A portable CRISPR Cas12a based lateral flow platform for sensitive detection of Staphylococcus aureus with double insurance

Recent Advances in Polysaccharide-Based Electrospun Nanofibers for Food Safety Detection

The continuous advancement of food safety analytical technologies is ensuring food safety and regulatory compliance. Electrospinning, a versatile fabrication platform, has emerged as a transformative methodology in materials science due to its unique capacity to generate nanoscale fibrous architectures with tunable morphologies. When combined with the inherent biodegradability and biocompatibility of polysaccharides, electrospun polysaccharide nanofibers are positioning themselves as crucial components in innovative applications in the fields of food science. This review systematically elucidates the fundamental principles and operational parameters governing electrospinning processes, with particular emphasis on polysaccharide-specific fiber formation mechanisms. Furthermore, it provides a critical analysis of state-of-the-art applications involving representative polysaccharide nanofibers (e.g., starch, chitosan, cellulose, sodium alginate, and others) in food safety detection, highlighting their innovative application in livestock (chicken, pork, beef), aquatic (yellow croaker, Penaeus vannamei, Plectorhynchus cinctus), fruit and vegetable (olive, peanut, coffee), and dairy (milk) products. The synthesis of current findings not only validates the unique advantages of polysaccharide nanofibers but also establishes new paradigms for advancing rapid, sustainable, and intelligent food safety technologies. This work further proposes a roadmap for translating laboratory innovations into industrial-scale applications while addressing existing technological bottlenecks.

Establishment and optimization of a system for the detection of Candida albicans based on enzymatic recombinase amplification and CRISPR/Cas12a system

Invasive candidiasis is a fungal infection caused by various pathogenic yeasts, with Candida albicans as the predominant pathogen. Traditional culturing and identification methods for C. albicans are slow, requiring several days to weeks to produce results, which hampers rapid diagnosis. In this study, we proposed three amplification methods to combine with CRISPR/Cas12a and selected the enzymatic recombinase amplification (ERA) and CRISPR/Cas12a two-step method for the detection of C. albicans in terms of sensitivity, and then the two-step method was optimized to a temperature-controlled one-step method for the detection of C. albicans by enzymatic recombinase amplification (ERA)-CRISPR/Cas12a. The temperature-controlled system employs a combination of liquid and solid paraffin wax to maintain the desired melting point, thus facilitating spatial separation of the ERA amplification system from the CRISPR/Cas12a detection system within a single tube. After a reaction at 37°C, the temperature is raised to 45°C, melting the wax and allowing the amplification system to merge with the detection system, initiating the reaction. This one-step detection platform simplifies and expedites the procedure, achieving a sensitivity level on par with that of two-step methods. The reaction completes in about 30 minutes, detecting as little as 100 ag/µL of genomic DNA from C. albicans pure cultures. It shows high specificity and resistance to clinical nucleic acid interference, without cross-reactivity. Additionally, the method eliminates the need to open the reaction tube, effectively preventing aerosol contamination and providing a stable, thus offering a new tool for the rapid clinical diagnosis of C. albicans.

IMPORTANCE

This study established a two-step method through optimization, compared its sensitivity, and then combined the specific detection capabilities of ERA and CRISPR/Cas12a. Furthermore, a one-step method was developed based on the two-step method, creating a one-step system for the detection of Candida albicans. This system does not require the lid to be opened during the reaction process, reducing aerosol contamination and minimizing the risk of false positives. This method does not require advanced instruments or equipment and shows strong specificity without being affected by other pathogens. It can serve as a new method for the detection of Candida albicans and has significant practical application prospects.

Dual recombinase polymerase amplification system combined with lateral flow immunoassay for simultaneous detection of Staphylococcus aureus and Vibrio parahaemolyticus

Development of a highly sensitive visualization platform for multiplex genetic detection could significantly improve efficiency and reliability of on-site detection of foodborne pathogens. In this study, coupling recombinase polymerase amplification (RPA) with lateral flow immunoassay (LFIA) readout system was proposed for Staphylococcus aureus and Vibrio parahaemolyticus detection. Taking the advantage of the isothermal amplification of RPA, dual primers modified with different labeling groups were designed to realize target signal amplification. LFIA coated with anti-digoxigenin antibody and streptavidin as test line 1 and 2 were designed to detect the two RPA products. The proposed method (dual RPA-LFIA) could realize visual detection using LFIA through rapid RPA amplification within 20 min, exhibiting a lowest detection limit of 4.6 × 102 CFU/mL for Staphylococcus aureus and Vibrio parahaemolyticus. The dual RPA-LFIA is characterized by simultaneous detection of dual targets in one RPA reaction and colorimetric readout through LFIA, thus ensuring high sensitivity and efficiency, and showing great potential to address the on-site detection of foodborne pathogens in the future.

Building the Future of Clinical Diagnostics: An Analysis of Potential Benefits and Current Barriers in CRISPR/Cas Diagnostics

Advancements in molecular diagnostics, such as polymerase chain reaction and next-generation sequencing, have revolutionized disease management and prognosis. Despite these advancements in molecular diagnostics, the field faces challenges due to high operational costs and the need for sophisticated equipment and highly trained personnel besides having several technical limitations. The emergent field of CRISPR/Cas sensing technology is showing promise as a new paradigm in clinical diagnostics, although widespread clinical adoption remains limited. This perspective paper discusses specific cases where CRISPR/Cas technology can surmount the challenges of existing diagnostic methods by stressing the significant role that CRISPR/Cas technology can play in revolutionizing clinical diagnostics. It underscores the urgency and importance of addressing the technological and regulatory hurdles that must be overcome to harness this technology effectively in clinical laboratories.

Trends in Aptasensing and the Enhancement of Diagnostic Efficiency and Accuracy

The field of healthcare diagnostics is navigating complex challenges driven by evolving patient demographics and the rapid advancement of new technologies worldwide. In response to these challenges, these biosensors offer distinctive advantages over traditional diagnostic methods, such as cost-effectiveness, enhanced specificity, and adaptability, making their integration with point-of-care (POC) platforms more feasible. In recent years, aptasensors have significantly evolved in diagnostic capabilities through the integration of emerging technologies such as microfluidics, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems, wearable devices, and machine learning (ML), driving progress in precision medicine and global healthcare solutions. Moreover, these advancements not only improve diagnostic accuracy but also hold the potential to revolutionize early detection, reduce healthcare costs, and improve patient outcomes, especially in resource-limited settings. This Account examines key advancements, focusing on how scientific breakthroughs, including artificial intelligence (AI), have improved sensitivity and precision. Additionally, the integration of aptasensors with these technologies has enabled real-time monitoring and data analysis, fostering advances in personalized healthcare. Furthermore, the potential commercialization of aptasensor technologies could increase their availability in clinical settings and support their use as widespread solutions for global health challenges. Hence, this review discusses technological improvements, practical uses, and prospects while also focusing on the challenges surrounding standardization, clinical validation, and interdisciplinary collaboration for widespread application. Finally, ongoing efforts to address these challenges are key to ensure that aptasensors can be effectively implemented in diverse healthcare systems.

Amplification-free sensitive detection of Staphylococcus aureus by spherical nucleic acid triggered CRISPR/Cas12a and Poly T-Cu reporter

A spherical nucleic acid (SNA, AuNPs-aptamer) into CRISPR/Cas12a system combined with poly T-template copper nanoparticles as fluorescence reporter was fabricated to establish an amplification-free sensitive method for Staphylococcus aureus (S. aureus) detection. This method, named PTCas12a, utilizes the concept that the bifunction of SNA recognizes the S. aureus and triggers the Cas12a cleavage activity. Then, the Cas12a enzyme cleaves the Poly T40 to generate a signal change in Poly T-Cu fluorescence, indicating the presence or absence of the target bacteria. The PTCas12a platform demonstrated a detection limit as low as 3.0 CFU/mL (3 N/S) in a wide response range of 1.0 × 101-1.0 × 106 CFU/mL for S. aureus detection, which holds significant potential in ensuring food safety and preventing the spread of diseases.

Recent advances of food safety detection by nucleic acid isothermal amplification integrated with CRISPR/Cas

Food safety problems have become one of the most important public health issues worldwide. Therefore, the development of rapid, effective and robust detection is of great importance. Amongst a range of methods, nucleic acid isothermal amplification (NAIA) plays a great role in food safety detection. However, the widespread application remains limited due to a few shortcomings. CRISPR/Cas system has emerged as a powerful tool in nucleic acid detection, which could be readily integrated with NAIA to improve the detection sensitivity, specificity, adaptability versatility and dependability. However, currently there was a lack of a comprehensive summary regarding the integration of NAIA and CRISPR/Cas in the field of food safety detection. In this review, the recent advances in food safety detection based on CRISPR/Cas-integrated NAIA were comprehensively reviewed. To begin with, the development of NAIA was summarized. Then, the types and working principles of CRISPR/Cas were introduced. The applications of the integration of NAIA and CRISPR/Cas for food safety were mainly introduced and objectively discussed. Lastly, current challenges and future opportunities were proposed. In summary, this technology is expected to become an important approach for food safety detection, leading to a safer and more reliable food industry.

Recent Advances in CRISPR/Cas System-Based Biosensors for the Detection of Foodborne Pathogenic Microorganisms

Foodborne pathogens pose significant risks to food safety. Conventional biochemical detection techniques are facing a series of challenges. In recent years, with the gradual development of CRISPR (clustered regularly interspaced short palindromic repeats) technology, CRISPR/Cas system-based biosensors, a newly emerging technology, have received much attention from researchers because of their supreme flexibility, sensitivity, and specificity. While numerous CRISPR-based biosensors have a broad application in the field of environmental monitoring, food safety, and point-of-care diagnosis, they remain in high demand to summarize recent advances in CRISPR/Cas system-based biosensors for foodborne pathogen detection. In this paper, we briefly classify and discuss the working principles of CRISPR/Cas systems with trans-cleavage activity in applications for the detection of foodborne pathogenic microorganisms. We highlight the current status, the unique feature of each CRISPR system and CRISPR-based biosensing platforms, and the integration of CRISPR-Cas with other techniques, concluding with a discussion of the advantages, disadvantages, and future directions.

Recent advances in the CRISPR/Cas system-based visual detection method

Currently, various infectious pathogens and bacterial toxins as well as heavy metal pollution pose severe threats to global environmental health and the socio-economic infrastructure. Therefore, there is a pressing need for rapid, sensitive, and convenient visual molecular detection methods. The rapidly evolving detection approach based on clustered regularly interspaced short palindromic repeats (CRISPR)/associated nucleases (Cas) has opened a new frontier in the field of molecular diagnostics. This paper reviews the development of visual detection methods in recent years based on different Cas and analyzes their advantages and disadvantages as well as the challenges of future research. Firstly, different CRISPR/Cas effectors and their working principles in the diagnosis of various diseases are briefly reviewed. Subsequently, the article focuses on the development of visual readout signals in point-of-care testing using laboratory-based CRISPR/Cas technology, including colorimetric, fluorescence, and lateral flow analysis. Finally, the challenges and prospects of visual detection methods based on CRISPR/Cas technology are discussed.

An RPA-Based CRISPR/Cas12a Assay in Combination with a Lateral Flow Assay for the Rapid Detection of Shigella flexneri in Food Samples

Among the pathogens that cause infectious diarrhea in China, Shigella is the most prominent. Shigellosis affects both adults and children, particularly those in developing nations, with nearly 190 million annual cases and a third resulting in fatalities. The recently emerged CRISPR/Cas system has also been increasingly applied for the detection of different biological targets. The lateral flow assay (LFA) has the advantages of short detection time, simple operation, high sensitivity, and low cost, and it provides an ideal platform for on-site detection. In this study, a recombinase polymerase amplification-CRISPR/Cas12a-LFA test for Shigella flexneri was constructed. The established method had good specificity and sensitivity, and the qualitative accuracy of 32 tested strains reached 100%. The detection limit of genomic DNA reached 8.3 copies/μL. With the advantages of high accuracy and portability, this diagnostic apparatus represents a novel method of identification and detection of Shigella flexneri, particularly in settings that lack complex laboratory infrastructure.

Research progress on detection of foodborne pathogens: The more rapid and accurate answer to food safety

In recent years, foodborne diseases have posed a serious threat to human health, and rapid detection of foodborne pathogens is particularly crucial for the prevention and control of such diseases. This article offers a detailed overview of the development of detection techniques for foodborne pathogens, transitioning from traditional microbiological culture methods to the current array of techniques, including immunological, molecular biological, and biosensor-based methods. It summarizes the technical principles, advantages, disadvantages, and research progress of these diverse methods. Furthermore, the article demonstrates that the combination of different methods enhances the efficiency and accuracy of pathogens detection. Specifically, the article focuses on the application and advantages of combining CRISPR/Cas systems with other detection methods in the detection of foodborne pathogens. CRISPR/Cas systems, with their high specificity, sensitivity, and ease of operation, show great potential in the field of foodborne pathogens detection. When integrated with other detection techniques such as immunological detection techniques, molecular biology detection techniques, and biosensors, the accuracy and efficiency of detection can be further improved. By fully utilizing these tools, early detection and control of foodborne diseases can be achieved, enhancing public health and preventing disease outbreaks. This article serves as a valuable reference for exploring more convenient, accurate, and sensitive field detection methods for foodborne pathogens, promoting the application of rapid detection techniques, and ensuring food safety and human health.

Decentralized food safety and authentication on cellulose paper-based analytical platform: A review

Food safety and authenticity analysis play a pivotal role in guaranteeing food quality, safeguarding public health, and upholding consumer trust. In recent years, significant social progress has presented fresh challenges in the realm of food analysis, underscoring the imperative requirement to devise innovative and expedient approaches for conducting on-site assessments. Consequently, cellulose paper-based devices (PADs) have come into the spotlight due to their characteristics of microchannels and inherent capillary action. This review summarizes the recent advances in cellulose PADs in various food products, comprising various fabrication strategies, detection methods such as mass spectrometry and multi-mode detection, sampling and processing considerations, as well as applications in screening food safety factors and assessing food authenticity developed in the past 3 years. According to the above studies, cellulose PADs face challenges such as limited sample processing, inadequate multiplexing capabilities, and the requirement for workflow integration, while emerging innovations, comprising the use of simplified sample pretreatment techniques, the integration of advanced nanomaterials, and advanced instruments such as portable mass spectrometer and the innovation of multimodal detection methods, offer potential solutions and are highlighted as promising directions. This review underscores the significant potential of cellulose PADs in facilitating decentralized, cost-effective, and simplified testing methodologies to maintain food safety standards. With the progression of interdisciplinary research, cellulose PADs are expected to become essential platforms for on-site food safety and authentication analysis, thereby significantly enhancing global food safety for consumers.

Seizing the Hidden Assassin: Current Detection Strategies for Staphylococcus aureus and Methicillin-Resistant S. aureus

Staphylococcus aureus (S. aureus) is a kind of pathogenic bacteria which can lead to food poisoning, hospital, and community infections. S. aureus and methicillin-resistant S. aureus (MRSA) have become headaches for public health worldwide. Therefore, strengthening the detection of S. aureus and MRSA is a critical step to prevent and control its spread and infection. This review summarized multiple detection methods (electrochemical, optical, and other biosensors) for sensitive and efficient detection of nonresistant and resistant S. aureus. First, we have introduced the principle and methods of detection platform for S. aureus and MRSA. We also contrasted various detection strategies. Finally, the current situation and prospect of S. aureus and MRSA detection in the future are explored in depth, and its development direction of detection methods is also predicted. In this review, we found that although biosensors have shown tremendous brilliance in the field of monitoring, they are currently in the experimental stage. It can be certain that we are very close to entering the commercialization stage. The point-of care testing available to nonprofessionals will become a new direction. We firmly believe that the monitoring system will be more perfect and stable and public life will be healthier and safer.

Nanotopology-Enabled On-Site Pathogen Detection for Managing Atopic Dermatitis

Atopic dermatitis (AD), a prevalent skin condition often complicated by microbial infection, poses a significant challenge in identifying the responsible pathogen for its effective management. However, a reliable, safe tool for pinpointing the source of these infections remains elusive. In this study, a novel on-site pathogen detection that combines chemically functionalized nanotopology with genetic analysis is proposed to capture and analyze pathogens closely associated with severe atopic dermatitis. The chemically functionalized nanotopology features a 3D hierarchical nanopillar array (HNA) with a functional polymer coating, tailored to isolate target pathogens from infected skin. This innovative nanotopology demonstrates superior pathogenic capture efficiency, favorable entrapment patterns, and non-cytotoxicity. An HNA-assembled stick is utilized to directly retrieve bacteria from infected skin samples, followed by extraction-free quantitative loop-mediated isothermal amplification (direct qLAMP) for validation. To mimic human skin conditions, porcine skin is employed to successfully capture Staphylococcus aureus, a common bacterium exacerbating AD cases. The on-site detection method exhibits an impressive detection limit of 103 cells mL-1. The HNA-assembled stick represents a promising tool for on-site detection of bacteria associated with atopic dermatitis. This innovative approach enables to deepen the understanding of AD pathogenesis and open avenues for more effective management strategies for chronic skin conditions.

CRISPR-Cas systems of lactic acid bacteria and applications in food science

CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) systems are widely distributed in lactic acid bacteria (LAB), contributing to their RNA-mediated adaptive defense immunity. The CRISPR-Cas-based genetic tools have exhibited powerful capability. It has been highly utilized in different organisms, accelerating the development of life science. The review summarized the components, adaptive immunity mechanisms, and classification of CRISPR-Cas systems; analyzed the distribution and characteristics of CRISPR-Cas system in LAB. The review focuses on the development of CRISPR-Cas-based genetic tools in LAB for providing latest development and future trend. The diverse and broad applications of CRISPR-Cas systems in food/probiotic industry are introduced. LAB harbor a plenty of CRISPR-Cas systems, which contribute to generate safer and more robust strains with increased resistance against bacteriophage and prevent the dissemination of plasmids carrying antibiotic-resistance markers. Furthermore, the CRISPR-Cas system from LAB could be used to exploit novel, flexible, programmable genome editing tools of native host and other organisms, resolving the limitation of genetic operation of some LAB species, increasing the important biological functions of probiotics, improving the adaptation of probiotics in complex environments, and inhibiting the growth of foodborne pathogens. The development of the genetic tools based on CRISPR-Cas system in LAB, especially the endogenous CRISPR-Cas system, will open new avenues for precise regulation, rational design, and flexible application of LAB.

CRISPR-Cas12a-Mediated Hue-Recognition Lateral Flow Assay for Point-of-Need Detection of Salmonella

Nucleic acid detection of pathogens in a point-of-need (PON) manner is of great significance yet remains challenging for sensitive and accurate visual discrimination. Here, we report a CRISPR-Cas12a-mediated lateral flow assay for PON detection of Salmonella typhimurium (S.ty) that is a prevailing pathogen disseminated through tainted food. The variation of the fluorescence color of the test line is exploited to interpret the results, enabling the discrimination between positive and negative samples on the basis of a hue-recognition mechanism. By leveraging the cleavage activity of Cas12a and hue-recognition readout, the assay facilitated by recombinase polymerase amplification can yield a visual detection limit of 1 copy μL-1 for S.ty genomic DNA within 1 h. The assay also displays a high specificity toward S.ty in fresh chicken samples, as well as a sensitivity 10-fold better than that of the commercial test strip. Moreover, a semiquantitative detection of S.ty ranging from 0 to 4 × 103 CFU/mL by the naked eye is made possible, thanks to the easily discernible color change of the test line. This approach provides an easy, rapid, accurate, and user-friendly solution for the PON detection of Salmonella and other pathogens.

Novel helix loop-mediated isothermal amplification (HAMP) assay for colorimetric detection of Staphylococcus aureus in milk

Staphylococcus aureus is an important and leading cause of foodborne diseases worldwide. Prompt detection and recall of contaminated foods are crucial to prevent untoward health consequences caused by S. aureus. Helix loop-mediated isothermal amplification (HAMP) is an exciting recent addition to the array of available isothermal-based nucleic acid amplification techniques. This study aimed to develop and evaluate a HAMP assay for detecting S. aureus in milk and milk products. The assay is completed in 75 minutes of isothermal temperature incubation (64 ˚C) and dye-based visual interpretation of results based on colour change. The specificity of the developed assay was ascertained using 27 S. aureus and 17 non S. aureus bacterial strains. The analytical sensitivity of the developed HAMP assay was 9.7 fg/µL of pure S. aureus DNA. The detection limit of the HAMP assay in milk (86 CFU/mL) was 1000x greater than the routinely used endpoint PCR (86 × 103 CFU/mL). The practicality of applying the HAMP assay was also assessed by analysing milk and milk product samples (n = 95) obtained from different dairy farms and retail outlets. The developed test is a more rapid, sensitive, and user-friendly method for the high-throughput screening of S. aureus in food samples and may therefore be suitable for field laboratories. To our knowledge, this is the first study to develop and evaluate the HAMP platform for detecting S. aureus.

Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests

Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.

Integration of a CRISPR Cas12a-assisted multicolor biosensor and a micropipette tip enables visible point-of-care testing of foodborne Vibrio vulnificus

Foodborne pathogens cause numerous food safety problems, and as a virulent bacterium falling under this category, Vibrio vulnificus (V. vulnificus) poses a huge threat to public health. The conventional methods used for the detection of V. vulnificus, including culture-based and molecular detection methods, have a variety of drawbacks, including being time-consuming and labor-intensive, the requirement of large-scale equipment, and the lack of professional operators. This paper establishes a visible detection platform for V. vulnificus based on CRISPR/Cas12a, which is integrated with nucleic acid isothermal amplification and β-galactosidase-catalyzed visible color reaction. The specific vvhA gene and a conservative segment in the 16S rDNA gene of the Vibrio genus were selected as the detection targets. By using spectrum analysis, this CRISPR detection platform achieved sensitive detection of V. vulnificus (1 CFU per reaction) with high specificity. Through the color transformation system, as low as 1 CFU per reaction of V. vulnificus in both bacterial solution and artificially contaminated seafood could be visibly observed with the naked eye. Furthermore, the consistency between our assay and the qPCR assay in the detection of V. vulnificus spiked seafood was confirmed. In general, this visible detection platform is user-friendly, accurate, portable, and equipment-free, and is expected to provide a powerful supplement in point-of-care testing of V. vulnificus and also holds good promise for future application in foodborne pathogen detection.

Loop-mediated isothermal amplification (LAMP)/Cas12a assay for detection of Ralstonia solanacearum in tomato

Introduction: Bacterial wilt (BW) caused by the aerobic, Gram-negative pathogenic species Ralstonia solanacearum (RS) is a major disease impacting commercial agriculture worldwide. Asian phylotype I of RS is the cause of tomato bacterial wilt, which has caused severe economic losses in southern China for many years. An urgent priority in control of bacterial wilt is development of rapid, sensitive, effective methods for detection of RS. Methods: We describe here a novel RS detection assay based on combination of loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a. crRNA1, with high trans-cleavage activity targeting hrpB gene, was selected out of four candidate crRNAs. Two visual detection techniques, involving naked-eye observation of fluorescence and lateral flow strips, were tested and displayed high sensitivity and strong specificity. Results and Discussion: The LAMP/Cas12a assay accurately detected RS phylotype Ⅰ in 14 test strains, and showed low detection limit (2.0 × 10⁰ copies). RS in tomato stem tissue and soil samples from two field sites with suspected BW infection was identified accurately, suggesting potential application of LAMP/Cas12a assay as point-of-care test (POCT). The overall detection process took less than 2 h and did not require professional lab equipment. Our findings, taken together, indicate that LAMP/Cas12a assay can be developed as an effective, inexpensive technique for field detection and monitoring of RS.

"Lock-and-key" recognizer-encoded lateral flow assays toward foodborne pathogen detection: An overview of their fundamentals and recent advances

In light of severe health risks of foodborne pathogenic bacterial diseases, the potential utility of point-of-care (POC) sensors is recognized for pathogens detection. In this regard, lateral flow assay (LFA) is a promising and user-friendly option for such application among various technological approaches. This article presents a comprehensive review of "lock-and-key" recognizer-encoded LFAs with respect to their working principles and detection performance against foodborne pathogenic bacteria. For this purpose, we describe various strategies for bacteria recognition including the antibody-based antigen-antibody interactions, nucleic acid aptamer-based recognition, and phage-mediated targeting of bacterial cells. In addition, we also outline the technological challenges along with the prospects for the future development of LFA in food analysis. The LFA devices built based upon many recognition strategies are found to have great potential for rapid, convenient, and effective POC detection of pathogens in complex food matrixes. Future developments in this field should emphasize the development of high-quality bio-probes, multiplex sensors, and intelligent portable readers.

CRISPR-based biosensors for pathogenic biosafety

Pathogenic biosafety is a worldwide concern. Tools for analyzing pathogenic biosafety, that are precise, rapid and field-deployable, are highly demanded. Recently developed biotechnological tools, especially those utilizing CRISPR/Cas systems which can couple with nanotechnologies, have enormous potential to achieve point-of-care (POC) testing for pathogen infection. In this review, we first introduce the working principle of class II CRISPR/Cas system for detecting nucleic acid and non-nucleic acid biomarkers, and highlight the molecular assays that leverage CRISPR technologies for POC detection. We summarize the application of CRISPR tools in detecting pathogens, including pathogenic bacteria, viruses, fungi and parasites and their variants, and highlight the profiling of pathogens' genotypes or phenotypes, such as the viability, and drug-resistance. In addition, we discuss the challenges and opportunities of CRISPR-based biosensors in pathogenic biosafety analysis.

Gold Nanomaterials-Implemented CRISPR-Cas Systems for Biosensing

Due to their superiority in the simple design and precise targeting, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have attracted significant interest for biosensing. On the one hand, CRISPR-Cas systems have the capacity to precisely recognize and cleave specific DNA and RNA sequences. On the other hand, CRISPR-Cas systems such as orthologs of Cas9, Cas12, and Cas13 exhibit cis-cleavage or trans-cleavage activities after recognizing the target sequence. Owing to the cleavage activities, CRISPR-Cas systems can be designed for biosensing by degrading tagged nucleic acids to produce detectable signals. To meet the requirements of point-of-care detection and versatile signal readouts, gold nanomaterials with excellent properties such as high extinction coefficients, easy surface functionalization, and biocompatibility are implemented in CRISPR-Cas-based biosensors. In combination with gold nanomaterials such as gold nanoparticles, gold nanorods, and gold nanostars, great efforts are devoted to fabricating CRISPR-Cas-based biosensors for the detection of diverse targets. This review focuses on the current advances in gold nanomaterials-implemented CRISPR-Cas-based biosensors, particularly the working mechanism and the performance of these biosensors. CRISPR-Cas systems, including CRISPR-Cas9, CRISPR-Cas12a, and CRISPR-Cas13a are discussed and highlighted. Meanwhile, prospects and challenges are also discussed in the design of biosensing strategies based on gold nanomaterials and CRISPR-Cas systems.

A critical review of microfluidic systems for CRISPR assays

Reviewed are nucleic acid detection assays that incorporate clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics and microfluidic devices and techniques. The review serves as a reference for researchers who wish to use CRISPR-Cas systems for diagnostics in microfluidic devices. The review is organized in sections reflecting a basic five-step workflow common to most CRISPR-based assays. These steps are analyte extraction, pre-amplification, target recognition, transduction, and detection. The systems described include custom microfluidic chips and custom (benchtop) chip control devices for automated assays steps. Also included are partition formats for digital assays and lateral flow biosensors as a readout modality. CRISPR-based, microfluidics-driven assays offer highly specific detection and are compatible with parallel, combinatorial implementation. They are highly reconfigurable, and assays are compatible with isothermal and even room temperature operation. A major drawback of these assays is the fact that reports of kinetic rates of these enzymes have been highly inconsistent (many demonstrably erroneous), and the low kinetic rate activity of these enzymes limits achievable sensitivity without pre-amplification. Further, the current state-of-the-art of CRISPR assays is such that nearly all systems rely on off-chip assays steps, particularly off-chip sample preparation.

Paper-based sensors for bacteria detection

The detection of pathogenic bacteria is essential to prevent and treat infections and to provide food security. Current gold-standard detection techniques, such as culture-based assays and polymerase chain reaction, are time-consuming and require centralized laboratories. Therefore, efforts have focused on developing point-of-care devices that are fast, cheap, portable and do not require specialized training. Paper-based analytical devices meet these criteria and are particularly suitable to deployment in low-resource settings. In this Review, we highlight paper-based analytical devices with substantial point-of-care applicability for bacteria detection and discuss challenges and opportunities for future development.

Thermophilic helicase-dependent amplification-based CRISPR/Cas12a system: Detection of stx2 in Escherichia coli O157:H7 by controlling primer dimers

BACKGROUND

s: To overcome the limitation of polymerase chain reaction (PCR), isothermal amplification methods such as thermophilic helicase-dependent amplification (tHDA) have been developed. However, formation of primer dimer due to the single amplification temperature are major problems of tHDA. When cross-dimerization of forward and reverse primer occurred, false-positive results can be found on the lateral flow assay (LFA) which is one of the major detection methods widely used as a point of care diagnosis. Therefore, specific method of detecting only the target amplicon is required.

RESULTS

In this study, a tHDA-based CRISPR/Cas12a system was developed to detect low levels of Escherichia coli O157:H7 in fresh salad mix without the false-positive results produced by primer dimers. For the comparison of the effect in eliminating false-positive results by CRISPR/Cas12a system, LFA was also evaluated. The tHDA-based CRISPR/Cas12a system detected as low as 10¹ CFU/mL E. coli O157:H7 in bacterial pure culture. In LFA false-positive results were produced due to the primer dimer, whereas the primer dimer produced by tHDA was not detected in the CRISPR/Cas12a system. These results indicated that the CRISPR/Cas12a system eliminated the formation of primer dimer. In fresh salad mix, the tHDA-based CRISPR/Cas12a system combined with the filter concentration method detected 10³ CFU/g E. coli O157:H7.

CONCLUSION

This study was the first to amplify stx2 of E. coli O157:H7 with tHDA as an isothermal amplification method and detected the amplicon without false-positive results by combining tHDA with CRISPR/Cas12a. Therefore, this study showed great potential for detecting low levels of E. coli O157:H7 present in fresh salad mix.

CRISPR-Cas based molecular diagnostics for foodborne pathogens

Foodborne pathogenic infection has brought multifaceted issues to human life, leading to an urgent demand for advanced detection technologies. CRISPR/Cas-based biosensors have the potential to address various challenges that exist in conventional assays such as insensitivity, long turnaround time and complex pretreatments. In this perspective, we review the relevant strategies of CRISPR/Cas-assisted diagnostics on foodborne pathogens, focusing on biosensing platforms for foodborne pathogens based on fluorescence, colorimetric, (electro)chemiluminescence, electrochemical, and surface-enhanced Raman scattering detection. It summarizes their detection principles by the clarification of foodborne pathogenic bacteria, fungi, and viruses. Finally, we discuss the current challenges or technical barriers of these methods against broad application, and put forward alternative solutions to improve CRISPR/Cas potential for food safety.

Computer vision enabled funnel adapted sensing tube (FAST) for power-free and pipette-free nucleic acid detection

A simple, portable, and low-cost microfluidic system-funnel adapted sensing tube (FAST) is developed as an integrated, power-free, and pipette-free biosensor for viral nucleic acids. This FAST chip consists of four reaction chambers separated by carbon fiber rods, and the reagents in each chamber are transferred and mixed by manually removing the rods. Rather than using electrical heaters, only a hand warmer pouch is used for an isothermal recombinase polymerase amplification (RPA) and CRISPR-Cas12a reaction. The signal produced by the RPA-CRISPR reaction is observed by the naked eye using an inexpensive flashlight as a light source. The FAST chip is fabricated using water-soluble polyvinyl alcohol (PVA) as a sacrificial core, which is simple and environmentally friendly. Using a SARS-CoV-2 fragment as a target, a ∼10 fM (6 × 10³ copies per μL) detection limit is achieved. To generalize standard optical readout for individuals without training, a linear kernel algorithm is created, showing an accuracy of ∼100% for identifying both positive and negative samples in FAST. This power-free, pipette-free, disposable, and simple device will be a promising tool for nucleic acid diagnostics in either clinics or low-resource settings.

Capturing nucleic acid variants with precision using CRISPR diagnostics

CRISPR/Cas systems have the ability to precisely target nucleotide sequences and enable their rapid identification and modification. While nucleotide modification has enabled the therapeutic correction of diseases, the process of identifying the target DNA or RNA has greatly expanded the field of molecular diagnostics in recent times. CRISPR-based DNA/RNA detection through programmable nucleic acid binding or cleavage has been demonstrated for a large number of pathogenic and non-pathogenic targets. Combining CRISPR detection with nucleic acid amplification and a terminal signal readout step allowed the development of numerous rapid and robust nucleic acid platforms. Wherever the Cas effector can faithfully distinguish nucleobase variants in the target, the platform can also be extended for sequencing-free rapid variant detection. Some initial PAM disruption-based SNV detection reports were limited to finding or integrating mutated/mismatched nucleotides within the PAM sequences. In this review, we try to summarize the developments made in CRISPR diagnostics (CRISPRDx) to date emphasizing CRISPR-based SNV detection. We also discuss the applications where such diagnostic modalities can be put to use, covering various fields of clinical research, SNV screens, disease genotyping, primary surveillance during microbial infections, agriculture, food safety, and industrial biotechnology. The ease of rapid design and implementation of such multiplexable assays can potentially expand the applications of CRISPRDx in the domain of affinity-based target sequencing, with immense possibilities for low-cost, quick, and widespread usage. In the end, in combination with proximity assays and a suicidal gene approach, CRISPR-based in vivo SNV detection and cancer cell targeting can be formulated as personalized gene therapy.

CRISPR-Cas systems mediated biosensing and applications in food safety detection

Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.

In Vitro CRISPR-Cpf1 Assay for Differentiation of Fine and Bulk Cocoa (Theobroma cacao L.)

Cocoa cultivation is dominated by the clone "Colleción Castro Naranjal 51" (CCN-51). In contrast, CCN-51 is the expensive and aromatic fine cocoa "Arriba Nacional" from Ecuador. The differences in the overall quality of the beans and in the prices show that it is necessary to develop a rapid and accurate method to distinguish these varieties and prevent food fraud. To this end, we used a CRISPR-Cpf1 assay suitable for AT-rich targets such as the chloroplast genome (cpGenome). SNPs in cocoa plastid genomes were selected to replace the canonical PAM sequence of Cpf1 (5'-TTTV-3'). We developed two assay systems to digest both Arriba and CCN-51. The results were tested qualitatively by agarose gel electrophoresis and quantitatively by capillary gel electrophoresis. Using the assay described here, we were able to reliably detect admixtures of 5% CCN-51 (P < 0.01) and 10% Arriba (P < 0.05). The application to processed cocoa products was also successful.

An ultrasensitive sandwich-type electrochemical aptasensor using silver nanoparticle/titanium carbide nanocomposites for the determination of Staphylococcus aureus in milk

A novel sandwich-type electrochemical aptasensor for the detection of Staphylococcus aureus (S. aureus) was developed. S. aureus aptamers were self-assembled onto the surface of a glassy carbon electrode (GCE) modified with nanocomposites comprising titanium carbide embedded with silver nanoparticles (AgNPs@Ti₃C₂) through hydrogen bonds and the chelation interaction between phosphate groups and Ti ions. In addition, the self-assembled aptamers were immobilized on CuO/graphene (GR) nanocomposites via π-π stacking interactions to serve as a signal probe. In the presence of the target S. aureus, the sandwich-type recognition system reacted on the surface of GCE, and the CuO/GR nanocomposites catalyzed the hydrogen peroxide + hydroquinone reaction producing a strong current response. Under the optimal experimental conditions, the current response of the aptasensor was linearly correlated with the concentration of S. aureus (52-5.2 × 10⁷ CFU mL^-1) with a low detection limit of 1 CFU mL^-1. The aptasensor displayed good repeatability and excellent selectivity for S. aureus detection. Moreover, this aptasensor was applied to the detection of S. aureus in cow, sheep, and goat milk samples, affording recoveries ranging from 92.64 to 109.58%. This research provides a new platform for the detection of pathogenic bacteria and other toxic and harmful substances in food.

CRISPR-Cas-based detection for food safety problems: Current status, challenges, and opportunities

Food safety is one of the biggest public issues occurring around the world. Microbiological, chemical, and physical hazards can lead to food safety issues, which may occur at all stages of the supply chain. In order to tackle food safety issues and safeguard consumer health, rapid, accurate, specific, and field-deployable detection methods meeting diverse requirements are one of the imperative measures for food safety assurance. CRISPR-Cas system, a newly emerging technology, has been successfully repurposed in biosensing and has demonstrated huge potential to establish conceptually novel detection methods with high sensitivity and specificity. This review focuses on CRISPR-Cas-based detection and its current status and huge potential specifically for food safety inspection. We firstly illustrate the pending problems in food safety and summarize the popular detection methods. We then describe the potential applications of CRISPR-Cas-based detection in food safety inspection. Finally, the challenges and futuristic opportunities are proposed and discussed. Generally speaking, the current food safety detection methods are still unsatisfactory in some ways such as being time-consuming, displaying unmet sensitivity and specificity standards, and there is a comparative paucity of multiplexed testing and POCT. Recent studies have shown that CRISPR-Cas-based biosensing is an innovative and fast-expanding technology, which could make up for the shortcomings of the existing methods or even replace them. To sum up, the implementation of CRISPR-Cas and the integration of CRISPR-Cas with other techniques is promising and desirable, which is expected to provide "customized" and "smart" detection methods for food safety inspection in the coming future.

CE-RAA-CRISPR Assay: A Rapid and Sensitive Method for Detecting Vibrio parahaemolyticus in Seafood

Vibrio parahaemolyticus is one of the major pathogenic Vibrio species that contaminate seafood. Rapid and accurate detection is crucial for avoiding foodborne diseases caused by pathogens and is important for food safety management and mariculture. In this study, we established a system that combines chemically enhanced clustered regularly interspaced short palindromic repeats (CRISPR) and recombinase-aided amplification (RAA) (CE–RAA–CRISPR) for detecting V. parahaemolyticus in seafood. The method combines RAA with CRISPR-associated protein 12a (Cas12a) for rapid detection in a one-pot reaction, effectively reducing the risk of aerosol contamination during DNA amplifier transfer. We optimized the primers for V. parahaemolyticus, determined the optimal crRNA/Cas12a ratio, and demonstrated that chemical additives (bovine serum albumin and L-proline) could enhance the detection capacity of Cas12a. The limit of detection (at optimal conditions) was as low as 6.7 × 10¹ CFU/mL in pure cultures and 7.3 × 10¹ CFU/g in shrimp. Moreover, this method exhibited no cross-reactivity with other microbial pathogens. The CE–RAA–CRISPR assay was compared with the quantitative polymerase chain reaction assay using actual food samples, and it showed 100% diagnostic agreement.

Recent advances in CRISPR-based systems for the detection of foodborne pathogens

There has long been a need for more advanced forms of pathogen detection in the food industry. Though in its infancy, biosensing based on clustered regularly interspaced short palindromic repeats (CRISPR) has the potential to solve many problems that cannot be addressed using conventional methods. In this review, we briefly introduce and classify the various CRISPR/Cas protein effectors that have thus far been used in biosensors. We then assess the current state of CRISPR technology in food-safety contexts; describe how each Cas effector is utilized in foodborne-pathogen detection; and discuss the limitations of the current technology, as well as how it might usefully be applied in other areas of the food industry. We conclude that, if the limitations of existing CRISPR/Cas-based detection methods are overcome, they can be deployed on a wide scale and produce a range of positive food-safety outcomes.

CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety

BACKGROUND

In the context of the current pandemic caused by the novel coronavirus, molecular detection is not limited to the clinical laboratory, but also faces the challenge of the complex and variable real-time detection fields. A series of novel coronavirus events were detected in the process of food cold chain packaging and transportation, making the application of molecular diagnosis in food processing, packaging, transportation, and other links urgent. There is an urgent need for a rapid detection technology that can adapt to the diversity and complexity of food safety.

SCOPE AND APPROACH

This review introduces a new molecular diagnostic technology-biosensor analysis technology based on CRISPR-Cas12a. Systematic clarification of its development process and detection principles. It summarizes and systematically organizes its applications in viruses, food-borne pathogenic bacteria, small molecule detection, etc. In the past four years, which provides a brand-new and comprehensive solution for food detection. Finally, this article puts forward the challenges and the prospects for food safety.

KEY FINDINGS AND CONCLUSIONS

The novel coronavirus hazards infiltrated every step of the food industry, from processing to packaging to transportation. The biosensor analytical technology based on CRISPR-Cas12a has great potential in the qualitative and quantitative analysis of infectious pathogens. CRISPR-Cas12a can effectively identify the presence of the specific nucleic acid targets and the small changes in sequences, which is particularly important for nucleic acid identification and pathogen detection. In addition, the CRISPR-Cas12a method can be adjusted and reconfigured within days to detect other viruses, providing equipment for nucleic acid diagnostics in the field of food safety. The future work will focus on the development of portable microfluidic devices for multiple detection. Shao et al. employed physical separation methods to separate Cas proteins in different microfluidic channels to achieve multiple detection, and each channel simultaneously detected different targets by adding crRNA with different spacer sequences. Although CRISPR-Cas12a technology has outstanding advantages in detection, there are several technical barriers in the transformation from emerging technologies to practical applications. The newly developed CRISPR-Cas12a-based applications and methods promote the development of numerous diagnostic and detection solutions, and have great potential in medical diagnosis, environmental monitoring, and especially food detection.

Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison

Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.

Direct Detection of Foodborne Pathogens via a Proximal DNA Probe-Based CRISPR-Cas12 Assay

Foodborne pathogens can cause illnesses. Existing tools for detecting foodborne pathogens are typically time-consuming or require complex protocols. Here, we report an assay to directly analyze pathogenic genes based on CRISPR-Cas12. This new test, termed proximal DNA probe-based CRISPR-Cas12 (PPCas12), facilitates the detection of foodborne pathogens without amplification steps. The elimination of the nucleic acid amplification process dramatically reduced the processing time, complexity, and costs in the analysis of foodborne pathogens. The substitution of the frequently used dually labeled DNA reporter with a proximal DNA probe in the PPCas12 assay led to a 4-fold sensitivity enhancement. PPCas12 offered a limit of detection of 619 colony-forming units in the detection of Salmonella enterica (S. enterica) without the nucleic acid amplification process. The specific recognition of genes via PPCas12 allowed distinguishing S. enterica from other foodborne pathogens. The PPCas12 assay was applied in the screening of S. enterica contamination on fresh eggs with high precision. Hence, the new PPCas12 assay will be a valuable tool for on-site monitoring of foodborne pathogens.