SERS based artificial peroxidase enzyme regulated multiple signal amplified system for quantitative detection of foodborne pathogens

Advances in signal amplification strategies applied in pathogenic bacteria apta-sensing analysis-A review

Pathogenic bacteria are primarily kinds of food hazards that provoke serious harm to human health via contaminated or spoiled food. Given that pathogenic bacteria continue to reproduce and expand once they contaminate food, pathogenic bacteria of high concentration triggers more serious losses and detriments. Hence, it is essential to detect low-dose pollution at an early stage with high sensitivity. Aptamers, also known as "chemical antibodies", are oligonucleotide sequences that have attracted much attention owing to their merits of non-toxicity, small size, variable structure as well as easy modification of functional group. Aptamer-based bioanalysis has occupied a critical position in the field of rapid detection of pathogenic bacteria. This is attributed to the unique advantage of using aptamers as recognition elements in signal amplification strategies. The signal amplification strategy is an effective means to improve the detection sensitivity. Some diverse signal amplification strategies emphasize the synthesis and assembly of nanomaterials with signal amplification capabilities, while others introduce various nucleic acid amplification techniques into the detection system. This review focuses on a variety of signal amplification strategies employed in aptamer-based detection approaches to pathogenic bacteria. Meanwhile, we provided a detailed introduction to the design principles and characteristics of signal amplification strategies, as well as the improvement of sensor sensitivity. Ultimately, the existing issues and development trends of applying signal amplification strategies in apta-sensing analysis of pathogenic bacteria are critically proposed and prospected. Overall, this review discusses from a new perspective and is expected to contribute to the further development of this field.

Construction of a point-of-care electrochemical biosensor for Escherichia coli 16S rRNA analysis based on MoS2 nanoprobes

Foodborne pathogens are harmful to human health because they can contaminate food and induce diseases. To efficiently distinguish and determine foodborne bacteria, an ultrasensitive point-of-care electrochemical biosensor was designed for 16S rRNA detection by coupling a signal amplification strategy with MoS2-based nanoprobes. Gold nanoparticles and thionine co-functionalized molybdenum disulfide (MoS2) nanocomposites (MoS2-Thi-AuNPs) were used to construct nanoprobes, which can efficiently monitor the detection process and amplify the detection signal. In the presence of Escherichia coli (E. coli) 16S rRNA, a classical sandwiched DNA structure was formed on the surface of a hierarchical flower-like gold nanostructure-decorated screen-printed carbon electrode (HFGN-SPCE), generating an obvious electrochemical signal from Thi. Under optimal conditions, this designed electrochemical biosensor showed a wide dynamic range (0-1.0 × 106 fM), low detection limit (2.8 fM), high selectivity and accepted stability for E. coli 16S rRNA detection in ideal buffers. Moreover, this biosensor can efficiently determine 16S rRNA in milk samples and 10 CFU mL-1 bacterial lysate. All experimental results suggested that this biosensor has a promising application in the detection of foodborne pathogens.

Research advances of SERS analysis method based on silent region molecules for food safety detection

Food safety is a critical issue that is closely related to people's health and safety. As a simple, rapid, and sensitive detection technique, surface-enhanced Raman scattering (SERS) technology has significant potential for food safety detection. Recently, researchers have shown a growing interest in utilizing silent region molecules for SERS analysis. These molecules exhibit significant Raman scattering peaks in the cellular Raman silent region between 1800 and 2800 cm-1 avoiding overlapping with the SERS spectrum of biological matrices in the range 600-1800 cm-1, which could effectively circumvent matrix effects and improve the SERS accuracy. In this review, the application of silent region molecules-based SERS analytical technique for food safety detection is introduced, detection strategies including label-free detection and labeled detection are discussed, and recent applications of SERS analysis technology based on molecules containing alkyne and nitrile groups, as well as Prussian blue (PB) in the detection of pesticides, mycotoxins, metal ions, and foodborne pathogens are highlighted. This review aims to draw the attention to the silent region molecules-based SERS analytical technique and to provide theoretical support for its further applications in food safety detection.

FRET-Based Single-Molecule Detection of Pathogen Protein IsdA Using Computationally Selected Aptamers

Iron-regulated surface determinant protein A (IsdA) is a key surface protein found in the foodborne bacteria─Staphylococcus aureus (S. aureus)─which is known to be critical for bacterial survival and colonization. S. aureus is pathogenic and has been linked to foodborne diseases; thus, early detection is critical to prevent diseases caused by this bacterium. Despite IsdA being a specific marker for S. aureus and several detection methods have been developed for sensitive detection of this bacteria such as cell culture, nucleic acids amplification, and other colorimetric and electrochemical methods, the detection of S. aureus through IsdA is underdeveloped. Here, by combining computational generation of target-guided aptamers and fluorescence resonance energy transfer (FRET)-based single-molecule analysis, we presented a widely applicable and robust detection method for IsdA. Three different RNA aptamers specific to the IsdA protein were identified and their ability to switch a FRET construct to a high-FRET state in the presence of protein was verified. The presented approach demonstrated the detection of IsdA down to picomolar levels (×10^-12 M, equivalent to ∼1.1 femtomoles IsdA) with a dynamic range extending to ∼40 nM. The FRET-based single-molecule technique that we reported here is capable of detecting the foodborne pathogen protein IsdA with high sensitivity and specificity and has a broader application in the food industry and aptamer-based sensing field by enabling quantitative detection of a wide range of pathogen proteins.

SERS detection of Hg2+ and aflatoxin B1 through on-off strategy of oxidase-like Au@HgNPs/carbon dots

In this work, cerium-doped carbon dots (Ce-CDs) both as a reducing agent and template hybrid gold nanoparticles (AuNPs) with weak oxidase-like (OXD) activity was synthesized for the detection of Hg²⁺ and aflatoxin B₁ (AFB₁). The AuNPs can catalyze efficiently mercury ion (Hg²⁺) reduction to the metallic (Hg⁰) to form Au-Hg amalgam (Au@HgNPs). The obtained Au@HgNPs with strong OXD-like activity oxidize without Raman-active leucomalachite green (LMG) into the Raman-active malachite green (MG) and simultaneously as the SERS substrates by the formed Raman "hot spot" through MG-induced Au@HgNPs aggregation. While AFB₁ was introduced resulting in the SERS intensity decreasing due to Hg²⁺ with AFB₁ via carbonyl group to inhibit the aggregation of Au@HgNPs. The work paves a new path for the design of a nanozyme-based SERS protocol for tracing Hg²⁺ and AFB₁ residues in foodstuff analysis.

Metal-Organic Frameworks-Based Optical Nanosensors for Analytical and Bioanalytical Applications

Metal-organic frameworks (MOFs)-based optical nanoprobes for luminescence and surface-enhanced Raman spectroscopy (SERS) applications have been receiving tremendous attention. Every element in the MOF structure, including the metal nodes, the organic linkers, and the guest molecules, can be used as a source to build single/multi-emission signals for the intended analytical purposes. For SERS applications, the MOF can not only be used directly as a SERS substrate, but can also improve the stability and reproducibility of the metal-based substrates. Additionally, the porosity and large specific surface area give MOF a sieving effect and target molecule enrichment ability, both of which are helpful for improving detection selectivity and sensitivity. This mini-review summarizes the advances of MOF-based optical detection methods, including luminescence and SERS, and also provides perspectives on future efforts.

Au nanoparticles decorated covalent organic framework composite for SERS analyses of malachite green and thiram residues in foods

A three-dimensional (3D) surface-enhanced Raman scattering (SERS) substrate composed of gold nanoparticles (AuNPs) self-assembled covalent organic frameworks (COFs) was fabricated via the electrostatic interaction between positively charged COFs and negatively charged AuNPs, which exhibited excellent SERS performance and were successfully applied for the analyses of malachite green (MG) residue in different seafood products as well as thiram residue in several kinds of fruit juice. The raspberry-like structure SERS substrate has a larger surface area that can provide more adsorption sites in testing and improve the efficiency of sample enrichment. By using this developed SERS substrate, the detection linearity ranges are 1.0 × 10^-9 mol·L^-1-1.0 × 10^-6 mol·L^-1 for MG and 5.0 × 10^-8 mol·L^-1-1.0 × 10^-5 mol·L^-1 for thiram (R² ≥ 0.995). The detection limits are 6.2 × 10^-10 mol·L^-1 for MG and 1.7 × 10^-8 mol·L^-1 for thiram, respectively. The COF-AuNPs substrate was actually applied for analysis of MG in seafood products and thiram in different fruit juice, with the recoveries in the ranges of 94.67-108.99 % for MG and 95.00-107.58 % for thiram, and both of the relative standard deviation (RSD) are no more than 5.88 %. This work indicates that the developed COF-AuNPs substrate is promising for SERS analyses and detections of residues in foods.

Multiple amplification-based fluorometric aptasensor for highly sensitive detection of Staphylococcus aureus

Rapid and accurate detection and identification of Staphylococcus aureus (S. aureus) are of great significance for food safety, environmental monitoring, early clinical diagnosis, and prevention of the spread of drug-resistant bacteria. Herein, we design a fluorometric aptasensor for ultra-sensitive, specific, and rapid detection of S. aureus. The apasensor combines the enrichment and separation of magnetic nanoparticles (MNPs), the biotin-streptavidin conjugation system, and a single S. aureus can release four signaling probes for signal amplification. Aptamer acts as a specific biorecognition element of S. aureus. Four FAM-labeled partially complementary sequences (FAM-pcDNAs) were used as signaling probes. The aptamers were sequential hybridized with the four FAM-pcDNAs to form aptamer&pcDNAs, which were then bound to MNPs via the biotin-streptavidin. When the aptamer specifically recognizes and binds to S. aureus, the FAM-pcDNAs signaling probes are replaced and released into the supernatant. The concentration of S. aureus can be quantified by measuring the fluorescence intensity (λexc/em = 492/520 nm) of the replaced signaling probe FAM-pcDNAs. The results show that the proposed fluorometric aptasensor displays good specificity, ultra-high sensitivity (1.23 cfu/mL), wide linear range (1 ~ 10⁸ cfu/mL), and fast detection speed (~ 1.5 h). The recovery test verifies further that the proposed fluorometric aptasensor can detect S. aureus in spiked blood samples. Since aptamers are easy to customize, we believe that fluorometric aptasensors based on multiple amplification have broad prospects in the construction of practical high-performance biosensors for bacterial detection. KEY POINTS: • Multiple amplification-based fluorometric aptasensor for S. aureus is developed • The aptasensor displays high specificity with a LOD of 1.23 CFU/mL • The aptasensor can directly detect S. aureus in spiked blood samples.

Progress on aptamer-based SERS sensors for food safety and quality assessment: methodology, current applications and future trends

It is well known that food safety has aroused extensive attentions from governments to researchers and to food industries. As a versatile technology based on molecular interactions, aptamer sensors which could specifically identify a wide range of food contaminants have been extensively studied in recent years. Surface-enhanced Raman spectroscopy integrated aptamer combines the advantages of both technologies, not only in the ability to specifically identify a wide range of food contaminants, but also in the ultra-high sensitivity, simplicity, portable and speed. To provide beneficial insights into the evaluation techniques in the field of food safety, we offer a comprehensive review on the design strategies for aptamer-SERS sensors in different scenarios, including non-nucleic acid amplification methods ("on/off" mode, sandwich mode, competition model and catalytic model) and nucleic acid amplification methods (hybridization chain reaction, rolling circle amplification, catalytic hairpin assembly). Meanwhile, a special attention is paid to the application of aptamer-SERS sensors in biological (foodborne pathogenic, bacteria and mycotoxins) and chemical contamination (drug residues, metal ions, and food additives) of food matrix. Finally, the challenges and prospects of developing reliable aptamer-SERS sensors for food safety were discussed, which are expected to offer a strong guidance for further development and extended applications.

Catalytic hairpin activated gold-magnetic/gold-core-silver-shell rapid self-assembly for ultrasensitive Staphylococcus aureus sensing via PDMS-based SERS platform

Staphylococcus aureus (S. aureus) has been identified as a marker of food contamination, closely associated with human health. This work designs a sensitive and rapid bio-detection strategy for S. aureus based on hybridization chain reaction-assisted surface enhanced Raman scattering (HCR-assisted-SERS) signal amplification. In this approach, the interaction between the aptamer (Apt) and its partial complementary DNA strands (cDNA) fabricated on the surface of gold-assisted magnetic nanoparticles (Au-MNPs) and the subsequent detachment of the cDNA results in the activation of the HCR process. In the HCR, a pair of hairpin structured DNA probes (H1 and H2) with sticky ends self-assembles to form a long DNA polymer. Subsequently, the output and amplification of the SERS signal were performed by conjugating 4-ATP modified Au@Ag NPs with the obtained DNA polymer via a specific Ag-S bond, and further collected through a self-administered polydimethylsiloxane (PDMS) cone-shaped support array. The precise quantification of S. aureus was performed in the concentration range of 28 to 2.8 × 10⁶ cfu/mL, achieving a detection limit of 0.25 cfu/mL. This strategy was further applied to S. aureus detection in spiked milk samples with good recoveries (91-102%) and the relative standard deviation (4.35-8.41%). The sensing platform also showed satisfactory validation results (p > 0.05) using the traditional plate counting method. The proposed HCR-assisted SERS probe can be extended to other foodborne pathogenic bacteria types via engineering appropriate Apt and DNA initiators, thus, inspiring widespread applications in food safety and biomedical research.

Comparative Transcriptomic Analysis of Staphylococcus aureus Reveals the Genes Involved in Survival at Low Temperature

In food processing, the temperature is usually reduced to limit bacterial reproduction and maintain food safety. However, Staphylococcus aureus can adapt to low temperatures by controlling gene expression and protein activity, although its survival strategies normally vary between different strains. The present study investigated the molecular mechanisms of S. aureus with different survival strategies in response to low temperatures (4 °C). The survival curve showed that strain BA-26 was inactivated by 6.0 logCFU/mL after 4 weeks of low-temperature treatment, while strain BB-11 only decreased by 1.8 logCFU/mL. Intracellular nucleic acid leakage, transmission electron microscopy, and confocal laser scanning microscopy analyses revealed better cell membrane integrity of strain BB-11 than that of strain BA-26 after low-temperature treatment. Regarding oxidative stress, the superoxide dismutase activity and the reduced glutathione content in BB-11 were higher than those in BA-26; thus, BB-11 contained less malondialdehyde than BA-26. RNA-seq showed a significantly upregulated expression of the fatty acid biosynthesis in membrane gene (fabG) in BB-11 compared with BA-26 because of the damaged cell membrane. Then, catalase (katA), reduced glutathione (grxC), and peroxidase (ahpC) were found to be significantly upregulated in BB-11, leading to an increase in the oxidative stress response, but BA-26-related genes were downregulated. NADH dehydrogenase (nadE) and α-glucosidase (malA) were upregulated in the cold-tolerant strain BB-11 but were downregulated in the cold-sensitive strain BA-26, suggesting that energy metabolism might play a role in S. aureus under low-temperature stress. Furthermore, defense mechanisms, such as those involving asp23, greA, and yafY, played a pivotal role in the response of BB-11 to stress. The study provided a new perspective for understanding the survival mechanism of S. aureus at low temperatures.

Rapid determination of process parameters during simultaneous saccharification and fermentation (SSF) of cassava based on molecular spectral fusion (MSF) features

Simultaneous saccharification and fermentation (SSF) of cassava is one of the key steps in the production of fuel ethanol. In order to improve the monitoring efficiency of the ethanol production process and the product yield, this study puts forward a new idea for monitoring of the cassava SSF process based on the molecular spectroscopy fusion (MSF) technique. Savisky-Golay (SG) combined with standard normal variable (SNV) was used to preprocess the obtained Raman spectra and near-infrared (NIR) spectra. Competitive adaptive reweighted sampling (CARS) was used to optimize the characteristic wavelengths of the preprocessed Raman spectra and the NIR spectra, and the optimized features were fused in the feature layer. The support vector machine (SVM) model of the process parameters during the cassava SSF based on the MSF features was established. The experimental results showed that compared with the best CARS-SVM model based on the single-molecule spectral features, the performance of the best CARS-SVM model based on fusion features has been significantly improved. For detection of the glucose content, the RMSEP, R_P² and RPD of the best CARS-SVM model were 5.398, 0.957 and 4.922, respectively. For detection of the ethanol content, the RMSEP, R_P² and RPD of the best CARS-SVM model were 4.394, 0.977 and 6.758, respectively. The obtained results reveal that the combination of MSF technique and appropriate chemometric methods can achieve high-precision quantitative detection of the process parameters during the cassava SSF. This study can provide technical basis and experimental reference for the development of portable spectrometer equipment for process monitoring of the cassava SSF.

The recent development of nanozymes for food quality and safety detection

As potential mimics of natural enzymes, nanozymes overcome many disadvantages of natural enzymes such as complex preparation and purification process, high price, poor stability and low recycling efficiency. Combined with...

A lab-on-a-tube biosensor for automatic detection of foodborne bacteria using rotated Halbach magnetic separation and Raspberry Pi imaging

A lab-on-a-tube biosensor was established to rapidly, sensitively and automatically detect foodborne bacteria through a rotatable Halbach magnet to form and rotate magnetic nanobead (MNB) chains for specific isolation of target bacteria, gold@platinum nanocatalysts (Au@PtNCs) to label target bacteria for efficient amplification of detection signal and Raspberry Pi App to collect and analyze the image of catalysate. First, the glass tube was successively preloaded with the mixture of MNBs, sample and Au@PtNCs, the washing buffer (skim milk) and the substrate (hydrogen peroxide-3,30,5,50-tetramethylbenzidine), and they were separated by air gaps. After the tube was placed on the biosensor, the MNB chains were stably formed and continuously rotated using the Halbach magnet and the mixture was moved back and forth using a programmable peristaltic pump, thus making the formation of MNB-bacteria-Au@PtNCs complexes. After the washing buffer was moved to wash the complexes, the substrate was then moved to resuspend the complexes, resulting in the catalytic reaction that changed the color of the substrate. Finally, the catalysate was moved to the designated area, the image of which was analyzed by the Raspberry Pi App to quantitatively determine the concentration of bacteria in the samples. This biosensor was able to detect Salmonella in spiked chicken samples in 1 h with lower detection limit of 8 CFU/50 μL and a recovery from 88.96% to 99.74%. This biosensor based on a single tube is very promising to automatically detect foodborne bacteria due to its low cost, high integration and simple operation.

Upconversion Nanoprobes Based on a Horseradish Peroxidase-Regulated Dual-Mode Strategy for the Ultrasensitive Detection of Staphylococcus aureus in Meat

Staphylococcus aureus (S. aureus) is one of the foodborne pathogens that can cause infectious diseases and food poisoning. Herein, colorimetric and fluorescent dual-mode nanoprobes were developed for ultrasensitive detection of S. aureus to immediately respond to public health emergencies, reduce false positives, and improve measurement accuracy and persuasiveness. The nanoprobe consists of aptamer-labeled magnetic nanoparticles (apt-MNPs) as the capture signal probe and horseradish peroxidase and complementary DNA-functionalized upconversion nanoparticles (HRP-UCNPs-cDNA) as the chromogenic signal probe. In the absence of S. aureus, the probe forms an immune complex through base complementation with an observable signal. When S. aureus is introduced to this system, it preferentially binds to the apt-MNPs, releasing HRP-UCNPs-cDNA from the apt-MNPs and restoring the chromogenic probe signal. Under optimum conditions, an ultrasensitive assay of S. aureus was obtained, with limits of detection of 22 CFU mL^-1 for fluorescence and 20 CFU mL^-1 for colorimetry in a linear range of 56-5.6 × 10⁶ CFU mL^-1. Additionally, the standard plate counting method confirmed the reliability and accuracy of the established nanoprobe with an insignificant difference. Hence, the developed dual-mode platform has extensive application prospects for speedy and specific determination of S. aureus in meat.

Recent advancement in nano-optical strategies for detection of pathogenic bacteria and their metabolites in food safety

Pathogenic bacteria and their metabolites are the leading risk factor in food safety and are one of the major threats to human health because of the capability of triggering diseases with high morbidity and mortality. Nano-optical sensors for bacteria sensing have been greatly explored with the emergence of nanotechnology and artificial intelligence. In addition, with the rapid development of cross fusion technology, other technologies integrated nano-optical sensors show great potential in bacterial and their metabolites sensing. This review focus on nano-optical strategies for bacteria and their metabolites sensing in the field of food safety; based on surface-enhanced Raman scattering (SERS), fluorescence, and colorimetric biosensors, and their integration with the microfluidic platform, electrochemical platform, and nucleic acid amplification platform in the recent three years. Compared with the traditional techniques, nano optical-based sensors have greatly improved the sensitivity with reduced detection time and cost. However, challenges remain for the simple fabrication of biosensors and their practical application in complex matrices. Thus, bringing out improvements or novelty in the pretreatment methods will be a trend in the upcoming future.