Quantitative Analysis of Salmonella typhimurium Based on Elemental-Tags Laser-Induced Breakdown Spectroscopy

An antifouling electrochemical biosensor using self-signal for Salmonella typhimurium direct detection in food sample

Eating food contaminated by foodborne pathogens can lead to illness. The development of electrochemical sensors for pathogen detection has received widespread attention. However, the analytical performance of electrochemical sensors is inevitably affected by the non-specific adsorption of molecules in the sample. Moreover, the external signal probes might be affected by the complex components in the sample accompanied with signal suppression. This work presents an electrochemical aptasensor for Salmonella typhimurium detection based on the self-signal of poly-xanthurenic acid and the antifouling ability of chondroitin sulfate. The detection time was 60 min. The linear range was from 101 to 107 CFU/mL, and the detection limit was 3 CFU/mL. The biosensors presented good repeatability and storage stability. And the biosensors has been successfully applied in milk and orange juice. This strategy is expected to be applied in the design of other antifouling biosensors, to achieve rapid detection of pathogens and ensure food safety.

Allosteric probe-triggered isothermal amplification to activate CRISPR/Cas12a for sensitive electrochemiluminescence detection of Salmonella

We report an electrochemiluminescence (ECL) sensor for Salmonella detection based on allosteric probe as a bio-recognition element and CRISPR/Cas12a as a signal amplification strategy. In the presence of Salmonella, the structure switching occurs on allosteric probes, resulting in their hybridization with primers to trigger isothermal amplification. Salmonella is then released to initiate the next reaction cycle accompanying by generating a large amount of dsDNA, which are subsequently recognized by CRISPR-gRNA for activating the trans-cleavage activity of Cas12a. Furthermore, the activated Cas12a can indiscriminately cut the ssDNA which is bound to the electrode, enabling the release of the ECL emitter porphyrinic Zr metal - organic framework (MOF, PCN-224) and exhibiting a decreased ECL signal accordingly. The linear range is 50 CFU·mL^-1-5 × 10⁶ CFU·mL^-1 and the detection limit is calculated to be 37 CFU·mL^-1. This method sensitively detects Salmonella in different types of real samples, indicating it is a promising strategy for Salmonella detection.

T-Shaped Aptamer-Based LSPR Biosensor Using Ω-Shaped Fiber Optic for Rapid Detection of SARS-CoV-2

SARS-CoV-2, especially the variant strains, is rapidly spreading around the world. Rapid detection methods for the virus are crucial for controlling the COVID-19 epidemic. Herein, a localized surface plasmonic resonance (LSPR) biosensor based on Ω-shaped fiber optic (Ω-FO) was developed for dual assays of SARS-CoV-2 monitoring. Due to its strong ability to control the orientation and density, a new T-shaped aptamer exhibits enhanced binding affinity toward N proteins. After being combined on the fiber optic surface, the T-shaped aptamer sensitively captured N proteins of SARS-CoV-2 for a direct assay. Further, core-shell structured gold/silver nanoparticles functionalized with a T-shaped aptamer (apt-Ag@AuNPs) can amplify the signal of N protein detection for a sandwich assay. The real-time analytical feature of the dual assays endows time-dependent sensitivity enhancement behavior, which provides a guideline to save analytical time. With those characteristics, the LSPR biosensor has been successfully used to rapidly identify 39 healthy volunteers and 39 COVID-19 patients infected with the ancestral or variant SARS-CoV-2. With the help of simple pretreatment, we obtain a true negative rate of 100% and a true positive rate of 92.3% with a short analysis time of 45 min using the direct assay. Further, the LSPR biosensor could also broaden the detection application range to the surface of cold-chain foods using a sandwich assay. Thus, the LSPR biosensor based on Ω-FO was demonstrated to have broad application potential to detect SARS-CoV-2 rapidly.

Molecularly imprinted 3D SERS sensor with inorganic frameworks for specific and recyclable SERS sensing application

Poor selectivity and reusability of Au/Ag nanostructures are the main challenges for surface-enhanced Raman spectroscopy (SERS) in real sample detection. Herein, a novel specific and reusable three-dimensional (3D) SERS sensor with dual functions of selective trapping and photocatalytic degradation was designed. Firstly, Au-Ag bimetallic nanoparticles decorated silicon nanowires array (SiNWs-AuAg) were prepared as 3D SERS substrate. Then, silicon-based inorganic-framework molecularly imprinted TiO₂ (TiO₂@SiMIP) was synthesized and immobilized on SiNWs-AuAg by using rhodamine 6G (R6G) as template molecule. Owing to the excellent SERS performance of SiNWs-AuAg and the specific affinity of TiO₂@SiMIP to template molecule, the prepared SERS sensor enables sensitive and selective detection of R6G in food samples with a limit of detection (LOD) of 0.27 nM. In addition, due to the photocatalysis of TiO₂ and the stability of silicon-based inorganic framework, the residual templates in TiO₂@SiMIP can be completely removed by UV irradiation, and the imprinted cavity of regenerated sensors still maintained good selectivity after regeneration by UV irradiation.

Construction of classification models for pathogenic bacteria based on LIBS combined with different machine learning algorithms

Bacteria, especially foodborne pathogens, seriously threaten human life and health. Rapid discrimination techniques for foodborne pathogens are still urgently needed. At present, laser-induced breakdown spectroscopy (LIBS), combined with machine learning algorithms, is seen as fast recognition technology for pathogenic bacteria. However, there is still a lack of research on evaluating the differences between different bacterial classification models. In this work, five species of foodborne pathogens were analyzed via LIBS; then, the preprocessing effect of five filtering methods was compared to improve accuracy. The preprocessed spectral data were further analyzed with a support vector machine (SVM), a backpropagation neural network (BP), and k-nearest neighbor (KNN). Upon comparing the capacity of the three algorithms to classify pathogenic bacteria, the most suitable one was selected. The signal-to-noise ratio and mean square error of the spectral data after applying a Savitzky-Golay filter reached 17.4540 and 0.0020, respectively. The SVM algorithm, BP algorithm, and KNN algorithm attained the highest classification accuracy for pathogenic bacteria, reaching 98%, 97%, and 96%, respectively. The results indicate that, with the support of a machine learning algorithm, LIBS technology demonstrates superior performance, and the combination of the two is expected to be a powerful tool for pathogen classification.

Dual-aptamer-based enzyme linked plasmonic assay for pathogenic bacteria detection

Development of rapid, sensitive, and selective method for pathogenic bacteria detection is of great importance for food safety, medical diagnostic, and environmental monitoring. Currently, most techniques for low numbers of bacteria detection require advanced instrumentation or skilled operators. Herein, we present a facile colorimetric detection platform for bacterial detection using Ag nanoplates as chromogenic substrate, which takes advantages of the high specificity and affinity of aptamer and the ability of catalase to hydrolyze H₂O₂ that can etch Ag nanoplates. By introducing catalase to the sandwich structure composed by dual-aptamer recognition strategy, bacteria detection signal is converted to the peak shift of LSPR and colorimetric change. This proposed method allows a fast naked-eye detection of S. aureus at the concentration of 60 CFU/mL based on the combination of streptavidin-biotin system and inherent sensitivity of plasmonic Ag nanoplates. Owing to the high selectivity and sensitivity, as well as the low-cost and good adaptability, this plasmonic assay is expected to be suitable for pathogenic bacteria detection in resource-limited settings.

Phage long tail fiber protein-immobilized magnetic nanoparticles for rapid and ultrasensitive detection of Salmonella

There is an urgent need to develop fast and sensitive detection methods for foodborne pathogens. But the conventional culture method that typically requires 2-3 days is not ideal for the rapid analysis. Food samples demonstrate a great challenge for direct detection due to the complex matrix. Hence, we present a new method based on the phage long-tail-fiber proteins (LTF4-a) immobilized magnetic nanoparticles (MNPs) for specific separation and concentration of Salmonella. The LTF4-a-MNP was prepared via the coupling of recombinant LTF4-a with MNPs and used to isolate and enrich Salmonella cells from contaminated food samples. The captured material was further integrated with the direct PCR program for accurate detection of Salmonella. Our study successfully established a new method for detecting contaminated food samples of Salmonella, the overall approach took no more than 3 h, which allowed a detection limit of 7 CFU/mL, demonstrating a promising alternative to the immunomagnetic separation method by replacing antibodies or aptamers, that is compatible with downstream analysis.

Recent Advances and Applications of Rapid Microbial Assessment from a Food Safety Perspective

Unsafe food is estimated to cause 600 million cases of foodborne disease, annually. Thus, the development of methods that could assist in the prevention of foodborne diseases is of high interest. This review summarizes the recent progress toward rapid microbial assessment through (i) spectroscopic techniques, (ii) spectral imaging techniques, (iii) biosensors and (iv) sensors designed to mimic human senses. These methods often produce complex and high-dimensional data that cannot be analyzed with conventional statistical methods. Multivariate statistics and machine learning approaches seemed to be valuable for these methods so as to "translate" measurements to microbial estimations. However, a great proportion of the models reported in the literature misuse these approaches, which may lead to models with low predictive power under generic conditions. Overall, all the methods showed great potential for rapid microbial assessment. Biosensors are closer to wide-scale implementation followed by spectroscopic techniques and then by spectral imaging techniques and sensors designed to mimic human senses.

A capillary-based SERS sensor for ultrasensitive and selective detection of Hg2+ by amalgamation with Au@4-MBA@Ag core-shell nanoparticles

A capillary-based SERS sensor was fabricated for ultrasensitive and selective detection of Hg²⁺ in water. Au@Ag core-shell NPs embedded with 4-mercaptobenzoic acid (4-MBA) (Au@4-MBA@Ag) were prepared by a seed growth method and fixed on the inner wall of the glass capillary to obtain the sensor. Owing to the amalgamation between Ag and Hg, the capillary-based SERS sensor can specifically recognize the reduced Hg²⁺ without any recognition element, and the resulted Ag/Hg amalgam can weaken the SERS activity of Ag shell; thus, the SERS intensity of the embedded 4-MBA at 1075 cm^-1 gradually decreased with the increase of Hg²⁺ concentration. Under the optimum condition, the fabricated sensor can sensitively determine Hg²⁺ in water with a limit of detection (LOD) as low as 0.03 nM. The capillary-based SERS sensor offers the advantages of simple preparation, superior stability, and high selectivity, which is promising for rapid and on-site detection of Hg²⁺ in water combined with a portable Raman device.

Single-digit Salmonella detection with the naked eye using bio-barcode immunoassay coupled with recombinase polymerase amplification and a CRISPR-Cas12a system

The ability to visually detect low numbers of Salmonella in food samples is highly valuable but remains a challenge. Here we present a novel platform for ultrasensitive and visual detection of Salmonella Typhimurium by integrating the bio-barcode immunoassay (BCA), recombinase polymerase amplification (RPA), and CRISPR-Cas12a cleavage in a single reaction system (termed as BCA-RPA-Cas12a). In the system, the target bacteria were separated by immunomagnetic nanoparticles and labeled with numerous barcode AuNPs, which carry abundant bio-barcode DNA molecules to amplify the signal. Afterwards, the bio-barcode DNA molecules were amplified by RPA and subsequently triggered the cleavage activity of Cas12a to generate the fluorescence signal. Due to this triplex signal amplification, the BCA-RPA-Cas12a system can selectively detect Salmonella Typhimurium at the single-digit level with the naked eye under blue light within 60 min. Meanwhile, this novel platform was successfully applied to detect Salmonella Typhimurium in spiked milk samples with a similar sensitivity and satisfactory recovery, indicating its potential application in real samples. Furthermore, in virtue of the versatility of the antibody in the stage of BCA, the BCA-RPA-Cas12a system can be extended to further application in other bacteria detection and food safety monitoring.

Multiplexing steganography based on laser-induced breakdown spectroscopy coupled with machine learning

This study proposes steganography based on laser-induced breakdown spectroscopy (LIBS) for the first time. LIBS inks containing different elements in varying concentrations were fabricated to write steganographic text. LIBS was combined with machine learning as an ideal tool to efficiently extract hidden information. The proposed steganography strategy has the advantages of low cost, high security, and good stability, thus providing a practical tool for information transfer.

A simple magnetic-assisted microfluidic method for rapid detection and phenotypic characterization of ultralow concentrations of bacteria

Isolation and enumeration of bacteria at ultralow concentrations and antibiotic resistance profiling are of great importance for early diagnosis and treatment of bacteremia. In this work, we describe a simple, rapid, and versatile magnetic-assisted microfluidic method for rapid bacterial detection. The developed method enables magnetophoretic loading of bead-captured bacteria into the microfluidic chamber under external static and dynamic magnetic fields in 4 min. A shallow microfluidic chamber design that enables the monolayer orientation and transportation of the beads and a glass substrate with a thickness of 0.17 mm was utilized to allow high-resolution fluorescence imaging for quantitative detection. Escherichia coli (E. coli) with green fluorescent protein (GFP)-expressing gene and streptavidin-modified superparamagnetic microbeads were used as model bacteria and capturing beads, respectively. The specificity of the method was validated using Lactobacillus gasseri as a negative control group. The limit of detection and limit of quantification values were determined as 2 CFU/ml and 10 CFU/ml of E. coli, respectively. The magnetic-assisted microfluidic method is a versatile tool for the detection of ultralow concentrations of viable bacteria with the linear range of 5-5000 CFU/ml E. coli in 1 h, and providing growth curves and phenotypic characterization bead-captured E. coli in the following 5 h of incubation. Our results are promising for future rapid and sensitive antibiotic susceptibility testing of ultralow numbers of viable cells.

An enzyme-mediated universal fluorescent biosensor template for pathogen detection based on a three-dimensional DNA walker and catalyzed hairpin assembly

An enzyme-mediated universal fluorescent biosensor template for rapid detection of pathogens was developed based on the strategy of a three-dimensional (3D) DNA walker and catalyzed hairpin assembly (CHA) reaction. In the bacterial recognition step, a strand displacement reaction between bacteria and the double-stranded complex caused the release of the walker strand. The walker strand triggered the DNA walker to produce an enzyme fragment, and the DNA walker used gold nanoparticles (AuNPs) as the track to provide an excellent DNA ligand anchoring area. In the CHA step, the enzyme fragment induced the CHA cycle to yield fluorescence signals, which greatly enhanced the conversion ratio of trigger DNA and the sensitivity of the fluorescent biosensor. The effect of the distance and density of the DNA ligand was studied by adjusting the length of poly-adenine (PolyA), and was further explored by its reaction kinetics. By comparing the maximum reaction rate (Vmax), Michaelis constant (Km) and turnover number (Kcat), the optimized PolyA probe was assessed and identified. In this work, the optimized PolyA-DNA probe exhibited an outstanding sensitivity in Salmonella typhimurium (S. ty) detection, which is 11.9 times and 4.6 times higher than those of the SH-DNA and the MCH treated SH-DNA. Meanwhile, a detection limit of 28.1 CFU mL-1 was achieved in Escherichia coli (E. coli) detection. Furthermore, the biosensor achieved good selectivity and high repeatability with recoveries of 91%-115% for real sample detection. Considering these advantages, this template has great potential as a routine tool for pathogen detection and has wide applications in the field of global public health and food safety.

A novel surface-enhanced Raman scattering (SERS) strategy for ultrasensitive detection of bacteria based on three-dimensional (3D) DNA walker

Bacteria seriously endanger human life and health, and the detection of bacteria is vital for the prevention and treatment of related diseases. Surface-enhanced Raman scattering (SERS) is considered as a powerful technique for bacterial detection due to the inherent richness of spectral data. In this work, a novel SERS strategy based on three-dimensional (3D) DNA walker was developed for quantitative analysis of Salmonella typhimurium (S. ty). The complimentary DNA of S.ty-recognizing aptamer (cApt) was replaced from the double-stranded DNA (dsDNA) of Apt@cApt in the presence of S.ty, which can trigger the endonuclease mediated "DNA walker" on the surface of gold modified magnetic nanoparticles (AuMNPs). The DNA residues on the surface of AuMNPs can bind to SERS tag through base complementary pairing, and the complex of "AuMNPs@SERS tag" can be separated from the fluid by an external magnetic field for SERS analysis. It was found that the SERS intensity showed a good linear relationship with both lower (10-10⁴ CFU/mL) and higher (10⁴-10⁶ CFU/mL) S.ty concentration. A superior limit of detection (LOD) as low as 4 CFU/mL was achieved due to the signal amplification effect of "DNA walker", and the preeminent selectivity of the proposed method was determined by the selectivity of the aptamer sequence. This strategy of separating the SERS tag from the biological matrix enables high stability and good repeatability of the SERS spectra, which presents a new method for SERS detection of biomaterials that can benefit various application scenarios.