the early diagnosis of precocious puberty due to its excellent analytical sensitivity.

Raman-based microarray readout: a review

For a quarter of a century, microarrays have been part of the routine analytical toolbox. Label-based fluorescence detection is still the commonest optical readout strategy. Since the 1990s, a continuously increasing number of label-based as well as label-free experiments on Raman-based microarray readout concepts have been reported. This review summarizes the possible concepts and methods and their advantages and challenges. A common label-based strategy is based on the binding of selective receptors as well as Raman reporter molecules to plasmonic nanoparticles in a sandwich immunoassay, which results in surface-enhanced Raman scattering signals of the reporter molecule. Alternatively, capture of the analytes can be performed by receptors on a microarray surface. Addition of plasmonic nanoparticles again leads to a surface-enhanced Raman scattering signal, not of a label but directly of the analyte. This approach is mostly proposed for bacteria and cell detection. However, although many promising readout strategies have been discussed in numerous publications, rarely have any of them made the step from proof of concept to a practical application, let alone routine use. Graphical Abstract Possible realization of a SERS (Surface-Enhanced Raman Scattering) system for microarray readout.

A rapid SERS method for label-free bacteria detection using polyethylenimine-modified Au-coated magnetic microspheres and Au@Ag nanoparticles

A rapid and efficient method for label-free SERS detection of bacteria in solution.

Design and preparation of a recyclable microfluidic SERS chip with integrated Au@Ag/TiO2 NTs

Design and preparation of a recyclable microfluidic SERS chip with integrated Au@Ag/TiO₂ NTs.

Label-free mapping of single bacterial cells using surface-enhanced Raman spectroscopy

Here we presented a simple, rapid and label-free surface-enhanced Raman spectroscopy (SERS) based mapping method for the detection and discrimination ofSalmonella entericaandEscherichia coli onsilver dendrites.

Early apoptosis real-time detection by label-free SERS based on externalized phosphatidylserine

Early apoptosis real-time detection by label-free SERS based on externalized phosphatidylserine usingin situsynthesized silver nanoparticles.