Magnetically modified bacteriophage-triggered ATP release activated EXPAR-CRISPR/Cas14a system for visual detection of Burkholderia pseudomallei

crRNA array-mediated CRISPR/Cas12a coupling with dual RPA for highly sensitive detection of Streptomyces aureofaciens Tü117 from hypertension with multi-signal output

Accurate and sensitive detection of Streptomyces aureofaciens Tü117 is crucial for hypertension classification and early warning. To achieve this, a dual recombinase polymerase amplification coupled with a crRNA array-mediated CRISPR/Cas12a assay (DR-CAMCas) was developed, enabling multi-signal output for precise identification and detection of S. aureofaciens Tü117. The 16S rDNA and LipReg4 genes of S. aureofaciens Tü117 are amplified simultaneously via one-step dual RPA, activating the crRNA array-mediated CRISPR/Cas12a system to cleave exogenous FQ-reporters, releasing fluorescent signals. DR-CAMCas offers high amplification efficiency, multi-site recognition through crRNA array signal superposition, and the programmability of CRISPR/Cas12a, achieving ultrasensitive detection with a linear range of 10 to 108 cfu/mL and a limit of detection of approximately 3 cfu/mL. DR-CAMCas successfully detected S. aureofaciens Tü117 in fecal samples from high-salt diet-induced hypertensive mice and hypertensive patients, matching qPCR results and demonstrating high reliability and practicality. Additionally, target-induced cleavage of a DNA linker by DR-CAMCas dispersed AuNPs-DNA probes, enabling colorimetric detection. Integrated onto lateral flow sensors, DR-CAMCas allows point-of-care testing via simple visual strip analysis. Its triple signal output meets diverse detection needs, offering a promising tool for diagnosing salt-sensitive hypertension.

CRISPR/Cas-powered nucleic acid amplification and amplification-free biosensors for public safety detection: Principles, advances and prospects

Rapid, accurate, cost-effective, and efficient ultrasensitive detection strategies are essential for public health safety (including food safety, disease prevention and environmental governance). The CRISPR/CRISPR-associated (Cas) detection is a cutting-edge technology that has been widely used in the detection of public health safety due to its targeted cleavage properties (signal amplification), attomolar level sensitivity, high specificity (recognizing single-base mismatches), and rapid turnover time. However, the current research about CRISPR/Cas-based biosensors is not clear, such as mechanism problem and application differences of integrating CRISPR/Cas system with other technologies, and how to further innovate and develop in the future. Therefore, further detailed analysis and comparative discussion of CRISPR/Cas-based biosensors is needed. Currently, CRISPR/Cas system powered biosensors can be mainly categorized into two types: CRISPR/Cas system powered nucleic acid amplification biosensors and CRISPR/Cas system powered nucleic acid amplification-free biosensors. The two biosensors have different characteristics and advantages. This paper first provides an in-depth investigation of the enzymatic mechanism of CRISPR/Cas system at the molecular level. Then, this paper summarizes the principles and recent advances of CRISPR/Cas system powered nucleic acid amplification biosensors and CRISPR/Cas system powered nucleic acid amplification-free biosensors and discusses their integration mechanisms in depth. More, the differences and application-oriented between the two biosensors are further discussed. Finally, the application orientation and future perspectives of the two biosensors are discussed, and unique insights into the future development of CRISPR/Cas system are provided.

Visual Counting of Influenza A Viruses with Magnetic T4 Phage SPR Probe

Influenza A virus (IAV) represents a considerable threat to both animal and human health, while current detection methods encounter challenges related to the spectrum, rapidity, and sensitivity of viral identification. Herein, we describe the development of a magnetic T4 phage surface plasmon resonance probe for universal, rapid, highly sensitive, and visually detectable IAV detection under dark field microscopy (DFM). Briefly, we initially fused the Soc protein of the T4 phage with a single-chain variable fragment (scFv) antibody that exhibits broad-spectrum affinity toward the hemagglutinins of group 1 and group 2 influenza viruses, resulting in the generation of the recombinant Soc-scFv protein. Additionally, we generated another recombinant protein called AviTag-Hoc by fusing the Hoc capsid protein of T4 phage with biotin receptor peptides (AviTag). These two recombinant proteins were assembled on the head region of the T4 phage lacking both Soc and Hoc proteins. Subsequently, the resulting assembly was covalently modified with biotin using biotin-protein ligase, enabling conjugation with streptavidin-modified magnetic nanoparticles (SA@MNPs) to generate the magnetic T4 phage probe (T4@scFv@MNPs). Binding experiments demonstrated that this magnetic phage probe specifically binds to a wide range of IAVs of group 1 and group 2. Furthermore, in the presence of influenza viruses, the magnetic T4 phage probe and antibodies functionalized chip can form a sandwich complex that appears as a distinct bright golden yellow fluorescence spot visible to the naked eye under DFM. The number of viruses in samples can be automatically counted using artificial intelligence-assisted software. Assay results from both pure and real virus samples show that our magnetic phage-based DFM strategy is highly time efficient, taking approximately 30 min to complete. The method also showed excellent virus binding efficiency (>85%) in both high and low concentration samples and an extremely low detection limit (1 PFU/μL).

Phage/aptamer dual-encoded hydrogel arrays integrated with microfluidic platforms for simultaneous detection of multiple food pathogens

Food pathogens pose significant threats to public health. This study presents a universal, sensitive and time-efficient microfluidic chip electrophoresis (MCE) platform for simultaneously detecting multiple food pathogens based on phage/aptamer dual-encoded hydrogel arrays. The arrays are comprised of "all-in-one" hydrogel slices embedded with the capturing probe of specific phages and sensing probe of ATP aptamer/complementary chain (A-Apt/cDNA) hybrid structures. The live bacteria are specifically captured and lysed by the corresponding phages to generate copious amounts of ATP. The ATP further combines with the A-Apt/cDNA hybrids to release the cDNA strands with various lengths from the hydrogel pores into the supernatant. Therefore, cDNA strands whose lengths are specific for each bacteria function as markers for ATP, the level of which represents the number of living bacteria. The qualitation and quantification of multiple bacteria is realized by isolating and analyzing various cDNA using MCE. Taking three food pathogens (i.e., E. coli, Salmonella typhimurium, Staphylococcus aureus) as target models, the platform were performed within 60 min, with detection limits of 20 CFU/mL, 30 CFU/mL and 15 CFU/mL, respectively. This study offers a universal and rapid strategy for multiple food pathogens analysis.