An isothermal recombinase polymerase amplification and lateral flow strip combined method for rapid on-site detection of Vibrio vulnificus in raw seafood

A One-Step RPA-CRISPR Assay Using crRNA Based on Suboptimal Protospacer Adjacent Motif for Vibrio vulnificus Detection

Vibrio vulnificus is a hazardous foodborne pathogen responsible for approximately 95% of seafood-related deaths. This highlights the urgent requirement for specialized detection tools to be developed and used by food enterprises and food safety authorities. The DETECTR (DNA endonuclease targeted CRISPR trans reporter) system that combines CRISPR/Cas and recombinase polymerase amplification (RPA) has been utilized to develop a molecular detection assay for V. vulnificus. However, because the incompatibility between RPA and Cas12a cleavage has not been addressed, it is a two-step assay that lacks convenience and presents contamination risk. Here, we developed a one-step RPA-CRISPR assay for V. vulnificus using a special crRNA targeting a sequence with a suboptimal protospacer adjacent motif (PAM). The entire assay, conducted at 37°C, takes only 40-60 min, yields results visualized under blue light, and exhibits exceptional specificity and sensitivity (detecting 4 pathogen genome copies per reaction). This study offers a valuable tool for detecting V. vulnificus, aiding in foodborne infection prevention, and exemplifies one-step RPA-CRISPR assays managing Cas-cleavage activity through PAM adjustments.

Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels

Global wild-capture fisheries are a large and diverse sector requiring various tools for fisheries-dependant data collection and effective Monitoring, Control and Surveillance (MCS). Here we present a novel protocol to collect eDNA from brine tanks onboard commercial longline vessels to reconstruct catch composition. We collected samples from nine vessels operating out of the Eastern Tuna Billfish Fishery, Australia, validating eDNA results with reliable catch data consisting of seven target and bycatch species. Environmental DNA was highly effective for detecting species retained on vessels without contamination or false positives. For four vessels, logbook data and eDNA were consistent with detections of all species. The remaining vessels detected all species except for rare catches of short-billed spearfish (Tetrapturus angustirostris). Similarities between rank abundance distributions of catch and eDNA reads were observed with logbook data mirrored when eDNA sequences were organised into rank order abundance. The method was effective at identifying highly abundant taxa retained in brine tanks- tuna (Thunnus spp.), swordfish (Xiphias gladius), marlin (Kajijia audax), and Atlantic Pomfret (Brama brama). Further research is required to validate how eDNA and other molecular monitoring tools can be scaled and applied to provide solutions for monitoring challenges in the fisheries sector.

Development of Multienzyme Isothermal Rapid Amplification (MIRA) Combined with Lateral-Flow Dipstick (LFD) Assay to Detect Species-Specific tlh and Pathogenic trh and tdh Genes of Vibrio parahaemolyticus

Vibrio parahaemolyticus causes severe gastroenteritis in humans after consuming contaminated raw or undercooked seafood. A species-specific marker, the thermolabile hemolysin (tlh) gene, and two pathogenic markers, thermostable-related hemolysin (trh) and thermostable-direct hemolysin (tdh) genes, have been used to identify V. parahaemolyticus and determine its pathogenicity using both PCR and qPCR assays. To enable testing in field conditions with limited resources, this study aimed to develop a simple and rapid method to detect the species-specific (tlh) and pathogenic (trh and tdh) genes of V. parahaemolyticus using multienzyme isothermal rapid amplification (MIRA) combined with a lateral-flow dipstick (LFD). The amplification of the tlh, trh, and tdh genes could be completed within 20 min at temperatures ranging from 30 to 45 °C (p < 0.05). The test yielded positive results for V. parahaemolyticus but produced negative results for nine Vibrio species and eighteen foodborne pathogenic bacterial species. MIRA-LFD could detect 10 fg of DNA and 2 colony-forming units (CFU) of V. parahaemolyticus per reaction, demonstrating a sensitivity level comparable to that of qPCR, which can detect 10 fg of DNA and 2 CFU per reaction. Both MIRA-LFD and qPCR detected seven tlh-positive results from thirty-six oyster samples, whereas one positive result was obtained using the PCR assay. No positive results for the trh and tdh genes were obtained from any oyster samples using MIRA-LFD, PCR, and qPCR. This study suggests that MIRA-LFD is a simple and rapid method to detect species-specific and pathogenic genes of V. parahaemolyticus with high sensitivity.

Water-soluble fluorine-functionalized chitooligosaccharide derivatives: Synthesis, characterization and antimicrobial activity

In this work, a series of water-soluble fluorine-functionalized chitooligosaccharide derivatives were synthesized by conjugating nicotinic acid to chitooligosaccharide via nicotinylation reaction, followed by nucleophilic reaction with ethyl bromide, benzyl bromide and fluorobenzyl bromides. Synthesized derivatives were identified structurally by Fourier Transform Infrared Spectroscopy and Nuclear Magnetic Resonance. In addition, the antibacterial activities of chitooligosaccharide derivatives against several disease-causing bacteria were assessed by the broth dilution method and Kirby-Bauer method, the mycelium growth rate method was used to assessing the antifungal properties of samples against three plant-threatening fungi. Among the chitooligosaccharide derivatives, those containing benzyl or fluorobenzyl exhibited noteworthy antimicrobial activity. Specifically, the chitooligosaccharide derivative containing 2,3,4-trifluorobenzyl displayed remarkable antimicrobial activity, with an inhibition index of 84.35% against Botryis cinerea at a concentration of 1.0 mg/mL. Additionally, its MIC value against Staphylococcus aureus was found to be 0.03125 mg/mL, while the MBC value was determined to be 0.0625 mg/mL. The findings of the study revealed that the incorporation of pyridinium cations and fluorine into the chitooligosaccharide backbone may play a critical role in strengthening its ability to combat harmful microorganisms. Furthermore, the cytotoxicities of chitooligosaccharide derivatives against Huvec cells were evaluated through MTT assay, and all samples were not toxic. As a consequence, the water-soluble fluorine-functionalized chitooligosaccharide derivatives possessed rapid microbicidal properties and good biocompatibility, which provided promising prospects for the development of a more effective and environmentally friendly antimicrobial agent.

A Novel RAA Combined Test Strip Method Based on Dual Gene Targets for Pathogenic Vibrio vulnificus in Aquatic Products

Vibrio vulnificus can cause disease in aquatic animals and humans, therefore, rapid and simple field detection of pathogenic V. vulnificus is important for early disease prevention. In this study, a novel recombinase-aided amplification (RAA) combined test strip with double T-lines (RAA-TS-DTL) was developed for the rapid detection of V. vulnificus in aquatic products. Pathogenic V. vulnificus was detected using the virulence vvhA gene and the housekeeping gene gyrB gene as the dual target of the test strip. The RAA-TS-DTL method showed 100% specificity for V. vulnificus, and no cross-reaction was observed with Vibrio spp. or other bacteria (n = 14). Furthermore, sensitive detection of V. vulnificus in oysters was achieved. The LODs of the gyrB and vvhA genes were 6 CFU/mL and 23 CFU/mL, respectively, which was about five times higher than that of the commercial test strip. The method was validated with spiked samples (n = 60) of fish, shrimp and oyster. The consistency between RAA-TS-DTL and the traditional culture method was 97.9%. In addition, the entire process of detection, including preparation of the sample, could be completed within 50 min. Our results indicated that the developed RAA-TS-DTL was a reliable and useful tool for rapid screening or on-site detection of pathogenic V. vulnificus in aquatic products and aquaculture water.

Development of Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay To Detect Hemolysin Gene of Vibrio vulnificus in Oysters

ABSTRACT

Vibrio vulnificus inhabits estuarine waters around the world and can cause severe infections in people who eat contaminated raw or undercooked oysters. Although current detection methods are sensitive and specific, there are continuous demands for the development of rapid and accurate methods without a trained operator and equipment in the field conditions. Herein, we developed a simple and rapid method by detecting the hemolysin (vvh) gene of V. vulnificus by using recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD). The RPA-LFD could detect 100 fg of DNA (P < 0.05) and 20 CFU of V. vulnificus per reaction within 30 min (P < 0.01) and showed the result with incubation temperature ranges from 30 to 45°C (P < 0.001). The test was specific only to V. vulnificus and was not responsive to 10 other closely related Vibrio species and 18 foodborne pathogenic bacteria. Compared with PCR, quantitative PCR, and colony hybridization assays by using naturally contaminated oyster samples, our RPA-LFD showed the same detection ability as quantitative PCR assay. Therefore, the current RPA-LFD would be a valuable tool to detect V. vulnificus in oysters, especially in field conditions.

HIGHLIGHTS

Visual Detection of Chicken Adulteration Based on a Lateral Flow Strip-PCR Strategy

The aim of this study was to develop an accurate, easy-to-use, and cost-effective method for the detection of chicken adulteration based on polymerase chain reaction (PCR) and lateral flow strip (LFS). We compared six DNA extraction methods, namely the cetyltrimethylammonium bromide (CTAB) method, salt method, urea method, SDS method, guanidine isothiocyanate method, and commercial kit method. The chicken cytb gene was used as a target to design specific primers. The specificity and sensitivity of the PCR-LFS system were tested using a self-assembled lateral flow measurement sensor. The results showed that the DNA concentration obtained by salt methods is up to 533 ± 84 ng µL⁻¹, is a suitable replacement for commercial kits. The PCR-LFS method exhibits high specificity at an annealing temperature of 62 °C and does not cross-react with other animal sources. This strategy is also highly sensitive, being able to detect 0.1% of chicken in artificial adulterated meat. The results of the test strips can be observed with the naked eye within 5 min, and this result is consistent with the electrophoresis result, demonstrating its high accuracy. Moreover, the detection system has already been successfully used to detect chicken in commercial samples. Hence, this PCR-LFS strategy provides a potential tool to verify the authenticity of chicken.

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.

Development of an isothermal recombinase-aided amplification assay for the rapid and visualized detection of Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae is a zoonotic opportunistic pathogen, leading to severe infections in dairy cows and humans. Efficient, on-site and accurate detection of K. pneumoniae is necessary to reduce the harm of cow mastitis and human infections. The objective of this study was to establish a recombinase-aided amplification (RAA) method combined with lateral flow dipstick (LFD) for rapid detection of K. pneumoniae.

RESULTS

The primer concentration, incubation temperature and incubation time of the RAA reaction were optimized. When the primer concentration was 100 nmol L^-1 , the strongest band could be obtained by incubation at 37 °C for 20 min. The RAA-LFD method had high specificity to K. pneumoniae and showed no cross-reaction with other pathogens. In addition, the detection limit of RAA-LFD for K. pneumoniae was 20 fg genomic DNA and 2.5 × 10²  CFU mL^-1 of bacteria in pure culture, which is 100 times higher than that of polymerase chain reaction (PCR) detection. Moreover, the RAA-LFD method can detect K. pneumoniae at initial concentrations as low as 2.5 CFU per 25 mL in artificially spiked milk samples after at least incubation for 6 h. Importantly, RAA-LFD had a high agreement with a test accuracy of 96.9%, compared with the biochemical identification method. Also, the detection accuracy of RAA-LFD was higher than that of the PCR assay (95.3%).

CONCLUSIONS

The results demonstrated that the RAA-LFD assay is an accurate, sensitive, simple and point-of-use detection method for K. pneumoniae, which could be used as a potential application in the research laboratory and for disease diagnosis. © 2021 Society of Chemical Industry.

Phenotyping Bacteria through a Black-Box Approach: Amplifying Surface-Enhanced Raman Spectroscopy Spectral Differences among Bacteria by Inputting Appropriate Environmental Stress

Surface-enhanced Raman spectroscopy (SERS) stands out in the field of microbial analysis due to its rich molecular information, fast analysis speed, and high sensitivity. However, achieving strain-level differentiation is still challenging because numerous bacterial species inevitably have very similar SERS profiles. Here, a method inspired by the black-box theory was proposed to boost the spectral differences, where the undifferentiated bacteria was considered as a type of black-box, external environmental stress was used as the input, and the SERS spectra of bacteria exposed to the same stress was output. For proof of the concept, three types of environmental stress were explored, i.e., ethanol, ultraviolet light (UV), and ultrasound. Enterococcus faecalis (E. faecalis) and three types of Escherichia coli (E. coli) were all subjected to the stimuli (stress) before SERS measurement. Then the collected spectra were processed only by simple principal component analysis (PCA) to achieve differentiation. The results showed that appropriate stress was beneficial to increase the differences in bacterial SERS spectra. When sonication at 490 W for 60 s was used as the input, the optimal differentiation of bacteria at the species (E. faecalis and E. coli) and strain-level (three E. coli) can be achieved.

The DNA-Cu nanocluster and exonuclease I integrated label-free reporting system for CRISPR/Cas12a-based SARS-CoV-2 detection with minimized background signal

CRISPR-driven biosensing is developing rapidly, but current works mostly adopt dye-labeled ssDNA as the signal reporter, which is costly and unstable. Herein, we developed a label-free and low-background reporter for...

Rapid and Sensitive Detection of Vibrio vulnificus Using CRISPR/Cas12a Combined With a Recombinase-Aided Amplification Assay

Vibrio vulnificus is an important zoonotic and aquatic pathogen and can cause vibriosis in humans and aquatic animals (especially farmed fish and shrimp species). Rapid and sensitive detection methods for V. vulnificus are still required to diagnose human vibriosis early and reduce aquaculture losses. Herein, we developed a rapid and sensitive diagnostic method comprising a recombinase-aided amplification (RAA) assay and the CRISPR/Cas12a system (named RAA-CRISPR/Cas12a) to detect V. vulnificus. The RAA-CRISPR/Cas12a method allows rapid and sensitive detection of V. vulnificus in 40 min without a sophisticated instrument, and the limit of detection is two copies of V. vulnificus genomic DNA per reaction. Meanwhile, the method shows satisfactory specificity toward non-target bacteria and high accuracy in the spiked blood, stool, and shrimp samples. Therefore, our proposed rapid and sensitive V. vulnificus detection method, RAA-CRISPR/Cas12a, has great potential for early diagnosis of human vibriosis and on-site V. vulnificus detection in aquaculture and food safety control.