Accurate Detection of Salmonella Based on Microfluidic Chip to Avoid Aerosol Contamination

Evaluation of amplicons by AF4 as assistant for deep comprehension of loop-mediated isothermal amplification combined with lateral flow assay

Loop-mediated isothermal amplification (LAMP) is a rapid and efficient method for DNA amplification, producing concatemers of varying lengths (amplicons). This study explores the characterization of LAMP amplicons using asymmetric flow field-flow fractionation (AF4) and their realization in LAMP - lateral flow assay (LFA) for point-of-care diagnostics. We examined LAMP products from the invA gene of Salmonella enterica using two specific primer sets and three methods: fluorescent staining with SYBR Green, electrophoretic detection, and AF4. LAMP products labeled with biotin and fluorescein (introduced through primers, 12 combinations) were detected by LFA due to binding the labels. The efficiency of amplicon detection by test strips varied depending on the primer combination: the color intensities for the best and worst combinations differed by more than 7 times. AF4 enabled precise detection of components from primers to amplicons up to 500 bp and revealed differences influenced by labeling and primer combinations. An important advantage of AF4, which was demonstrated for the first time, was the characterization of native complexes of amplicons with receptors. The analysis of amplicons in complexes with streptavidin, anti-fluorescein antibodies, or both receptors together using AF4 revealed significant differences in the fractograms. The shape and maxima of the absorption peaks at 260 nm depended on retention time in the range from 20 to 35 min, indicating the formation of complexes of different compositions. AF4 and LFA showed that smaller amplicons (200-300 bp) primarily contribute to the binding of detected labels, while longer amplicons (1000-1500 bp) do not enhance the signal due to structural complexities. Our findings demonstrate the potential of AF4 as a tool for deep comprehension of LAMP processes and the composition of the formed amplicon-receptor complexes, offering valuable insights for enhancing LAMP-LFA systems. This work provides a foundation for the advanced application of AF4 for nucleic acid amplification technologies.

Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications

Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.

High-resolution melting real-time polymerase chain reaction assays for subtyping of five diarrheagenic Escherichia coli by a single well in milk

Diarrheagenic Escherichia coli (DEC) is a kind of foodborne pathogen that poses a significant threat to both food safety and human health. To address the current challenges of high prevalence and difficult subtyping of DEC, this study developed a method that combined multiplex PCR with high-resolution melting (HRM) analysis for subtyping 5 kinds of DEC. The target genes are amplified by multiplex PCR in a single well, and HRM curve analysis was applied for distinct amplicons based on different melting temperature (Tm) values. The method enables discrimination of different DEC types based on characteristic peaks and distinct Tm values in the thermal melting curve. The assay exhibited 100% sensitivity and 100% specificity with a detection limit of 0.5 to 1 ng/μL. The results showed that different DNA concentrations did not influence the subtyping results, demonstrating this method owed high reliability and stability. In addition, the method was also used for the detection and subtyping of DEC in milk. This method streamlines operational procedures, shorts the detection time, and offers a novel tool for subtyping DEC.

Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton

The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 109 copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R2 = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R2 = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.

Accurate molecular identification of different meat adulterations without carryover contaminations on a microarray chip PCR-directed microfluidic lateral flow strip device

Meat adulteration-based food fraud has recently become one of the global major economical, illegal, religious, and public health concerns. In this work, we developed a microarray chip polymerase chain reaction (PCR)-directed microfluidic lateral flow strip (LFS) device that facilitates the accurate and simultaneous identification of beef adulterated with chicken, duck, and pork, especially in processed beef products. To realize this goal, four pairs of amplification primers were designed and applied for specifically amplifying genomic DNA extracted from mixed meat powders in microarray chip. With the prominent advantage of this device lies in the flexible combination and integration of sample loading, detection, and reporting in microstructures, all the DNA amplicons can be individually visualized on the LFS unit, leading to the appearance of test lines (TC line, TD line, TP line, or TB line) as well as the control line (C line) for the species identification and quantification in beef products. Based on this new method, the adulterants were successfully distinguished and identified in mixtures down to 0.01% (wt.%) while the carryover aerogel contamination in routine molecular diagnostic laboratories was effectively avoided. The practicability, accuracy, and reliability of the device were further confirmed by using real-time PCR as a gold standard control on the successful identification of 50 processed ground meat samples sourced from local markets. The method and device proposed herein could be a useful tool for on-site identification of food authentication.

Sensitive and Portable Signal Readout Strategies Boost Point-of-Care CRISPR/Cas12a Biosensors

Point-of-care (POC) detection is getting more and more attention in many fields due to its accuracy and on-site test property. The CRISPR/Cas12a system is endowed with excellent sensitivity, target identification specificity, and signal amplification ability in biosensing because of its unique trans-cleavage ability. As a result, a lot of research has been made to develop CRISPR/Cas12a-based biosensors. In this review, we focused on signal readout strategies and summarized recent sensitivity-improving strategies in fluorescence, colorimetric, and electrochemical signaling. Then we introduced novel portability-improving strategies based on lateral flow assays (LFAs), microfluidic chips, simplified instruments, and one-pot design. In the end, we also provide our outlook for the future development of CRISPR/Cas12a biosensors.

Enzymatic Catalysis in Size and Volume Dual-Confined Space of Integrated Nanochannel-Electrodes Chip for Enhanced Impedance Detection of Salmonella

Nanochannel-based confinement effect is a fascinating signal transduction strategy for high-performance sensing, but only size confinement is focused on while other confinement effects are unexplored. Here, a highly integrated nanochannel-electrodes chip (INEC) is created and a size/volume-dual-confinement enzyme catalysis model for rapid and sensitive bacteria detection is developed. The INEC, by directly sandwiching a nanochannel chip (60 µm in thickness) in nanoporous gold layers, creates a micro-droplet-based confinement electrochemical cell (CEC). The size confinement of nanochannel promotes the urease catalysis efficiency to generate more ions, while the volume confinement of CEC significantly enriches ions by restricting diffusion. As a result, the INEC-based dual-confinement effects benefit a synergetic enhancement of the catalytic signal. A 11-times ion-strength-based impedance response is obtained within just 1 min when compared to the relevant open system. Combining this novel nanoconfinement effects with nanofiltration of INEC, a separation/signal amplification-integrated sensing strategy is further developed for Salmonella typhimurium detection. The biosensor realizes facile, rapid (<20 min), and specific signal readout with a detection limit of 9 CFU mL-1 in culturing solution, superior to most reports. This work may create a new paradigm for studying nanoconfined processes and contribute a new signal transduction technique for trace analysis application.

Towards Point of Care CRISPR-Based Diagnostics: From Method to Device

Rapid, accurate, and portable on-site detection is critical in the face of public health emergencies. Infectious disease control and public health emergency policymaking can both be aided by effective and trustworthy point of care tests (POCT). A very promising POCT method appears to be the clustered regularly interspaced short palindromic repeats and associated protein (CRISPR/Cas)-based molecular diagnosis. For on-site detection, CRISPR/Cas-based detection can be combined with multiple signal sensing methods and integrated into smart devices. In this review, sensing methods for CRISPR/Cas-based diagnostics are introduced and the advanced strategies and recent advances in CRISPR/Cas-based POCT are reviewed. Finally, the future perspectives of CRISPR and POCT are summarized and prospected.