Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations

Infrared spectroscopy-based machine learning algorithms for rapid detection of Klebsiella pneumoniae isolated directly from patients' urine and determining its susceptibility to antibiotics

Among the most prevalent and detrimental bacteria causing urinary tract infections (UTIs) is Klebsiella (K.) pneumoniae. A rapid determination of its antibiotic susceptibility can enhance patient treatment and mitigate the spread of resistant strains. In this study, we assessed the viability of using infrared spectroscopy-based machine learning as a rapid and precise approach for detecting K. pneumoniae bacteria and determining its susceptibility to various antibiotics directly from a patient's urine sample. In this study, 2333 bacterial samples, including 636 K. pneumoniae were investigated using infrared micro-spectroscopy. The obtained spectra (27996spectra) were analyzed with XGBoost classifier, achieving a success rate exceeding 95 % for identifying K. pneumoniae. Moreover, this method allows for the simultaneous determination of K. pneumoniae susceptibility to various antibiotics with sensitivities ranging between 74 % and 81 % within approximately 40 min after receiving the patient's urine sample.

Rapid Concentration and Detection of Bacteria in Milk Using a Microfluidic Surface Acoustic Wave Activated Nanosieve

Rapid detection of microbes is a key feature for monitoring food quality. Unfortunately, current detection systems rely on labor-intensive and time-consuming lab-based processes that are not suitable for point-of-interest applications and typically require several days before results are available. Here, we demonstrate a microfluidic system capable of rapidly concentrating, fluorescent staining, and detecting bacteria in unprocessed complex biological media such as milk. This concentration is done using a surface acoustic wave-driven microfluidic device which operates based on the Bjerknes force, a force generated on one particle by another in its close proximity. We exploit this effect by exciting a tightly packed bed of 50 μm polystyrene microparticles temporarily with surface acoustic waves within a microfluidic device to capture and release bacterial cells on demand. The bacterial cells are fluorescently stained during capture and then detected using fluorescence microscopy upon release. This device offers a high capturing efficiency (>80%) and a 34 Colony Forming Units (CFU)/mL limit of detection, which is 1 order of magnitude below that of plate counting at 30 CFU per standard 100 μL plate (or 300 CFU/mL). This can be attained in just 1 h of processing at 10 μL/min. With this system, we demonstrate that bacterial detection from extremely low concentration samples down to the order of ∼10 CFU/mL is possible without requiring any additional external pre- or postprocessing.

Phage tailspike protein coated gold nanoparticles combined with smartphone for rapid bacterial detection and photothermal sterilization

The integration of recognition and therapeutic functions in multifunctional biosensors is of great importance in guaranteeing food security and reducing the occurrence of foodborne illness caused by foodborne pathogens. In this study, a biosensor utilizing a "sense-and-treat" approach was developed by integrating phage tailspike protein (TSP) with gold nanoparticles (AuNPs@TSP). The synthesized AuNPs@TSP showed strong binding affinity towards Salmonella typhimurium causing color changes and exhibited effective bactericidal activity when exposed to near-infrared (NIR) irradiation. This biosensor facilitated rapid colorimetric detection of S. typhimurium in 50 min, with a LOD (limit of detection) of 2.53 × 103 CFU/mL output on a smartphone APP after analyzing the red-green-blue (RGB) values from color rendering results. Furthermore, the biosensor displayed high selectivity, rapid response time, and broad applicability when tested with real samples. Moreover, the biosensor exhibited a remarkably efficient antibacterial efficacy of 100 % against S. typhimurium under 808 nm light irradiation for 6 min. This study provides a comprehensive investigation into the potential utilization of biosensors for rapid detection and eradication of foodborne pathogens in food industry.

Hyperspectral upgrade solution for biomicroscope combined with Transformer network to classify infectious bacteria

Infectious diseases caused by bacterial pathogens pose a significant public health threat, emphasizing the need for swift and accurate bacterial species detection methods. Hyperspectral microscopic imaging (HMI) offers nondestructive, rapid, and data-rich advantages, making it a promising tool for microbial detection. In this research, we present a highly compatible and cost-effective approach to extend a standard biomicroscope system into a hyperspectral biomicroscope using a prism-grating-prism configuration. Using this prototype, we generate 600 hyperspectral data cubes for Listeria, Bacillus typhi, Bacillus pestis, and Bacillus anthracis. Additionally, we propose a Transformer-based classification network that achieves a 99.44% accuracy in classifying these infectious pathogens, outperforming traditional methods. Our results suggest that the successful combination of HMI and the optimized Transformer-based classification network highlights the potential for rapid and precise detection of infectious disease pathogens .

Rapid Detection of Broad-Spectrum Pathogenic Bacteria Based on Highly Sensitive Proton Response of the Nucleic Acid Amplification SPQC Platform

Pathogenic bacteria significantly contribute to elevated morbidity and mortality rates, highlighting the urgent need for early and precise detection. Currently, there is a paucity of effective broad-spectrum methods for detecting pathogenic bacteria. We have developed an innovative proton-responsive series piezoelectric quartz crystal (PR-SPQC) platform for the broad-spectrum identification of pathogenic bacteria. This was achieved by retrieving and aligning sequences from the NCBI GenBank database to identify and validate 16S rRNA oligonucleotide sequences that are signatures of pathogenic bacteria but absent in humans or fungi. The hyperbranched rolling circle amplification, activated exclusively by the screened target, exponentially generates protons that are detected by SPQC through a 2D polyaniline (PANI) film. The PR-SPQC platform demonstrates broad-spectrum capabilities in detecting pathogenic bacteria, with a detection limit of 2 CFU/mL within 90 min. Clinical testing of blood samples yielded satisfactory results. With its advantages in miniaturization, cost efficiency, and suitability for point-of-care testing, PR-SPQC has the potential to be extensively used for the rapid identification of diverse pathogenic bacteria within clinical practice and public health sectors.

Establishment of a Simple, Sensitive, and Specific Salmonella Detection Method Based on Recombinase-Aided Amplification Combined with dsDNA-Specific Nucleases

Salmonella is a common foodborne pathogen that can cause food poisoning, posing a serious threat to human health. Therefore, quickly, sensitively, and accurately detecting Salmonella is crucial to ensuring food safety. For the Salmonella hilA gene, we designed Recombinase-aided amplification (RAA) primers and dsDNA-specific nuclease (DNase) probes. The ideal primer and probe combination was found when conditions were optimized. Under UV light, a visual Salmonella detection technique (RAA-dsDNase) was developed. Additionally, the RAA-dsDNase was modified to further reduce pollution hazards and simplify operations. One-pot RAA-dsDNase-UV or one-pot RAA-dsDNase-LFD was developed as a Salmonella detection method, using UV or a lateral flow dipstick (LFD) for result observation. Among them, one-pot RAA-dsDNase and one-pot RAA-dsDNase-LFD had detection times of 50 min and 60 min, respectively, for detecting Salmonella genomic DNA. One-pot RAA-dsDNase-UV had a detection limit of 101 copies/μL and 101 CFU/mL, while one-pot RAA-dsDNase-LFD had a sensitivity of 102 copies/μL and 102 CFU/mL. One-pot RAA-dsDNase-UV and one-pot RAA-dsDNase-LFD assays may identify 17 specific Salmonella serovars witho ut causing a cross-reaction with the remaining 8 bacteria, which include E. coli. Furthermore, Salmonella in tissue and milk samples has been reliably detected using both approaches. Overall, the detection method developed in this study can quickly, sensitively, and accurately detect Salmonella, and it is expected to become an important detection tool for the prevention and control of Salmonella in the future.

Development of rapid nucleic acid testing techniques for common respiratory infectious diseases in the Chinese population

Background: Most respiratory viruses can cause serious lower respiratory diseases at any age. Therefore, timely and accurate identification of respiratory viruses has become even more important. This study focused on the development of rapid nucleic acid testing techniques for common respiratory infectious diseases in the Chinese population. Methods: Multiplex fluorescent quantitative polymerase chain reaction (PCR) assays were developed and validated for the detection of respiratory pathogens including the novel coronavirus (SARS-CoV-2), influenza A virus (FluA), parainfluenza virus (PIV), and respiratory syncytial virus (RSV). Results: The assays demonstrated high specificity and sensitivity, allowing for the simultaneous detection of multiple pathogens in a single reaction. These techniques offer a rapid and reliable method for screening, diagnosis, and monitoring of respiratory pathogens. Conclusion: The implementation of these techniques might contribute to effective control and prevention measures, leading to improved patient care and public health outcomes in China. Further research and validation are needed to optimize and expand the application of these techniques to a wider range of respiratory pathogens and to enhance their utility in clinical and public health settings.

PEI-Mediated Assembly of Fe3O4 onto SiO2-Encapsulated CsPbBr3 for Highly Sensitive Fluorescent Lateral Flow Immunoassay

The conventional lateral flow immunoassay (LFIA) method using colloidal gold nanoparticles (Au NPs) as labeling agents faces two inherent limitations, including restricted sensitivity and poor quantitative capability, which impede early viral infection detection. Herein, we designed and synthesized CsPbBr3 perovskite quantum dot-based composite nanoparticles, CsPbBr3@SiO2@Fe3O4 (CSF), which integrated fluorescence detection and magnetic enrichment properties into LFIA technology and achieved rapid, sensitive, and convenient quantitative detection of the SARS-CoV-2 virus N protein. In this study, CsPbBr3 served as a high-quantum-yield fluorescent signaling probe, while SiO2 significantly enhanced the stability and biomodifiability of CsPbBr3. Importantly, the SiO2 shell shows relatively low absorption or scattering toward fluorescence, maintaining a quantum yield of up to 74.4% in CsPbBr3@SiO2. Assembly of Fe3O4 nanoparticles mediated by PEI further enhanced the method's sensitivity and reduced matrix interference through magnetic enrichment. Consequently, the method achieved a fluorescent detection range of 1 × 102 to 5 × 106 pg·mL-1 after magnetic enrichment, with a limit of detection (LOD) of 58.8 pg·mL-1, representing a 13.3-fold improvement compared to nonenriched samples (7.58 × 102 pg·mL-1) and a 2-orders-of-magnitude improvement over commercial colloidal gold kits. Furthermore, the method exhibited 80% positive and 100% negative detection rates in clinical samples. This approach holds promise for on-site diagnosis, home-based quantitative tests, and disease procession evaluation.

Characterization of Antimicrobial Activities of Bifidobacterium lactis BB-12 and Their Inhibitory Effect Against Some Foodborne Pathogens

Bifidobacterium animalis subsp. lactis BB-12, a probiotic, has shown potential to promote health benefits and control pathogens. This study aimed to investigate the effectiveness of BB-12 and its cell-free supernatant (CFS) in inhibiting the growth of Listeria monocytogenes and Salmonella enterica serovar Typhimurium. To assess the antimicrobial activity of BB-12, agar well diffusion, disk diffusion, and minimum inhibitory concentration (MIC) tests were conducted. The bicinchoninic acid (BCA) assay was performed to measure the protein concentration in CFS. The study's results indicated that the BB-12 strain inhibited the pathogens' growth. The disk diffusion test using BB-12 showed inhibitory results ranging from 11 to 14 mm for both bacteria. The agar well diffusion test reported the zone of inhibition ranging from 11.6 to 16 mm for both bacteria. The MIC test was conducted as a confirmatory test, which demonstrated the highest inhibitory zone using 2 McFarland (6 × 108 CFU/mL) concentrations of probiotics on L. monocytogenes (44.98%) and S. Typhimurium (66.41%). The disk diffusion test revealed that the probiotic CFS had a significant inhibitory impact on S. Typhimurium with a 16.6 mm zone of inhibition. The BCA test findings indicated that the 24- and 48-h CFSs exhibited inhibitory properties against infections. Notably, the 24-h CFS, including a protein level of 78.47 μg/mL, demonstrated a more pronounced inhibitory impact on both pathogens. The findings highlight that utilizing the BB-12 strain and its CFS can serve as a viable approach to battle infections, enhancing food safety and public health.

A novel multifunctional SERS microfluidic sensor based on ZnO/Ag nanoflower arrays for label-free ultrasensitive detection of bacteria

This study proposes a microfluidic platform for rapid enrichment and ultrasensitive SERS detection of bacteria. The platform comprises ZnO nanoflower arrays decorated with silver nanoparticles to enhance the SERS sensitivity. The ZnO nanoflower array substrate with a 3D reticular columnar structure is prepared using the hydrothermal method. SEM analysis depicts the 3.05 μm gap distribution of the substrate array to intercept the most bacteria in the particle sizes range of 0.5 to 3 μm. Then, silver nanoparticles are deposited on the ZnO nano-array surface by liquid evaporation self-assembly. TEM and SEM analysis indicate nanosize of Ag particles, evenly distributed on the substrate, enhancing the SERS efficiency and improving sensing reproducibility. The probe molecules (R6G) are tested to demonstrate the high SERS activity of the proposed microfluidic sensor. Then, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis, and Bacillus subtilis are selected, demonstrating the sensor's excellent bacterial capture and sensitive recognition capabilities, with a detection limit as low as 102 CFU mL-1. Additionally, the antibacterial properties of ZnO/Ag heterojunction nanostructures are studied, suggesting their ability to inactivate bacteria. Compared with the traditional Au-enhanced chip, the sensor preparation is easy, safe, reliable, and low-cost. Moreover, the ZnO nano-array exhibits a large specific surface area, high interception ability, stronger and uniform SERS performance, and effective and reliable detection of trace pathogens. This work provides potential future ZnO/Ag microfluidic SERS sensor applications for rapid, unlabeled, and trace pathogens detection in clinical and environmental applications, potentially achieving breakthroughs in early detection, prevention, and treatment.

Electrochemical biosensors for pathogenic microorganisms detection based on recognition elements

The worldwide spread of pathogenic microorganisms poses a significant risk to human health. Electrochemical biosensors have emerged as dependable analytical tools for the point-of-care detection of pathogens and can effectively compensate for the limitations of conventional techniques. Real-time analysis, high throughput, portability, and rapidity make them pioneering tools for on-site detection of pathogens. Herein, this work comprehensively reviews the recent advances in electrochemical biosensors for pathogen detection, focusing on those based on the classification of recognition elements, and summarizes their principles, current challenges, and prospects. This review was conducted by a systematic search of PubMed and Web of Science databases to obtain relevant literature and construct a basic framework. A total of 171 publications were included after online screening and data extraction to obtain information of the research advances in electrochemical biosensors for pathogen detection. According to the findings, the research of electrochemical biosensors in pathogen detection has been increasing yearly in the past 3 years, which has a broad development prospect, but most of the biosensors have performance or economic limitations and are still in the primary stage. Therefore, significant research and funding are required to fuel the rapid development of electrochemical biosensors. The overview comprehensively evaluates the recent advances in different types of electrochemical biosensors utilized in pathogen detection, with a view to providing insights into future research directions in biosensors.

Force-Encoding DNA Nanomachines for Simultaneous and Direct Detection of Multiple Pathogenic Bacteria in Blood

Pathogen detection is growing in importance in the early stages of bacterial infection and treatment due to the significant morbidity and mortality associated with bloodstream infections. Although various diagnostic approaches for pathogen detection have been proposed, most of them are time-consuming, with insufficient sensitivity and limited specificity and multiplexing capability for clinical use. Here, we report a force-encoding DNA nanomachine for simultaneous and high-throughput detection of multiple pathogens in blood through force-induced remnant magnetization spectroscopy (FIRMS). The force-encoding DNA nanomachines coupled with DNA walkers enable analytical sensitivity down to a single bacterium via a cascade signal amplification strategy. More importantly, it allows for rapid and specific profiling of various pathogens directly in blood samples, without being affected by factors such as light color and solution properties. We expect that this magnetic sensing platform holds great promise for various applications in biomedical research and clinical diagnostics.

Siamese Networks for Clinically Relevant Bacteria Classification Based on Raman Spectroscopy

Identifying bacterial strains is essential in microbiology for various practical applications, such as disease diagnosis and quality monitoring of food and water. Classical machine learning algorithms have been utilized to identify bacteria based on their Raman spectra. However, convolutional neural networks (CNNs) offer higher classification accuracy, but they require extensive training sets and retraining of previous untrained class targets can be costly and time-consuming. Siamese networks have emerged as a promising solution. They are composed of two CNNs with the same structure and a final network that acts as a distance metric, converting the classification problem into a similarity problem. Classical machine learning approaches, shallow and deep CNNs, and two Siamese network variants were tailored and tested on Raman spectral datasets of bacteria. The methods were evaluated based on mean sensitivity, training time, prediction time, and the number of parameters. In this comparison, Siamese-model2 achieved the highest mean sensitivity of 83.61 ± 4.73 and demonstrated remarkable performance in handling unbalanced and limited data scenarios, achieving a prediction accuracy of 73%. Therefore, the choice of model depends on the specific trade-off between accuracy, (prediction/training) time, and resources for the particular application. Classical machine learning models and shallow CNN models may be more suitable if time and computational resources are a concern. Siamese networks are a good choice for small datasets and CNN for extensive data.

On-Site Bioaerosol Sampling and Airborne Microorganism Detection Technologies

Bioaerosols are small airborne particles composed of microbiological fragments, including bacteria, viruses, fungi, pollens, and/or by-products of cells, which may be viable or non-viable wherever applicable. Exposure to these agents can cause a variety of health issues, such as allergic and infectious diseases, neurological disorders, and cancer. Therefore, detecting and identifying bioaerosols is crucial, and bioaerosol sampling is a key step in any bioaerosol investigation. This review provides an overview of the current bioaerosol sampling methods, both passive and active, as well as their applications and limitations for rapid on-site monitoring. The challenges and trends for detecting airborne microorganisms using molecular and immunological methods are also discussed, along with a summary and outlook for the development of prompt monitoring technologies.

Sensitive Methods to Detect Single-Stranded Nucleic Acids of Food Pathogens Based on Cell-Free Protein Synthesis and Retroreflection Signal Detection

Cell-free protein synthesis (CFPS) has recently gained considerable attention as a new platform for developing methods to detect various molecules, ranging from small chemicals to biological macromolecules. Retroreflection has been used as an alternative signal to develop analytical methods because it can be detected by using a simple instrument comprising a white light source and a camera. Here, we report a novel reporter protein that couples the capability of CFPS and the simplicity of retroreflection signal detection. The design of the reporter was based on two pairs of protein-peptide interactions, SpyCatcher003-SpyTag003 and MDM2-PMI(N8A). MDM2-MDM2-SpyCatcher003 was decided as the reporter protein, and the two peptides, SpyTag003 and PMI(N8A), were immobilized on the surfaces of retroreflective Janus particles and microfluidic chips, respectively. The developed retroreflection signal detection system was combined with a previously reported CFPS reaction that can transduce the presence of a single-stranded nucleic acid into protein synthesis. The resulting methods were applied to detect 16S rRNAs of several foodborne pathogens. Concentration-dependent relationships were observed over a range of 10° fM to 102 pM, with the limits of detection being single-digit femtomolar concentrations. Considering the designability of the CFPS system for other targets, the retroreflection signal detection method will enable the development of novel methods to detect various molecules.

Verification of a Rapid Analytical Method for the Qualitative Detection of Listeria spp. and Listeria monocytogenes by a Real-Time PCR Assay according to EN UNI ISO 16140-3:2021

Microbial contamination and foodborne infections are a significant global public health concern. For this reason, the detection, monitoring, and characterization of pathogens represent a significant challenge in quality control settings. Standard approaches, such as culture methods and biochemical tests, are known to be very time-consuming and intensive. Conversely, molecular technologies based on the genomic identification of bacteria are quick and low-cost. Listeria monocytogenes is an opportunistic pathogen and a major concern especially in food industries. It is important to understand and implement multiple quality control measures to control Listeria infection risk and prevent the contamination of products. Standardized detection and confirmation tests such as the API Listeria test, MALDI-TOF MS, and PCR analysis are available. The aim of our work is to provide a specific molecular method, designed according to the EN UNI ISO 16140-3:2021, for the specific detection, monitoring, and characterization of Listeria spp. and Listeria monocytogenes contamination. The verification of this new rapid approach by real-time PCR (qPCR) overcomes the limitations of culture-based techniques, meeting all the verification criteria required by ISO guidelines, including implementation and item confirmation. This system offers a powerful approach to the real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection.

Temperature and particles interact to affect human norovirus and MS2 persistence in surface water

Modeling the fate and transport of viruses and their genetic material in surface water is necessary to assess risks associated with contaminated surface waters and to inform environmental surveillance efforts. Temperature has been identified as a key variable affecting virus persistence in surface waters, but the effects of the presence of biological and inert particles and of their interaction with temperature have not been well characterized. We assessed these effects on the persistence of human norovirus (HuNoV) genotype II.4 purified from stool and MS2 in surface water. Raw or filter-sterilized creek water microcosms were inoculated and incubated in the dark at 10 °C, 15 °C, and 20 °C. HuNoV (i.e., genome segments and intact capsids) and MS2 (i.e., infectious MS2, genome segments, and intact capsids) concentrations were followed over 36 days. The range in positive, significant first-order decay rate constants for HuNoV in this study was 0.14 to 0.69 day-1 compared with 0.026 to 0.71 day-1 for that of MS2. Decay rate constants for HuNoV genome segments and infectious MS2 were largest in creek water that included biological and inert particles and incubated at higher temperatures. In addition, for HuNoV and MS2 incubated in raw or filter-sterilized creek water at 15 °C, capsid damage was not identified as a dominant inactivation mechanism. Environmental processes and events that affect surface water biological and inert particles, temperature, or both could lead to variable virus decay rate constants. Incorporating the effects of particles, temperature, and their interaction could enhance models of virus fate and transport in surface water.

Microfluidic advances in food safety control

Food contamination is a global concern, particularly in developing countries. Two main types of food contaminants-chemical and biological-are common problems that threaten human health. Therefore, rapid and accurate detection methods are required to address the threat of food contamination. Conventional methods employed to detect these two types of food contaminants have several limitations, including high costs and long analysis time. Alternatively, microfluidic technology, which allows for simple, rapid, and on-site testing, can enable us to control food safety in a timely, cost-effective, simple, and accurate manner. This review summarizes advances in microfluidic approaches to detect contaminants in food. Different detection methods have been applied to microfluidic platforms to identify two main types of contaminants: chemical and biological. For chemical contaminant control, the application of microfluidic approaches for detecting heavy metals, pesticides, antibiotic residues, and other contaminants in food samples is reviewed. Different methods including enzymatic, chemical-based, immunoassay-based, molecular-based, and electrochemical methods for chemical contaminant detection are discussed based on their working principle, the integration in microfluidic platforms, advantages, and limitations. Microfluidic approaches for foodborne pathogen detection, from sample preparation to final detection, are reviewed to identify foodborne pathogens. Common methods for foodborne pathogens screening, namely immunoassay, nucleic acid amplification methods, and other methods are listed and discussed; highlighted examples of recent studies are also reviewed. Challenges and future trends that could be employed in microfluidic design and fabrication process to address the existing limitations for food safety control are also covered. Microfluidic technology is a promising tool for food safety control with high efficiency and applicability. Miniaturization, portability, low cost, and samples and reagents saving make microfluidic devices an ideal choice for on-site detection, especially in low-resource areas. Despite many advantages of microfluidic technology, the wide manufacturing of microfluidic devices still demands intensive studies to be conducted for user-friendly and accurate food safety control. Introduction of recent advances of microfluidic devices will build a comprehensive understanding of the technology and offer comparative analysis for future studies and on-site application.

Advances, limitations, and considerations on the use of vibrational spectroscopy towards the development of management decision tools in food safety

Food safety and food security are two of the main concerns for the modern food manufacturing industry. Disruptions in the food supply and value chains have created the need to develop agile screening tools that will allow the detection of food pathogens, spoilage microorganisms, microbial contaminants, toxins, herbicides, and pesticides in agricultural commodities, natural products, and food ingredients. Most of the current routine analytical methods used to detect and identify microorganisms, herbicides, and pesticides in food ingredients and products are based on the use of reliable and robust immunological, microbiological, and biochemical techniques (e.g. antigen-antibody interactions, extraction and analysis of DNA) and chemical methods (e.g. chromatography). However, the food manufacturing industries are demanding agile and affordable analytical methods. The objective of this review is to highlight the advantages and limitations of the use of vibrational spectroscopy combined with chemometrics as proxy to evaluate and quantify herbicides, pesticides, and toxins in foods.

Recent Advances in the Detection of Food Toxins Using Mass Spectrometry

Edibles are the only source of nutrients and energy for humans. However, ingredients of edibles have undergone many physicochemical changes during preparation and storage. Aging, hydrolysis, oxidation, and rancidity are some of the major changes that not only change the native flavor, texture, and taste of food but also destroy the nutritive value and jeopardize public health. The major reasons for the production of harmful metabolites, chemicals, and toxins are poor processing, inappropriate storage, and microbial spoilage, which are lethal to consumers. In addition, the emergence of new pollutants has intensified the need for advanced and rapid food analysis techniques to detect such toxins. The issue with the detection of toxins in food samples is the nonvolatile nature and absence of detectable chromophores; hence, normal conventional techniques need additional derivatization. Mass spectrometry (MS) offers high sensitivity, selectivity, and capability to handle complex mixtures, making it an ideal analytical technique for the identification and quantification of food toxins. Recent technological advancements, such as high-resolution MS and tandem mass spectrometry (MS/MS), have significantly improved sensitivity, enabling the detection of food toxins at ultralow levels. Moreover, the emergence of ambient ionization techniques has facilitated rapid in situ analysis of samples with lower time and resources. Despite numerous advantages, the widespread adoption of MS in routine food safety monitoring faces certain challenges such as instrument cost, complexity, data analysis, and standardization of methods. Nevertheless, the continuous advancements in MS-technology and its integration with complementary techniques hold promising prospects for revolutionizing food safety monitoring. This review discusses the application of MS in detecting various food toxins including mycotoxins, marine biotoxins, and plant-derived toxins. It also explores the implementation of untargeted approaches, such as metabolomics and proteomics, for the discovery of novel and emerging food toxins, enhancing our understanding of potential hazards in the food supply chain.

Identification and characterization of a novel bacteriocin gene cluster in Lysinibacillus boronitolerans

Although the antibiotics inhibit or kill pathogens, the abuse leads to the resistance formation and even "Super Bacteria." Therefore, it is urgent to explore the natural and safe alternatives such as bacteriocin. In this study, an uncharacterized bacteriocin gene cluster for Lysinibacillus boronitolerans was first predicted by genome sequencing and bioinformatics analysis, of which including two biosynthetic genes, a regulatory gene, a transport-related gene, and six other genes. Subsequently, the 10.24-kb gene cluster was expressed in Escherichia coli BL21, and the lysate effectively inhibited the growths of pathogenic bacteria containing Bacillus pumilus, Bacillus velezensis, Pseudomonas syringae pv. tomato DC3000, and Xanthomonas axonopodis pv. manihotis. The antibacterial substance was purified by 70% ammonium sulfate precipitation and further identified by liquid chromatography-tandem mass spectrometry. The results showed that the antibacterial substance consisted of 44 amino acids and had 24.1% sequence identity with the cyanobacterin Piricyclamide 7005 E4 PirE4, a bacteriocin analogue. The minimal set of genes required for the biosynthesis of the antibacterial substance was determined by site-directed mutagenesis, suggesting both a transcriptional repressor and a phosphohydroxythreonine transaminase were essential. Subsequently, the evolution and conservation of the two proteins were analyzed among 22 Lysinibacillus species. Among them, the residues responsible for functions were identified. Collectively, our results set a solid foundation for investigation of the biosynthesis and application of bacteriocin.

Recent advances in nanobiosensors for sustainable healthcare applications: A systematic literature review

The need for novel healthcare treatments and drugs has increased due to the expanding human population, detection of newer diseases, and looming pandemics. The development of nanotechnology offers a platform for cutting-edge in vivo non-invasive monitoring and point-of-care-testing (POCT) for rehabilitative disease detection and management. The advancement and uses of nanobiosensors are currently becoming more common in a variety of scientific fields, such as environmental monitoring, food safety, biomedical, clinical, and sustainable healthcare sciences, since the advent of nanotechnology. The identification and detection of biological patterns connected to any type of disease (communicable or not) have been made possible in recent years by several sensing techniques utilizing nanotechnology concerning biosensors and nanobiosensors. In this work, 2218 articles are drawn and screened from six digital databases out of which 17 were shortlisted for this review by using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) technique. As a result, this study uses a systematic methodology to review some recently developed extremely sensitive nanobiosensors, along with their biomedical, point-of-care diagnostics (POCD), or healthcare applications and their capabilities, particularly for the prediction of some fatal diseases based on a few of the most recent publications. The potential of nanobiosensors for medicinal, therapeutic, or other sustainable healthcare applications, notably for ailments diagnostics, is also recognized as a way forward in the manifestation of future trends.

In situ Tracking of Exoenzyme Activity Using Droplet Luminescence Concentrators for Ratiometric Detection of Bacteria

We demonstrate a novel, rapid, and cost-effective biosensing paradigm that is based on an in situ visualization of bacterial exoenzyme activity using biphasic Janus emulsion droplets. Sensitization of the droplets toward dominant extracellular enzymes of bacterial pathogens is realized via selective functionalization of one hemisphere of Janus droplets with enzyme-cleavable surfactants. Surfactant cleavage results in an interfacial tension increase at the respective droplet interface, which readily transduces into a microscopically detectable change of the internal droplet morphologies. A macroscopic fluorescence read-out of such morphological transitions is obtained via ratiometrically recording the angle-dependent anisotropic emission signatures of perylene-containing droplets from two different angles. The optical read-out method facilitates detection of marginal morphological responses of polydisperse droplet samples that can be easily produced in any environment. The performance of Janus droplets as powerful optical transducers and signal amplifiers is highlighted by rapid (<4 h) and cost-effective antibody and DNA-free identification of three major foodborne pathogens, with detection thresholds of below 10 CFU mL-1 for Salmonella and <102 to 103 CFU mL-1 for Listeria and Escherichia coli.

Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans

Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.

Enhanced detection of Listeria monocytogenes using tetraethylenepentamine-functionalized magnetic nanoparticles and LAMP-CRISPR/Cas12a-based biosensor

BACKGROUND

Listeria monocytogenes is a pathogenic bacterium that can lead to severe illnesses, especially among vulnerable populations. Therefore, the development of rapid and sensitive detection methods is vital to prevent and manage foodborne diseases. In this study, we used tetraethylenepentamine (TEPA)-functionalized magnetic nanoparticles (MNPs) and a loop-mediated isothermal amplification (LAMP)-based CRISPR/Cas12a-based biosensor to concentrate and detect, respectively, L. monocytogenes. LAMP enables DNA amplification at a constant temperature, providing a highly suitable approach for point-of-care testing (POCT). The ability of CRISPR/Cas12a to cleave ssDNA reporter, coupled with TEPA-functionalized MNPs effective attachment to negatively charged bacteria, forms a promising biosensor.

RESULTS

The LAMP assay was meticulously developed by selecting specific primers and designing crRNA sequences targeting a specific region within the hly gene of L. monocytogenes. We selected primer and refined the amplification conditions by systematically exploring a temperature range from 59 °C to 69 °C, ensuring the attainment of optimal performance. This process was complemented by systematic optimization of LAMP-CRISPR/Cas12a system parameters. In particular, we successfully established the optimal ssDNA reporter concentrations (0-1.2 μM) and Cas12a-mediated trans-cleavage times (0-20 min), crucial components that underpin the effectiveness of the LAMP-CRISPR/Cas12a-based biosensor. For optimizing parameters in capturing L. monocytogenes using TEPA-functionalized MNPs, capture efficiency was significantly enhanced through adjustments in TEPA-functionalized MNPs concentration, incubation times, and magnetic separation duration. Large-volume (20 mL) magnetic separation exhibited a 10-fold sensitivity improvement over conventional methods. Utilizing TEPA-functionalized MNPs, the LAMP-CRISPR/Cas12a-based biosensor achieved detection limits of 100 CFU mL-1 in pure cultures and 100 CFU g-1 in enoki mushrooms.

SIGNIFICANCE

The integration of this novel technique with the LAMP-CRISPR/Cas12a-based biosensor enhances the accuracy and sensitivity of L. monocytogenes detection in foods, and it can be a promising biosensor for POCT. The 10-fold increase in sensitivity compared to conventional methods makes this approach a groundbreaking advancement in pathogenic bacteria detection for food safety and public health.

Population dynamics of Listeria spp., Salmonella spp., and Escherichia coli on fresh produce: A scoping review

Collation of the current scope of literature related to population dynamics (i.e., growth, die-off, survival) of foodborne pathogens on fresh produce can aid in informing future research directions and help stakeholders identify relevant research literature. A scoping review was conducted to gather and synthesize literature that investigates population dynamics of pathogenic and non-pathogenic Listeria spp., Salmonella spp., and Escherichia coli on whole unprocessed fresh produce (defined as produce not having undergone chopping, cutting, homogenization, irradiation, or pasteurization). Literature sources were identified using an exhaustive search of research and industry reports published prior to September 23, 2021, followed by screening for relevance based on strict, a priori eligibility criteria. A total of 277 studies that met all eligibility criteria were subjected to an in-depth qualitative review of various factors (e.g., produce commodities, study settings, inoculation methodologies) that affect population dynamics. Included studies represent investigations of population dynamics on produce before (i.e., pre-harvest; n = 143) and after (i.e., post-harvest; n = 144) harvest. Several knowledge gaps were identified, including the limited representation of (i) pre-harvest studies that investigated population dynamics of Listeria spp. on produce (n = 13, 9% of pre-harvest studies), (ii) pre-harvest studies that were carried out on non-sprouts produce types grown using hydroponic cultivation practices (n = 7, 5% of pre-harvest studies), and (iii) post-harvest studies that reported the relative humidity conditions under which experiments were carried out (n = 56, 39% of post-harvest studies). These and other knowledge gaps summarized in this scoping review represent areas of research that can be investigated in future studies.

Next-Generation Rapid and Ultrasensitive Lateral Flow Immunoassay for Detection of SARS-CoV-2 Variants

The coronavirus disease 2019 (COVID-19) pandemic highlighted the need for rapid and accurate viral detection at the point-of-care testing (POCT). Compared with nucleic acid detection, lateral flow immunoassay (LFIA) is a rapid and flexible method for POCT detection. However, the sensitivity of LFIA limits its use for early identification of patients with COVID-19. Here, an innovative surface-enhanced Raman scattering (SERS)-LFIA platform based on two-dimensional black phosphorus decorated with Ag nanoparticles as important antigen-capturing and Raman-signal-amplification unit was developed for detection of SARS-CoV-2 variants within 5-20 min. The novel SERS-LFIA platform realized a limit of detection of 0.5 pg/mL and 100 copies/mL for N protein and SARS-CoV-2, demonstrating 1000 times more sensitivity than the commercial LFIA strips. It could reliably detect seven different SARS-CoV-2 variants with cycle threshold (Ct) < 38, with sensitivity and specificity of 97 and 100%, respectively, exhibiting the same sensitivity with q-PCR. Furthermore, the detection results for 48 SARS-CoV-2-positive nasopharyngeal swabs (Ct = 19.8-38.95) and 96 negative nasopharyngeal swabs proved the reliability of the strips in clinical application. The method also had good specificity in double-blind experiments involving several other coronaviruses, respiratory viruses, and respiratory medications. The results showed that the innovative SERS-LFIA platform is expected to be the next-generation antigen detection technology. The inexpensive amplification-free assay combines the advantages of rapid low-cost POCT and highly sensitive nucleic acid detection, and it is suitable for rapid detection of SARS-CoV-2 variants and other pathogens. Thus, it could replace existing antigens and nucleic acids to some extent.

Microfluidic Sensor Based on Cell-Imprinted Polymer-Coated Microwires for Conductometric Detection of Bacteria in Water

The rapid, inexpensive, and on-site detection of bacterial contaminants using highly sensitive and specific microfluidic sensors is attracting substantial attention in water quality monitoring applications. Cell-imprinted polymers (CIPs) have emerged as robust, cost-effective, and versatile recognition materials with selective binding sites for capturing whole bacteria. However, electrochemical transduction of the binding event to a measurable signal within a microfluidic device to develop easy-to-use, compact, portable, durable, and affordable sensors remains a challenge. For this paper, we employed CIP-functionalized microwires (CIP-MWs) with an affinity towards E. coli and integrated them into a low-cost microfluidic sensor to measure the conductometric transduction of CIP-bacteria binding events. The sensor comprised two CIP-MWs suspended perpendicularly to a PDMS microchannel. The inter-wire electrical resistance of the microchannel was measured before, during, and after exposure of CIP-MWs to bacteria. A decline in the inter-wire resistance of the sensor after 30 min of incubation with bacteria was detected. Resistance change normalization and the subsequent analysis of the sensor's dose-response curve between 0 to 109 CFU/mL bacteria revealed the limits of detection and quantification of 2.1 × 105 CFU/mL and 7.3 × 105 CFU/mL, respectively. The dynamic range of the sensor was 104 to 107 CFU/mL where the bacteria counts were statistically distinguishable from each other. A linear fit in this range resulted in a sensitivity of 7.35 μS per CFU/mL. Experiments using competing Sarcina or Listeria cells showed specificity of the sensor towards the imprinted E. coli cells. The reported CIP-MW-based conductometric microfluidic sensor can provide a cost-effective, durable, portable, and real-time solution for the detection of pathogens in water.

Updates on developing and applying biosensors for the detection of microorganisms, antimicrobial resistance genes and antibiotics: a scoping review

Background

The inappropriate use of antibiotics in clinical and non-clinical settings contributes to the increasing prevalence of multidrug-resistant microorganisms. Contemporary endeavours are focused on exploring novel technological methodologies, striving to create cost-effective and valuable alternatives for detecting microorganisms, antimicrobial resistance genes (ARGs), and/or antibiotics across diverse matrices. Within this context, there exists an increasingly pressing demand to consolidate insights into potential biosensors and their implications for public health in the battle against antimicrobial resistance (AMR).

Methods

A scoping review was carried out to map the research conducted on biosensors for the detection of microorganisms, ARGs and/or antibiotics in clinical and environmental samples. The Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) checklist was used. Articles published from 1999 to November 2022 and indexed in the following databases were included: MEDLINE, EMBASE, Web of Science, BIOSIS Citation index, Derwent Innovations index, and KCI-Korean Journal.

Results

The 48 studies included in the scoping review described the development and/or validation of biosensors for the detection of microorganisms, ARGs and/or antibiotics. At its current stage, the detection of microorganisms and/or ARGs has focused primarily on the development and validation of biosensors in clinical and bacterial samples. By contrast, the detection of antibiotics has focused primarily on the development and validation of biosensors in environmental samples. Asides from target and samples, the intrinsic characteristics of biosensors described in the scoping review were heterogenous. Nonetheless, the number of studies assessing the efficacy and validation of the aforementioned biosensor remained limited, and there was also a lack of comparative analyses against conventional molecular techniques.

Conclusion

Promoting high-quality research is essential to facilitate the integration of biosensors as innovative technologies within the realm of public health challenges, such as antimicrobial resistance AMR. Adopting a One-Health approach, it becomes imperative to delve deeper into these promising and feasible technologies, exploring their potential across diverse sample sets and matrices.

Fluorescent optotracers for bacterial and biofilm detection and diagnostics

Effective treatment of bacterial infections requires methods that accurately and quickly identify which antibiotic should be prescribed. This review describes recent research on the development of optotracing methodologies for bacterial and biofilm detection and diagnostics. Optotracers are small, chemically well-defined, anionic fluorescent tracer molecules that detect peptide- and carbohydrate-based biopolymers. This class of organic molecules (luminescent conjugated oligothiophenes) show unique electronic, electrochemical and optical properties originating from the conjugated structure of the compounds. The photophysical properties are further improved as donor-acceptor-donor (D-A-D)-type motifs are incorporated in the conjugated backbone. Optotracers bind their biopolymeric target molecules via electrostatic interactions. Binding alters the optical properties of these tracer molecules, shown as altered absorption and emission spectra, as well as ON-like switch of fluorescence. As the optotracer provides a defined spectral signature for each binding partner, a fingerprint is generated that can be used for identification of the target biopolymer. Alongside their use for in situ experimentation, optotracers have demonstrated excellent use in studies of a number of clinically relevant microbial pathogens. These methods will find widespread use across a variety of communities engaged in reducing the effect of antibiotic resistance. This includes basic researchers studying molecular resistance mechanisms, academia and pharma developing new antimicrobials targeting biofilm infections and tests to diagnose biofilm infections, as well as those developing antibiotic susceptibility tests for biofilm infections (biofilm-AST). By iterating between the microbial world and that of plants, development of the optotracing technology has become a prime example of successful cross-feeding across the boundaries of disciplines. As optotracers offers a capacity to redefine the way we work with polysaccharides in the microbial world as well as with plant biomass, the technology is providing novel outputs desperately needed for global impact of the threat of antimicrobial resistance as well as our strive for a circular bioeconomy.

Diagnostic efficiency of the FilmArray blood culture identification (BCID) panel: a systematic review and meta-analysis

Introduction. The FilmArray blood culture identification panel (BCID) panel is a multiplex PCR assay with high sensitivity and specificity to identify the most common pathogens in bloodstream infections (BSIs).Hypothesis. We hypothesize that the BCID panel has good diagnostic performance for BSIs and can be popularized in clinical application.Aim: To provide summarized evidence for the diagnostic accuracy of the BCID panel for the identification of positive blood cultures.Methodology. We searched the MEDLINE, EMBASE and Cochrane databases through March 2021 and assessed the efficacy of the diagnostic test of the BCID panel. We performed a meta-analysis and calculated the summary sensitivity and specificity of the BCID panel. Systematic review protocols were registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42021239176).Results. A total of 16 full-text articles were eligible for analysis. The overall sensitivities of the BCID panel on Gram-positive bacteria, Gram-negative bacteria and fungi were 97 % (95 % CI, 0.96-0.98), 100 % (95 % CI, 0.98-01.00) and 99 % (95 % CI, 0.87-1.00), respectively. The pooled diagnostic specificities were 99 % (95 % CI, 0.97-1.00), 100 % (95 % CI, 1.00-1.00) and 100 % (95 % CI, 1.00-1.00) for Gram-positive bacteria, Gram-negative bacteria and fungi, respectively.Conclusions. The BCID panel has high rule-in value for the early detection of BSI patients. The BCID panel can still provide valuable information for ruling out bacteremia or fungemia in populations with low pretest probability.

Responsive Janus droplets as modular sensory layers for the optical detection of bacteria

The field of biosensor development is fueled by innovations in new functional transduction materials and technologies. Material innovations promise to extend current sensor hardware limitations, reduce analysis costs, and ensure broad application of sensor methods. Optical sensors are particularly attractive because they enable sensitive and noninvasive analyte detection in near real-time. Optical transducers convert physical, chemical, or biological events into detectable changes in fluorescence, refractive index, or spectroscopic shifts. Thus, in addition to sophisticated biochemical selector designs, smart transducers can improve signal transmission and amplification, thereby greatly facilitating the practical applicability of biosensors, which, to date, is often hampered by complications such as difficult replication of reproducible selector-analyte interactions within a uniform and consistent sensing area. In this context, stimuli-responsive and optically active Janus emulsions, which are dispersions of kinetically stabilized biphasic fluid droplets, have emerged as a novel triggerable material platform that provides as a versatile and cost-effective alternative for the generation of reproducible, highly sensitive, and modular optical sensing layers. The intrinsic and unprecedented chemical-morphological-optical coupling inside Janus droplets has facilitated optical signal transduction and amplification in various chemo- and biosensor paradigms, which include examples for the rapid and cost-effective detection of major foodborne pathogens. These initial demonstrations resulted in detection limits that rival the capabilities of current commercial platforms. This trend article aims to present a conceptual summary of these initial efforts and to provide a concise and comprehensive overview of the pivotal kinetic and thermodynamic principles that govern the ability of Janus droplets to sensitively and selectively respond to and interact with bacteria.

Nanomaterial interfaces designed with different biorecognition elements for biosensing of key foodborne pathogens

Foodborne diseases caused by pathogen bacteria are a serious problem toward the safety of human life in a worldwide. Conventional methods for pathogen bacteria detection have several handicaps, including trained personnel requirement, low sensitivity, laborious enrichment steps, low selectivity, and long-term experiments. There is a need for precise and rapid identification and detection of foodborne pathogens. Biosensors are a remarkable alternative for the detection of foodborne bacteria compared to conventional methods. In recent years, there are different strategies for the designing of specific and sensitive biosensors. Researchers activated to develop enhanced biosensors with different transducer and recognition elements. Thus, the aim of this study was to provide a topical and detailed review on aptamer, nanofiber, and metal organic framework-based biosensors for the detection of food pathogens. First, the conventional methods, type of biosensors, common transducer, and recognition element were systematically explained. Then, novel signal amplification materials and nanomaterials were introduced. Last, current shortcomings were emphasized, and future alternatives were discussed.

Absorbance biosensors-based hybrid [Formula: see text] nanosheets for Escherichia coli detection

Detecting Escherichia coli is essential in biomedical, environmental, and food safety applications. In this paper, we have developed a simple, rapid, sensitive, and selective E. coli DNA sensor based on the novel hybrid-type [Formula: see text] and [Formula: see text] nanosheets. The sensor uses the absorbance measurement to distinguish among the DNA of E. coli, Vibrio proteolyticus, and Bacillus subtilis when implemented in conjunction with [Formula: see text]-probes. Our experiments showed that the absorbance increased when sensors detected E. coli DNA, whereas it decreased when sensors detected V. proteolyticus and B. subtilis DNA. To the best of authors' knowledge, there are no reports using the novel hybrid-[Formula: see text] and [Formula: see text] materials for differentiating three types of DNA using cost-effective and rapid absorbance measurements. In addition, the label-free E. coli DNA biosensor exhibited a linear response in the range of 0 fM to 11.65 fM with a limit of detection of 2 fM. The effect of [Formula: see text]-probes on our sensors' working performance is also investigated. Our results will facilitate further research in pathogen detection applications, which have not been fully developed yet.

Enterocin LD3 from Enterococcus hirae LD3 Inhibits the Growth of Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311 in Fruit Juice

In order to prevent the growth of pathogens in food, bacteriocins produced by various probiotic lactic acid bacteria have been recognized as potential substitutes of chemical preservatives. In this study, enterocin LD3 was purified from the cell-free supernatant of a food isolate, Enterococcus hirae LD3 using multistep chromatography. In the fruit juice, lethal concentration (LC₅₀) of enterocin LD3 was found to be 260 µg/mL against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The cells treated with enterocin LD3 were red colour indicating dead cells after propidium iodide staining, while untreated cells were found blue after staining with 4', 6-diamidino-2-phenylindole. The mechanism of cell killing was analyzed using infrared spectrum of cells treated with enterocin LD3 which was found altered in the range of 1,094.30 and 1,451.82 cm^-1 corresponding to nucleic acids and phospholipids, respectively. The morphology of target cells were severely ruptured and lysed as observed under electron microscopy. Thus, the present study suggested that enterocin LD3 showed bactericidal activity against Salm. enterica subsp. enterica serovar Typhimurium ATCC 13311 and may be applied as a bio-preservative for the safety of fruit juices.

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.

Development of Optical Label-Free Biosensor Method in Detection of Listeria monocytogenes from Food

The present work describes an alternative method for detecting and identifying Listeria monocytogenes in food samples by developing a nanophotonic biosensor containing bioreceptors and optical transducers. The development of photonic sensors for the detection of pathogens in the food industry involves the implementation of procedures for selecting probes against the antigens of interest and the functionalization of the sensor surfaces on which the said bioreceptors are located. As a previous step to functionalizing the biosensor, an immobilization control of these antibodies on silicon nitride surfaces was carried out to check the effectiveness of in plane immobilization. On the one hand, it was observed that a Listeria monocytogenes-specific polyclonal antibody has a greater binding capacity to the antigen at a wide range of concentrations. A Listeria monocytogenes monoclonal antibody is more specific and has a greater binding capacity only at low concentrations. An assay for evaluating selected antibodies against particular antigens of Listeria monocytogenes bacteria was designed to determine the binding specificity of each probe using the indirect ELISA detection technique. In addition, a validation method was established against the reference method for many replicates belonging to different batches of meat-detectable samples, with a medium and pre-enrichment time that allowed optimal recovery of the target microorganism. Moreover, no cross-reactivity with other nontarget bacteria was observed. Thus, this system is a simple, highly sensitive, and accurate platform for L. monocytogenes detection.

Development of Shortened Enrichment Methods for Detection of Salmonella Typhimurium Spiked in Milk

Rapid and accurate testing of pathogenic Salmonella enterica in dairy products could reduce the risk of exposure to the bacterial pathogens for consumers. This study aimed to reduce the assessment time needed for enteric bacteria recovery and quantification in food using the natural growth properties of Salmonella enterica Typhimurium (S. Typhimurium) in cow's milk and efficiently using rapid PCR methods. Over 5 h of 37 °C enrichment, culture and PCR methods measured increases in the non-heat-treated S. Typhimurium concentration at similar rates, with an average increase of 2.7 log10 CFU/mL between the start of enrichment and 5 h. In contrast, no bacteria were recovered by culture after S. Typhimurium in milk received heat treatment, and the number of gene copies of heat-treated Salmonella detected by PCR did not increase with the enrichment time. Thus, comparing culture and PCR data over just 5 h of enrichment time can detect and differentiate between replicating bacteria and dead bacteria.

Point-of-Care Testing of the MTF1 Osteoarthritis Biomarker Using Phenolphthalein-Soaked Swabs

Osteoarthritis (OA) is the most common joint disease, which accompanies pain and inconvenience in daily life owing to degradation of cartilage and adjacent tissues. In this study, we propose a simple point-of-care testing (POCT) kit for the detection of the MTF1 OA biomarker to achieve on-site clinical diagnosis of OA. The kit contains an FTA card for patient sample treatments, a sample tube for loop-mediated isothermal amplification (LAMP), and a phenolphthalein-soaked swab for naked eye detection. The MTF1 gene was isolated from synovial fluids using an FTA card and amplified using the LAMP method at 65 °C for 35 min. A test part of the phenolphthalein-soaked swab was decolorized in the presence of the MTF1 gene due to the pH change after the LAMP, but the color remained pink in the absence of the MTF1 gene. The control part of the swab served as a reference color in relation to the test part. When real-time LAMP (RT-LAMP), gel electrophoresis, and colorimetric detection of the MTF1 gene were performed, the limit of detection (LOD) was confirmed at 10 fg/μL, and the overall processes were completed in 1 h. The detection of an OA biomarker in the form of POCT was reported for the first time in this study. The introduced method is expected to serve as a POCT platform directly applicable by clinicians for easy and rapid identification of OA.

Current and emerging trends in techniques for plant pathogen detection

Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations

Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.

Salmonella typhimurium detection and ablation using OmpD specific aptamer with non-magnetic and magnetic graphene oxide

Foodborne diseases have increased in the last few years due to the increased consumption of packaged and contaminated food. Major foodborne bacteria cause diseases such as diarrhea, vomiting, and sometimes death. So, there is a need for early detection of foodborne bacteria as pre-existing detection techniques are time-taking and tedious. Aptamer has gained interest due to its high stability, specificity, and sensitivity. Here, aptamer has been developed against Salmonella Typhimurium through the Cell-Selex method, and to further find the reason for specificity and sensitivity, OmpD protein was isolated, and binding studies were done. Single molecular FRET experiment using aptamer and graphene oxide studies has also been done to understand the mechanism of FRET and subsequently used for target bacterial detection. Using this assay, Salmonella Typhimurium can be detected up to 10 CFU/mL. Further, Magnetic Graphene oxide was used to develop an assay to separate and ablate bacteria using 808 nm NIR where temperature increase was more than 60 °C within 30 s and has been shown by plating as well as a confocal live dead assay. Thus, using various techniques, bacteria can be detected and ablated using specific aptamer and Graphene oxide.

Detection of Salmonella Enteritidis in Milk Using Conductometric Immunosensor Coated on Polyaniline/Zinc Oxide Nanocomposite

The demand for rapid and accurate detection methods for Salmonella Enteritidis necessitates the development of highly sensitive and specific biosensors to ensure proper monitoring of food safety and quality requirements in the food sector and to secure human health. This study focused on development of a polyaniline/zinc oxide (PANI/ZnO) nanocomposite film on a gold electrode conductometric immunosensor for detection of Salmonella Enteritidis. The sensor was modified with monoclonal anti-Salmonella Enteritidis antibodies as biorecognition elements. The fabricated sensor was able to detect and quantify the target pathogen within 30 min and showed a good detection range from 10¹ to 10⁵ colony-forming units (CFU)/mL for Salmonella Enteritidis and a minimum detection limit of 6.44 CFU/mL in 0.1% peptone water. Additionally, the fabricated sensor showed good selectivity and detection limit toward the target bacterium and successfully determined Salmonella Enteritidis content in ultrahigh heat-treated skim milk samples without pretreatment of the food sample.

A Review of Modern Methods for the Detection of Foodborne Pathogens

Despite the recent advances in food preservation techniques and food safety, significant disease outbreaks linked to foodborne pathogens such as bacteria, fungi, and viruses still occur worldwide indicating that these pathogens still constitute significant risks to public health. Although extensive reviews of methods for foodborne pathogens detection exist, most are skewed towards bacteria despite the increasing relevance of other pathogens such as viruses. Therefore, this review of foodborne pathogen detection methods is holistic, focusing on pathogenic bacteria, fungi, and viruses. This review has shown that culture-based methods allied with new approaches are beneficial for the detection of foodborne pathogens. The current application of immunoassay methods, especially for bacterial and fungal toxins detection in foods, are reviewed. The use and benefits of nucleic acid-based PCR methods and next-generation sequencing-based methods for bacterial, fungal, and viral pathogens' detection and their toxins in foods are also reviewed. This review has, therefore, shown that different modern methods exist for the detection of current and emerging foodborne bacterial, fungal, and viral pathogens. It provides further evidence that the full utilization of these tools can lead to early detection and control of foodborne diseases, enhancing public health and reducing the frequency of disease outbreaks.

Rapid Escherichia coli Cloned DNA Detection in Serum Using an Electrical Double Layer-Gated Field-Effect Transistor-Based DNA Sensor

In this study, a rapid diagnosis platform was developed for the detection of Escherichia coli O157:H7. An electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) as a point-of-care testing device is demonstrated with its high sensitivity, portability, high selectivity, quick response, and ease of use. The specially designed ssDNA probe was immobilized on the extended gate electrode to bind the target complementary DNA segment of E. coli, resulting in a sharp drain current change within minutes. The limit of detection for target DNA is validated to a concentration of 1 fM in buffer solution and serum. Meanwhile, the results of a Kelvin probe force microscope were shown to have reduced surface potential of the DNA immobilized sensors before and after the cDNA detection, which is consistent with the decreased drain current of the BioFET. A 1.2 kb E. coli duplex DNA synthesized in plasmid was sonicated and detected in serum samples with the sensor array. Gel electrophoresis was used to confirm the efficiency of sonication by elucidating the length of DNA. Those results show that the EDL-gated BioFET system is a promising platform for rapid identification of pathogens for future clinical needs.

A Lab-on-a-Tube Biosensor Combining Recombinase-Aided Amplification and CRISPR-Cas12a with Rotated Magnetic Extraction for Salmonella Detection

BACKGROUND

Foodborne pathogenic bacteria threaten worldwide public health, and simple bacterial detection methods are in urgent need. Here, we established a lab-on-a-tube biosensor for simple, rapid, sensitive, and specific detection of foodborne bacteria.

METHODS

A rotatable Halbach cylinder magnet and an iron wire netting with magnetic silica beads (MSBs) were used for simple and effective extraction and purification of DNA from the target bacteria, and recombinase-aided amplification (RAA) was combined with clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins12a(CRISPR-Cas12a) to amplify DNA and generate fluorescent signal. First, 15 mL of the bacterial sample was centrifuged, and the bacterial pellet was lysed by protease to release target DNA. Then, DNA-MSB complexes were formed as the tube was intermittently rotated and distributed uniformly onto the iron wire netting inside the Halbach cylinder magnet. Finally, the purified DNA was amplified using RAA and quantitatively detected by the CRISPR-Cas12a assay.

RESULTS

This biosensor could quantitatively detect Salmonella in spiked milk samples in 75 min, with a lower detection limit of 6 CFU/mL. The fluorescent signal of 10² CFU/mL Salmonella Typhimurium was over 2000 RFU, while 10⁴ CFU/mL Listeria monocytogenes, Bacillus cereus, and E. coli O157:H7 were selected as non-target bacteria and had signals less than 500 RFU (same as the negative control).

CONCLUSIONS

This lab-on-a-tube biosensor integrates cell lysis, DNA extraction, and RAA amplification in one 15 mL tube to simplify the operation and avoid contamination, making it suitable for low-concentration Salmonella detection.

Superior possibilities and upcoming horizons for nanoscience in COVID-19: noteworthy approach for effective diagnostics and management of SARS-CoV-2 outbreak

The outbreak of COVID-19 has caused great havoc and affected many parts of the world. It has imposed a great challenge to the medical and health fraternity with its ability to continue mutating and increasing the transmission rate. Some challenges include the availability of current knowledge of active drugs against the virus, mode of delivery of the medicaments, its diagnosis, which are relatively limited and do not suffice for further prognosis. One recently developed drug delivery system called nanoparticles is currently being utilized in combating COVID-19. This article highlights the existing methods for diagnosis of COVID-19 such as computed tomography scan, reverse transcription-polymerase chain reaction, nucleic acid sequencing, immunoassay, point-of-care test, detection from breath, nanotechnology-based bio-sensors, viral antigen detection, microfluidic device, magnetic nanosensor, magnetic resonance platform and internet-of-things biosensors. The latest detection strategy based on nanotechnology, biosensor, is said to produce satisfactory results in recognizing SARS-CoV-2 virus. It also highlights the successes in the research and development of COVID-19 treatments and vaccines that are already in use. In addition, there are a number of nanovaccines and nanomedicines currently in clinical trials that have the potential to target COVID-19.

Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review

Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.

Development of a lateral flow dipstick test for the detection of 4 strains of Salmonella spp. in animal products and animal production environmental samples based on loop-mediated isothermal amplification

OBJECTIVE

This study aimed to develop loop-mediated isothermal amplification (LAMP) combined with lateral flow dipstick (LFD) and compare it with LAMP-AGE, polymerase chain reaction (PCR), and standard Salmonella culture as reference methods for detecting Salmonella contamination in animal products and animal production environmental samples.

METHODS

The SalInvA01 primer, derived from the InvA gene and designed as a new probe for LFD detection, was used in developing this study. Adjusting for optimal conditions by temperature, time, and reagent concentration includes evaluating the specificity and limit of detection. The sampling of 120 animal product samples and 350 animal production environmental samples was determined by LAMP-LFD, comparing LAMP-AGE, PCR, and the culture method.

RESULTS

Salmonella was amplified using optimal conditions for the LAMP reaction and a DNA probe for LFD at 63°C for 60 minutes. The specificity test revealed no cross-reactivity with other microorganisms. The limit of detection of LAMP-LFD in pure culture was 3×102 CFU/mL (6 CFU/reaction) and 9.01 pg/μL in genomic DNA. The limit of detection of the LAMP-LFD using artificially inoculated in minced chicken samples with 5 hours of pre-enrichment was 3.4×104 CFU/mL (680 CFU/reaction). For 120 animal product samples, Salmonella was detected by the culture method, LAMP-LFD, LAMP-AGE, and PCR in 10/120 (8.3%). In three hundred fifty animal production environmental samples, Salmonella was detected in 91/350 (26%) by the culture method, equivalent to the detection rates of LAMP-LFD and LAMP-AGE, while PCR achieved 86/350 (24.6%). When comparing sensitivity, specificity, positive predictive value, and accuracy, LAMP-LFD showed the best results at 100%, 95.7%, 86.3%, and 96.6%, respectively. For Kappa index of LAMP-LFD, indicated nearly perfect agreement with culture method.

CONCLUSION

The LAMP-LFD Salmonella detection, which used InvA gene, was highly specific, sensitive, and convenient for identifying Salmonella. Furthermore, this method could be used for Salmonella monitoring and primary screening in animal products and animal production environmental samples.