A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens

Reference Gene-Assisted LAMP-LFD for Sensitive and Specific Detection of Soy DNA as a Marker for Allergen Presence in Complex Food Products

Sensitive, selective screening for allergenic ingredients with internal control is crucial to identify food adulteration and remove allergens from the food chain. Here, loop-mediated isothermal amplification combined with a lateral flow device (LAMP-LFD) was developed for the fast and easy detection of soy DNA. The integrated quality controls included a regular control line to ensure proper implementation (extraction and amplification control) and a second LAMP-LFD assay for the cytochrome oxidase gene, which is a housekeeping gene in plants. The developed LAMP assay showed a limit of detection of only 5 pg DNA input per reaction, for both pure soy and spiked food samples. The test was subsequently implemented for the examination of 32 real food products with different compositions and declared soy contents, and benchmarked against qPCR. Then, this system was combined with a digital cube reader, allowing direct interpretation of the test results, facilitating the point-of-need applicability.

CRISPR revolution: Unleashing precision pathogen detection to safeguard public health and food safety

Foodborne pathogens represent a significant challenge to global food safety, causing widespread illnesses and economic losses. The growing complexity of food supply chains and the emergence of antimicrobial resistance necessitate rapid, sensitive, and portable diagnostic tools. CRISPR technology has emerged as a transformative solution, offering unparalleled precision and adaptability in pathogen detection. This review explores CRISPR's role in addressing critical gaps in traditional and modern diagnostic methods, emphasizing its advantages in sensitivity, specificity, and scalability. CRISPR-based diagnostics, such as Cas12 and Cas13 systems, enable rapid detection of bacterial and viral pathogens, as well as toxins and chemical hazards, directly in food matrices. Their integration with isothermal amplification techniques and portable biosensors enhances field applicability, making them ideal for decentralized and real-time testing. Additionally, CRISPR's potential extends beyond food safety, contributing to public health efforts by monitoring antimicrobial resistance and supporting One Health frameworks. Despite these advancements, challenges remain, including issues with performance in complex food matrices, scalability, and regulatory barriers. This review highlights future directions, including AI integration for assay optimization, the development of universal CRISPR platforms, and the adoption of sustainable diagnostic solutions. By tackling these challenges, CRISPR has the potential to redefine global food safety standards and create a more resilient food system. Collaborative research and innovation will be critical to fully unlocking its transformative potential in food safety and public health.

Multi-target microfluidic loop-mediated isothermal amplification technology for the detection of foodborne pathogens in various food matrices

BACKGROUND

Nutritional foods are susceptible to foodborne pathogens. Loop-mediated isothermal amplification (LAMP) technology has great potential in detecting foodborne pathogens, but conventional LAMP suffers from drawbacks such as complex operation and low detection throughput. Therefore, there is an urgent need to develop a multi-targeted and simultaneous LAMP detection platform to identify pathogens across various food matrices, in order to effectively manage food quality and safeguard human health.

RESULTS

The integration of LAMP with a microfluidic chip is proposed to enable the simultaneous and rapid detection of four pathogenic bacteria across eight different food matrices. We focused on designing and screening specific LAMP primers for Vibrio parahaemolyticus, Escherichia coli O157: H7, Yersinia enterocolitica, and Bacillus cereus. Then, we employed 10-well microfluidic chips to improve detection efficiency and reduce interference. We tested the feasibility and accuracy of detecting all four pathogens simultaneously on this chip platform. Our findings showed that the microfluidic LAMP detection platform could successfully identify the four pathogens with a low LOD (from 1.78 × 104 to 1.59 × 105 copies/mL) within 45 min. Furthermore, the platform specifically detected pathogens in a wide range of artificially simulated contaminated food matrices. All of these results could be observed with naked eyes and analyzed using fluorescence.

SIGNIFICANCE AND NOVELTY

The microfluidic LAMP platform, characterized by isothermal reactions, visualization features, robust immunity, and high throughput, presents an efficient, user-friendly, and highly sensitive approach for on-site detection. This technology has significant potential for future applications in the field of food safety monitoring.

Development of dual polymerase spiral reaction for detection of Listeria monocytogenes and Staphylococcus aureus simultaneously

Listeria monocytogenes and Staphylococcus aureus are prevalent foodborne pathogens responsible for poisoning humans with food. The present study was devoted to the establishment of a method based on dual polymerase spiral reaction (dual-PSR) and melting curve analysis for concurrent identification L. monocytogenes and S. aureus. Specifically, the primer pairs were aimed at the conserved hlyA gene of L. monocytogenes and that of S. aureus (nuc). These reactions were carried out isothermally at 65 °C for 45 min within the same reaction vessel, and the amplified products were analyzed in a melting curve. Different average temperatures of melting allow the discrimination in the dual-PSR assay between the two target bacteria. The limits of simultaneous determination of L. monocytogenes and S. aureus in artificially contaminated fresh-cut fruit samples were 1 × 10-4 ng of genomic DNA and 1 × 102 CFU/g, respectively. This method is characterized by its expeditious nature and simultaneous detection capability, and it promises to be a valuable technology for the monitoring of pathogenic microorganisms around health and quality control of foodstuffs within that industry.

Sample-to-answer microfluidic device towards the point-of-need detection of Staphylococcus aureus enterotoxin genes in ruminant milk

Milk is commonly screened both for indicators of animal disease and health, but also for foodborne hazards. Included in these analyses is the detection of Staphylococcus aureus, that can produce an enterotoxin, causing staphylococcal food poisoning (SFP), which often leads to sudden onset of significant gastrointestinal symptoms in humans. Epidemiological data on SFP are limited, particularly in low- and middle-income countries. Many conventional assays for the detection of staphylococcal enterotoxins rely on the detection of the genes coding for them, either directly in food samples or after bacterial culture. Currently, many of the nucleic acid-based methods used require specific expertise and equipment, whilst bacterial culture takes 24-48 hours; both are contributory factors that limit efforts either during food safety emergencies or routine screening. Here we present the development of a "sample-to-answer" isothermal nucleic acid loop-mediated amplification (LAMP) assay in a microfluidic device for the detection of Staphylococcus aureus enterotoxin genes in ruminant milk. A multiplex LAMP assay targeting two of the most prevalent S. aureus enterotoxin-encoding genes (A and B) was integrated into a microfluidic device combining simple 1 : 10 dilution for sample preparation and a lateral flow assay for easy readout. We achieved a limit of detection of 104 colony forming units per ml in spiked cow and goat milk samples, an order of magnitude more sensitive than the European recommendation for the maximum allowable presence of coagulase-positive staphylococci in raw milk. The assay showed no cross-reactivity in detecting other tested non-enterotoxigenic S. aureus strains or associated foodborne pathogens. The test integrated the simplicity of use of microfluidic devices with the sensitivity, specificity and rapidity of a nucleic acid-based assay, and a simple lateral flow readout to provide an appropriate device to ensure the safety of milk for human consumption. To illustrate its potential for point-of-need practical applications, the test was performed in agricultural settings in rural Turkey in a limited feasibility exercise.

Optimizing Poultry Nutrition to Combat Salmonella: Insights from the Literature

Salmonella infections in poultry production are a significant and pervasive concern, posing substantial risks to both animal and human health. This comprehensive literature review examines the current body of research on the use of various nutritional manipulations as a promising strategy to effectively control and mitigate the prevalence of Salmonella in poultry. The review covers a range of dietary interventions, particularly the utilization of probiotics, prebiotics, organic acids, and phytochemicals, and thoroughly evaluates their efficacy in reducing Salmonella colonization within poultry flocks. Furthermore, the review delves into the potential underlying mechanisms of action for these nutritional approaches to control Salmonella and the far-reaching implications for overall food safety. By providing a thorough analysis of the existing literature, this review aims to elucidate the most promising nutritional strategies that can be employed to control Salmonella in poultry production, ultimately safeguarding animal welfare and public health.

Chemical Heating for Minimally Instrumented Point-of-Care (POC) Molecular Diagnostics

The minimal instrumentation of portable medical diagnostic devices for point-of-care applications is facilitated by using chemical heating in place of temperature-regulated electrical heaters. The main applications are for isothermal nucleic acid amplification tests (NAATs) and other enzymatic assays that require elevated, controlled temperatures. In the most common implementation, heat is generated by the exothermic reaction of a metal (e.g., magnesium, calcium, or lithium) with water or air, buffered by a phase-change material that maintains a near-constant temperature to heat the assay reactions. The ability to incubate NAATs electricity-free and to further to detect amplification with minimal instrumentation opens the door for fully disposable, inexpensive molecular diagnostic devices that can be used for pathogen detection as needed in resource-limited areas and during natural disasters, wars, and civil disturbances when access to electricity may be interrupted. Several design approaches are reviewed, including more elaborate schemes for multiple stages of incubation at different temperatures.

Optimization of loop-mediated isothermal amplification assay for sunflower mildew disease detection

Loop-Mediated Isothermal Amplification (LAMP) represents a valuable technique for DNA/RNA detection, known for its exceptional sensitivity, specificity, speed, accuracy, and affordability. This study focused on optimizing a LAMP-based method to detect early signs of Plasmopara halstedii, the casual pathogen of sunflower downy mildew, a severe threat to sunflower crops. Specifically, a set of six LAMP primers (two outer, two inner, and two loop) were designed from P. halstedii genomic DNA, targeting the ribosomal Large Subunit (LSU). These primers were verified by in silico analysis and experimental validation using both target and non-target species' DNAs. Optimizations encompassing reaction conditions (temperature, time) and component concentrations (magnesium, Bst DNA polymerase, primers, and dNTP) were determined. Validation of these optimizations was performed by agarose gel electrophoresis. Furthermore, various colorimetric chemicals (Neutral Red, Hydroxynaphthol Blue, SYBR Safe, Thiazole Green) were evaluated to facilitate method analysis, and the real-time analysis has been optimized, presenting multiple approaches for detecting sunflower downy mildew using the LAMP technique. The analytical sensitivity of the method was confirmed by detecting P. halstedii DNA concentrations as low as 0.5 pg/μl. This pioneering study, establishing P. halstedii detection through the LAMP method, stands as unique in its field. The precision, robustness, and practicality of the LAMP protocol make it an ideal choice for studies focusing on sunflower mildew, emphasizing its recommended use due to its operational ease and reliability.

Recent advances and challenges in plant viral diagnostics

Accurate and timely diagnosis of plant viral infections plays a key role in effective disease control and maintaining agricultural productivity. Recent advances in the diagnosis of plant viruses have significantly expanded our ability to detect and monitor viral pathogens in agricultural crops. This review discusses the latest advances in diagnostic technologies, including both traditional methods and the latest innovations. Conventional methods such as enzyme-linked immunosorbent assay and DNA amplification-based assays remain widely used due to their reliability and accuracy. However, diagnostics such as next-generation sequencing and CRISPR-based detection offer faster, more sensitive and specific virus detection. The review highlights the main advantages and limitations of detection systems used in plant viral diagnostics including conventional methods, biosensor technologies and advanced sequence-based techniques. In addition, it also discusses the effectiveness of commercially available diagnostic tools and challenges facing modern diagnostic techniques as well as future directions for improving informed disease management strategies. Understanding the main features of available diagnostic methodologies would enable stakeholders to choose optimal management strategies against viral threats and ensure global food security.

Inhibitors of LAMP used to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease in Akoya pearl oysters, and additives to reduce the effect of the inhibitors

Black-spot shell disease is an unresolved disease that decreases pearl quality and threatens pearl oyster survival. In previous studies, the bacterium Tenacibaculum sp. strain Pbs-1 was isolated from diseased Akoya pearl oysters Pinctada fucata, and a rapid, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting this pathogen was established. This technology has considerable potential for routine diagnosis of strain Pbs-1 in oyster hatcheries and/or pearl farms; therefore, it is vital to identify substances in environmental samples that might inhibit LAMP and to find additives that can reduce the inhibition. In this study, we investigated the effects of six chemicals or proteins, otherwise known as conventional PCR inhibitors, on LAMP, using the DNA of strain Pbs-1 as template: humic acid, urea, iron (III) chloride hexahydrate, melanin, myoglobin, and Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA; pH 6.5). Next, to reduce the effects of identified inhibitors, we tested the addition of bovine serum albumin (BSA) or T4 gene 32 protein (gp32) to the LAMP assay. When 50 ng of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, and 10 mM of EDTA (pH 6.5) inhibited the LAMP reaction, whereas myoglobin, urea, and FeCl3 had no effect. When 50 pg of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, 4 μg/μL of myoglobin, 10 μg/μL of urea, and 10 mM of EDTA inhibited the LAMP reaction. Thus, it was shown that the gene-amplification inhibitory effect of melanin, humic acid, and urea could be reduced by adding BSA or gp32 to the LAMP reaction mixture. This technique could be applied as part of a protocol to prevent mass mortalities of pearl oysters; moreover, the results enhance our knowledge about substances that inhibit LAMP and methods to reduce the inhibition, which have rarely been reported.

A comprehensive review on novel synthetic foods: Potential risk factors, detection strategies, and processing technologies

Nowadays, the food industry is facing challenges due to the simultaneous rise in global warming, population, and food consumption. As the integration of synthetic biology and food science, novel synthetic foods have obtained high attention to address these issues. However, these novel foods may cause potential risks related to human health. Four types of novel synthetic foods, including plant-based foods, cultured meat, fermented foods, and microalgae-based foods, were reviewed in the study. The original food sources, consumer acceptance, advantages and disadvantages of these foods were discussed. Furthermore, potential risk factors, such as nutritional, biological, and chemical risk factors, associated with these foods were described and analyzed. Additionally, the current detection methods (e.g., enzyme-linked immunosorbent assay, biosensors, chromatography, polymerase chain reaction, isothermal amplification, and microfluidic technology) and processing technologies (e.g., microwave treatment, ohmic heating, steam explosion, high hydrostatic pressure, ultrasound, cold plasma, and supercritical carbon dioxide) were reviewed and discussed critically. Nonetheless, it is crucial to continue innovating and developing new detection and processing technologies to effectively evaluate these novel synthetic foods and ensure their safety. Finally, approaches to enhance the quality of these foods were briefly presented. It will provide insights into the development and management of novel synthetic foods for food industry.

Rapid detection of FadA in Fusobacterium nucleatum using the quantitative LAMP colorimetric phenol red method in stool samples from colorectal cancer patients

The study aimed to develop a quantitative colorimetric loop-mediated isothermal amplification technique using the phenol red indicator (QLAMP-PhR) for detecting Fusobacterium nucleatum (Fn) levels in colorectal cancer (CRC) patients and healthy individuals. QLAMP-PhR assays were conducted on 251 stool samples specific for the Fn FadA gene. Six primers were synthesized and utilized with master mix reagents, and a phenol red indicator was employed to enhance the QLAMP-PhR technique. A standard quantitative analysis curve was generated using a logarithmic function (absorbance vs. concentration) by serially diluting the copy number of genomic DNA templates (Fn ATCC25586). The CRC group exhibited a significantly higher abundance of Fn compared to the healthy control group (P < 0.001). These findings suggest that the QLAMP-PhR technique effectively identifies Fn specifically by its gene for the key virulence factor FadA. Additionally, ideas for developing a real-time QLAMP-PhR test were presented. Compared to the traditional polymerase chain reaction (PCR) technique, QLAMP-PhR offers several advantages including rapidity, simplicity, specificity, sensitivity, and cost-effectiveness method that can quantitatively screen for Fn presence in normal populations. The QLAMP-PhR method represents a sensitive and specific amplification assay for the rapid detection of the Fn pathogen. To the best of our knowledge, this study is the first to report the application of QLAMP-PhR for detecting FadA in Fn.

Development of a loop-mediated isothermal amplification assay for the rapid detection of Styphnolobium japonicum (L.) Schott as an adulterant of Ginkgo biloba (L.)

BACKGROUND

Species adulteration is a concern in herbal products, especially when plant substitutes of lower economic value replace valuable botanicals. Styphnolobium japonicum is well known as a potential adulterant of Ginkgo biloba, which is one of the most demanded medicinal plants due to its wide use in pharmaceuticals, food supplements, and traditional medicine. Despite bearing some resemblance to ginkgo's flavonol composition, S. japonicum lacks many of G. biloba's desired therapeutic properties. To prevent adulteration practices, it is crucial to implement rigorous quality control measures, including fast and simple diagnostic tools that can be used on-field.

PURPOSE

This study aims to develop for the first time a species-specific loop-mediated isothermal amplification (LAMP) method for the fast identification of S. japonicum in ginkgo-containing products.

METHODS

A set of four specific primers (SjF3, SjB3, SjFIP, and SjBIP) and loop primers (SjLF and SjLB) were designed for a LAMP based assay using the 5.8S partial sequence and the internal transcribed spacer 2 of nuclear ribosomal DNA of S. japonicum.

RESULTS

The successful amplification of the LAMP assay was inspected through visual detection, with the highest intensity recorded at the optimal conditions set at 68 °C for 40 min. The primers showed high specificity and were able to accurately discriminate S. japonicum from G. biloba and 49 other species of medicinal plants. Furthermore, the proposed LAMP assay proved to be fast, selective, and highly sensitive, as demonstrated by the absolute and relative limits of detection, which were reached at 0.5 pg for S. japonicum DNA and 0.01 % S. japonicum in G. biloba, respectively.

CONCLUSIONS

This novel approach allows easy identification and discrimination of S. japonicum as a potential adulterant of G. biloba, thus being a useful tool for quality control. Compared to chromatographic or PCR-based methods, the assay proved to be fast, sensitive and did not require expensive equipment, thus offering the possibly usage in field analysis.

Development of a PMA‐LAMP visual detection assay for viable Cronobacter sakazakii

Cronobacter sakazakii in powdered infant formula (PIF) can infect infants with a mortality rate of up to 80%. In this study, a propidium monoazide–loop‐mediated isothermal amplification (PMA‐LAMP) assay was developed for fast and cost‐effective visual detection of viable C. sakazakii. The detection could be finished in 75 min and the results could be identified by the naked eye. The detection limits of the assay were as low as 1.2 × 101 cfu/mL and 1.2 × 102 cfu/mL for gel electrophoresis and naked eyes respectively. Finally, the assay also showed good reliability in the artificially contaminated PIF.

Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow

Salmonella species are prominent foodborne microbial pathogens transmitted through contaminated food or water and pose a significant threat to human health. Accurate and rapid point-of-care (POC) diagnosis is gaining attention in effectively preventing outbreaks of foodborne disease. However, the presence of dead bacteria can interfere with an accurate diagnosis, necessitating the development of methods for the rapid, simple, and efficient detection of viable bacteria only. Herein, we used an improved propidium monoazide (PMAxx) to develop a nucleic acid lateral flow (NALF) assay based on recombinase polymerase amplification (RPA) to differentiate viable Salmonella Typhimurium. We selected an RPA primer set targeting the invA gene and designed a probe for NALF. RPA-based NALF was optimized for temperature (30-43 °C), time (1-25 min), and endonuclease IV concentration (0.025-0.15 unit/µL). PMAxx successfully eliminated false-positive results from dead S. Typhimurium, enabling the accurate detection of viable S. Typhimurium with a detection limit of 1.11 × 102 CFU/mL in pure culture. The developed method was evaluated with spiked raw chicken breast and milk with analysis completed within 25 min at 39 °C. This study has potential as a tool for the POC diagnostics of viable foodborne pathogens with high specificity, sensitivity, rapidity, and cost-effectiveness.

Naked-eye detection with loop-mediated isothermal amplification for P. carotovorum subsp. carotovorum in agricultural products

Pectobacterium carotovorum causing soft-rot disease requires on-site detection before the distribution of agricultural products. Loop-mediated isothermal amplification (LAMP), which is resistant to food inhibitors, is known for its high detection sensitivity for pathogens and when coupled with lateral flow immunoassay (LFA) enables visualizations. For detection of soft-rot disease, we developed a LAMP-LFA system targeting 16S ribosomal RNA, a partial sequence gene of P. carotovorum subsp. carotovorum. The LAMP-LFA was performed at 60 °C for 50 min followed by hybridization of digoxygenin-labeled LAMP amplicon and biotinylated probe. Detection sensitivity was 3.22 × 101 CFU/mL in pure culture, which specifically detected the target. In Chinese cabbage and potato, the target was detected up to low levels of 1.57 × 102 CFU/g and 1.29 × 102 CFU/g, respectively. This study showed potential applicability as a sensitive point-of-care system for soft-rot disease bacteria detection in agricultural products.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01315-z.

Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

This article presents a review of recent advancements in the utilization of NAA-based techniques for detecting foodborne pathogens in food products, focusing on studies conducted within the past five years. This review revealed that recent research efforts have primarily aimed at enhancing sensitivity and specificity by improving sample pre-treatment/preparation, DNA isolation, and readout methods. Isothermal-based amplification methods, such as LAMP, RPA, RAA, and RCA, have emerged as promising approaches, providing rapid results within one h and often demonstrating comparable or superior sensitivity to conventional or qPCR methods. However, the attention paid to specific pathogens varies, with Salmonella spp., Listeria spp., E. coli, and V. parahaemolyticus receiving more focus than norovirus and other similar pathogens. NAA-based methods have the potential to significantly contribute to food safety and public health protection. However, further advancements are necessary to fully realize their benefits.

Enhancement of loop mediated isothermal amplification's sensitivity and speed by multiple inner primers for more efficient identification of Vibrio parahaemolyticus

The modified loop-mediated isothermal amplification (LAMP), called multiple hybrid, inner primers (MHP)-LAMP, was developed to enhance the efficiency of the existing LAMP-based assay for Vibrio parahaemolyticus detection. The method was built on a conventional LAMP assay by employing 2 newly designed extra sets of primers to increase the initial binding sites of core primers on the V. parahaemolyticus's rpoD gene from 8 to 12. With this strategy, the assay detection sensitivity was increased by 10 folds, with the detection limit (DL) approaching 100 copies of purified target genomic DNA (gDNA) as analyzed by real-time turbidity measurement and gel electrophoresis. The MHP also accelerated the rate of DNA amplification by 30%, rendering the assay faster. The MHP-LAMP assay did not cross- react with other pathogens, indicating that it was highly specific for V. parahaemolyticus detection. Whilst V. parahaemolyticus was used as a study model herein, our idea of using MHP to maximize assay sensitivity and speed is considered as a universal strategy that can be applied to enhance efficiency of LAMP-based assays for detecting any DNA and RNA of interest. •The strategy of using multiple hybrid, inner primers (MHP) to enhance LAMP assay's efficiency was demonstrated with success.•The MHP enhanced the sensitivity and speed of the existing LAMP assay, designed to detect V. parahaemolyticus, by 10 times and 30%, respectively.•The proposed strategy can be applied to boost up any other LAMP-based assay's diagnostic performance.

Diverse methods of reducing and confirming false-positive results of loop-mediated isothermal amplification assays: A review

Loop-mediated isothermal amplification (LAMP), a rapid and sensitive isothermal nucleic acid amplification method, is a promising alternative to other molecular amplification techniques due to its superior specificity and sensitivity. However, due to primer dimerization, LAMP results in nonspecific and nontemplate amplification. And during the amplification confirmation process, there is carry-over contamination. These factors can result in false-positive results that overestimate the amount of DNA, preventing accurate detection. This review outlined several techniques for reducing false-positive LAMP results before amplification and confirming false-positive results after amplification. Before the amplification step, DNA polymerase activity can be decreased with organic additives such as dimethyl sulfoxide, betaine, and pullulan to prevent nonspecific amplification. The enzyme uracil-DNA-glycosylase (UDG) can eliminate false-positive results caused by carry-over contamination, and the hot-start effect with gold nanoparticles can reduce nonspecific amplification. When confirming false-positive results using clustered regularly interspaced short palindromic repeats, guide RNA accurately detects LAMP amplification, allowing differentiation from nonspecific amplification. By confirming amplification, the colorimetric change in the deoxyribozyme (DNAzyme) formed by the reaction of the G-quadruplex sequence of the LAMP amplicon and hemin can distinguish false-positive results. Lateral flow immunoassay can distinguish false-positive results by accurately recognizing hybridized probes to LAMP amplicons.

Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.

Detection of SARS-CoV-2 Based on Nucleic Acid Amplification Tests (NAATs) and Its Integration into Nanomedicine and Microfluidic Devices as Point-of-Care Testing (POCT)

The coronavirus SARS-CoV-2 has highlighted the criticality of an accurate and rapid diagnosis in order to contain the spread of the virus. Knowledge of the viral structure and its genome is essential for diagnosis development. The virus is still quickly evolving and the global scenario could easily change. Thus, a greater range of diagnostic options is essential to face this threat to public health. In response to the global demand, there has been a rapid advancement in the understanding of current diagnostic methods. In fact, innovative approaches have emerged, leveraging the benefits of nanomedicine and microfluidic technologies. Although this development has been incredibly fast, several key areas require further investigation and optimization, such as sample collection and preparation, assay optimization and sensitivity, cost effectiveness, scalability device miniaturization, and portability and integration with smartphones. Addressing these gaps in the knowledge and these technological challenges will contribute to the development of reliable, sensitive, and user-friendly NAAT-based POCTs for the diagnosis of SARS-CoV-2 and other infectious diseases, facilitating rapid and effective patient management. This review aims to provide an overview of current SARS-CoV-2 detection methods based on nucleic acid detection tests (NAATs). Additionally, it explores promising approaches that combine nanomedicine and microfluidic devices with high sensitivity and relatively fast 'time to answer' for integration into point-of-care testing (POCT).

Copper: DNA extraction and solid phase detection agent for all-in-one molecular diagnostic device coupled with isothermal amplification

In this study, an all-in-one poly(methyl methacrylate) (PMMA) device integrating two novel techniques - DNA extraction employing a CuSO₄/H₂O₂ system and DNA detection utilizing solid phase copper tape - coupled with loop-mediated isothermal amplification (LAMP) is developed for on-site pathogen detection. The CuSO₄/H₂O₂ system, also known as Fenton-like reaction, is used to produce hydroxyl radicals, which can disrupt bacterial membranes via lipid peroxidation and release DNA at room temperature. The released DNA is subsequently amplified by LAMP reaction. The acidic environment resulting from the production of hydrogen ions in the presence of target DNA in the LAMP reaction can stimulate the color change on copper tape due to the corrosion, while the innate alkaline environment in a negative sample not containing target DNA cannot stimulate the corrosion. The fabricated PMMA device integrates all the functionalities necessary for molecular diagnostics such as DNA extraction, amplification, and detection, and a carbon paste-based heater is fabricated for LAMP reaction. Using the PMMA device, Enterococcus faecium was detected as low as 4.67 × 10² CFU/mL within 90 min. E. faecium spiked in milk was successfully detected using the all-in-one PMMA device. The equipment-free techniques for decentralized diagnostics and naked-eye readout of results coupled with the portable heater serves as a promising solution for point-of-care testing particularly in a resource-limited environment.

Identification of Pseudomonas fuscovaginae, Pseudomonas syringae and Xanthomonas translucens in wheat seeds using PCR

The causative agents of grain crops bacteriosis viz. Pseudomonas fuscovaginae , Pseudomonas syringae and Xanthomonas translucens are regulated by phytosanitary requirements of the largest importers of Russian grain - Egypt, Turkey, Bangladesh, Nigeria and Pakistan. Therefore, it requires the development of rapid methods for their diagnosis. The PCR method, which is the fastest and most reliable in testing laboratories, needs optimal preparation of the test material. The aim of the study was to optimize the process of preparing seed samples for subsequent detection and identification of P. fuscovaginae, P. syringae and X. translucens by PCR. Wheat grain samples were soaked in phosphate-buffered saline (PBS) for 2 hours and infected with suspensions of P. fuscovaginae, P. syringae pv. coronafaciens and X. translucens at various concentrations. Then, the infected grain samples were crushed and subjected to two-stage centrifugation. DNA was isolated from the obtained analytical samples and species-specific PCR was performed for each bacterial species. It was found that a two-hour soaking of the seeds and their treatment with a homogenizer is sufficient to effectively destroy each grain in the sample and ensure the release of bacteria into the liquid part of the sample. The first low-speed centrifugation allowed the crushed grain to settle efficiently and remove excess starch from the supernatant. High-speed centrifugation of the supernatant made it possible to obtain a concentrated microbiota contained in the grain sample. To obtain DNA of sufficient quality for PCR test, the kit Proba-GS (AgroDiagnostika, Russia) was used for DNA extraction. Using Pseudomonas fuscovaginae-RT kit (Syntol, Russia) and PsyF/PsyR and 4F1/4R 1 primers, DNA of P. fuscovaginae P. syringae and X. translucens , respectively, was successfully detected in each of the samples infected with these bacteria at concentrations of 103 CFU/ml. The absence of PCR inhibition was noted. The method of removing starch from samples for molecular diagnostics of phytopathogens was used for the first time. Application of these methods will allow diagnosing pathogens of bacterioses within one day.

Udder Health Monitoring for Prevention of Bovine Mastitis and Improvement of Milk Quality

To maximize milk production, efficiency, and profits, modern dairy cows are genetically selected and bred to produce more and more milk and are fed copious quantities of high-energy feed to support ever-increasing milk volumes. As demands for increased milk yield and milking efficiency continue to rise to provide for the growing world population, more significant stress is placed on the dairy cow's productive capacity. In this climate, which is becoming increasingly hotter, millions of people depend on the capacity of cattle to respond to new environments and to cope with temperature shocks as well as additional stress factors such as solar radiation, animal crowding, insect pests, and poor ventilation, which are often associated with an increased risk of mastitis, resulting in lower milk quality and reduced production. This article reviews the impact of heat stress on milk production and quality and emphasizes the importance of udder health monitoring, with a focus on the use of emergent methods for monitoring udder health, such as infrared thermography, biosensors, and lab-on-chip devices, which may promote animal health and welfare, as well as the quality and safety of dairy products, without hindering the technological flow, while providing significant benefits to farmers, manufacturers, and consumers.

Development of Loop-Mediated Isothermal Amplification (LAMP) Assays for the Rapid Authentication of Three Swimming Crab Species

Blue swimming crab meat is easily adulterated by other crab meats with a lower price. A potential authentication method is required to prevent mislabeling. LAMP assays were established to identify the meat of blue swimming crab, crucifix crab, and three spotted swimming crab. The primers were designed using PrimerExplorer V5. The specificity of the LAMP assay was tested compared to the PCR method. The sensitivity was conducted at the DNA concentrations of 0.4-50 ng/reaction. The results demonstrated that both LAMP and PCR could discriminate all species of crabs. LAMP showed a superior sensitivity to PCR in the three spotted swimming crab, while a similar result between LAMP and PCR was obtained in blue swimming crab. No changes in the detection efficacy were attained when boiled and steamed crab meats were applied. Therefore, the LAMP assay developed could potentially be applicable to detect the adulteration or mislabeling of raw or cooked crab meat in markets.

Performance of Loop-Mediated Isothermal Amplification Technique in Milk Samples for the Diagnosis of Bovine Tuberculosis in Dairy Cattle Using a Bayesian Approach

This study aimed to estimate the sensitivity (Se) and specificity (Sp) of loop-mediated isothermal amplification (LAMP) and single intradermal tuberculin (SIT) tests for the diagnosis of bovine tuberculosis (bTB) in dairy cattle in Thailand using a Bayesian approach. The SIT test was performed in 203 lactating dairy cattle from nine dairy farms located in Chiang Mai province, Thailand. Milk samples were collected for the LAMP test. Kappa analysis was performed to determine the agreement between the two tests. A one-population conditional independence Bayesian model was applied to estimate the Se and Sp of the two tests. Of 203 dairy cattle, 2 were positive for the SIT test using standard interpretation, whereas 38 were positive for the LAMP test. A poor agreement (kappa = 0) was observed between the two tests. The median Se and Sp of the SIT test using standard interpretation were 63.5% and 99.1%, respectively. The median Se and Sp of the LAMP test were 67.2% and 82.0%, respectively. The estimated true prevalence of bTB was 3.7%. The LAMP test with milk samples can potentially be used as a non-invasive screening test for the diagnosis of bTB in dairy cattle.