Multiplex PCR method for simultaneous detection of five pathogenic bacteria closely related to foodborne diseases

Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

Rapid and Sensitive Fluorescence Detection of Staphylococcus aureus Based on Polyethyleneimine-Enhanced Boronate Affinity Isolation

There are increasing demands for fast and simple detection of pathogens in foodstuffs. Fluorescence analysis has demonstrated significant advantages for easy operation and high sensitivity, although it is usually hindered by a complex matrix, low bacterial abundance, and long-term bacterial enrichment. Effective enrichment procedures are required to meet the requirements for food detection. Here, boronate-functionalized cellulose filter paper and specific fluorescent probes were combined. An integrated approach for the enrichment of detection of Staphylococcus aureus was proposed. The modification of polyethyleneimine demonstrated a significant effect in enhancing the bacterial enrichment, and the boronate affinity efficiency of the paper was increased by about 51~132%. With optimized conditions, the adsorption efficiency for S. aureus was evaluated as 1.87 × 10⁸ CFU/cm², the linear range of the fluorescent analysis was 10⁴ CFU/mL~10⁸ CFU/mL (R² = 0.9835), and the lowest limit of detection (LOD) was calculated as 2.24 × 10² CFU/mL. Such efficiency was validated with milk and yogurt samples. These results indicated that the material had a high enrichment capacity, simple operation, and high substrate tolerance, which had the promising potential to be the established method for the fast detection of food pathogens.

Optimization and evaluation of a multiplex PCR assay for detection of Staphylococcus aureus and its major virulence genes for assessing food safety

Staphylococcus aureus is a natural commensal microflora of humans which causes opportunistic infections due to its large arsenal of exotoxins, invasion, immune evasion, and antibiotic resistance mechanisms. The primary goal of this study is to develop a multiplex PCR (mPCR) assay for simultaneous detection of Staphylococcus aureus (nuc) and its virulence genes coding for prominent exotoxins namely alpha hemolysin (hla), enterotoxins A (sea), enterotoxin B (seb), toxic shock syndrome toxin (tsst-1), and the gene coding for methicillin resistance (mecA). A competitive internal amplification control (IAC) was included in the assay to exclude the false negative outcomes. Highly specific primer pairs were designed for the target genes using in silico resources. At the outset, monoplex PCRs were standardized using reference S. aureus strains. Primer specificity to the target genes was authenticated through restriction digestion analysis of amplified PCR products. Multiplex PCR was optimized in increments of one gene starting with nuc and IAC amplified simultaneously using one pair of primers (nuc) in a competitive manner. The mPCR assay was found to be highly sensitive with a detection limit of ~10 CFUs per reaction for pure cultures. Multiplex PCR assay was further evaluated on the retail and processed food samples to test the prevalence of S. aureus and study their exotoxin profiles. Of the 57 samples examined, 13 samples (22.80%) were found to be contaminated with S. aureus whose DNA was extracted after a 6-h enrichment period. Among these, a high percentage of hemolytic and enterotoxin A positive strains were encountered. The mPCR assay developed in this study would be a useful tool for rapid and reliable monitoring of S. aureus for food quality testing and from clinical infections.

A novel SERS method for the detection of Staphylococcus aureus without immobilization based on Au@Ag NPs/slide substrate

Here, an aptamer-based SERS method for the detection of Staphylococcus aureus (S. aureus) without immobilization using Au@Ag NPs/slide as enhanced substrate was constructed. ROX-aptamer of S. aureus was modified on the surface of Au@Ag NPs/slide through electrostatic interaction. Based on the specific binding effect of the aptamer to S. aureus, the ROX-aptamer fell off from the surface of the substrate, resulting in a decrease of the SERS signal intensity of the substrate. Under the optimal experimental conditions, a good linear relationship was found between SERS intensity at 1500 cm^-1 and the logarithm of concentration of S. aureus in the range of 10² cfu/mL-10⁷ cfu/mL (y = 6623-796lgx, R² = 0.994) with a detection limit of 6 cfu/mL. The selectivity analysis revealed that the method had higher selectivity toward the corresponding target. The results for milk sample using the developed SERS method for the detection of S. aureus were similar to those of the plate counting method. The recovery ratio was from 90.60% to 107.26%, indicating the accuracy and reliability of the developed method. This method eliminates the need for bacterial immobilization and improves the convenience and efficiency of detection.

Research progress on detection techniques for point-of-care testing of foodborne pathogens

The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.

Hapten-labeled fusion-polymerase chain reaction of multiple marker genes for the application of immunochromatographic test

A variety of methods have been reported using polymerase chain reaction (PCR)-based nucleic acid testing (NAT) because of its potential to be used in highly sensitive inspection systems. Among these NATs, fusion-PCR (also called as overlap-extension-PCR) has been focused on this study and adopted to generate the fused amplicon composed of plural marker gene fragments for detection. Generally, conventional agarose gel electrophoresis followed by gel staining is employed to check the PCR results. However, these are time-consuming processes that use specific equipment. To overcome these disadvantages, the immunochromatographic test (ICT) for the detection of PCR amplicons with hapten-labels that were generated by PCR using hapten-labeled primers was also adopted in this study. Based on these concepts, we constructed the systems of hapten-labeled fusion-PCR (HL-FuPCR) followed by ICT (HL-FuPCR-ICT) for the two and three marker genes derived from pathogenic microbe. As a result, we successfully developed a two marker genes system for the pathogenic influenza A virus and a three marker genes system for the penicillin-resistant Streptococcus pneumoniae. These detection systems of HL-FuPCR-ICT are characterized by simple handling and rapid detection within few minutes, and also showed the results as clear lines. Thus, the HL-FuPCR-ICT system introduced in this study has potential for use as a user-friendly inspection tool with the advantages especially in the detection of specific strains or groups expressing the characteristic phenotype(s) such as antibiotic resistance and/or high pathogenicity even in the same species.

A PCR-free genosensing platform for detection of Shigella dysenteriae in human plasma samples by porous and honeycomb-like biochar decorated with ultrathin flower-like MoS2 nanosheets incorporated with Au nanoparticles

Shigella dysenteriae, a gram-negative bacterium, which results in the most infectious of bacterial shigellosis and dysenteries. In this study, an innovative gene detection platform based on label-free DNA sequences was developed to detect Shigella dysenteriae in human plasma samples. The porous and honeycomb-like structure of biochar (BC) was first synthesized through a pyrolysis process. Then, the produced biochar was effectively decorated with flower-like MoS₂ nanosheets (MoS₂/BC). The resulting nanocomposite was incorporated with Au nanoparticles (AuNPs) by applying chronoamperometry technique, and then the subsequent product including MoS₂ nanosheets, biochar and AuNPs were immobilized on the Au electrode surface and used for modifier agent in electrochemical bio-assays. Structural and morphological study of the synthesized compounds were investigated using various characterization methods such as FE-SEM, TEM, EDS, FTIR, and XRD. Various electrochemical techniques including cyclic voltammetry (CV) and Differential pulse anodic stripping voltammetry (DPASV) have been used to investigate the applicability of the fabricated genosensing bio-assay. Under optimal conditions, LOD and LOQ were calculated 9.14 fM and 0.018 pM respectively. In addition, a linear range from 0.01 to 100 pM was obtained for single stranded-target DNA (ss-tDNA), with R² of 0.9992. The recoveries ranged from 98.0 to 101.3%. The fabricated bio-detection assay demonstrated high selectivity for 1, 2, and 3 base mismatch sequences. In addition, a negative control of the gene detection platform which was performed to study selectivity was provided by ss-tDNA from Haemophilusinfluenzae, and Salmonella typhimurium. Moreover, it is important to mention that the organized bioassay is simply reusable and reproducible with the RSD% (relative standard deviation) ˂ 5 to next detection assays.

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.