A rapid Salmonella detection method involving thermophilic helicase-dependent amplification and a lateral flow assay

Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

Review of Detection Limits for Various Techniques for Bacterial Detection in Food Samples

Foodborne illnesses can be infectious and dangerous, and most of them are caused by bacteria. Some common food-related bacteria species exist widely in nature and pose a serious threat to both humans and animals; they can cause poisoning, diseases, disabilities and even death. Rapid, reliable and cost-effective methods for bacterial detection are of paramount importance in food safety and environmental monitoring. Polymerase chain reaction (PCR), lateral flow immunochromatographic assay (LFIA) and electrochemical methods have been widely used in food safety and environmental monitoring. In this paper, the recent developments (2013-2023) covering PCR, LFIA and electrochemical methods for various bacterial species (Salmonella, Listeria, Campylobacter, Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli)), considering different food sample types, analytical performances and the reported limit of detection (LOD), are discussed. It was found that the bacteria species and food sample type contributed significantly to the analytical performance and LOD. Detection via LFIA has a higher average LOD (24 CFU/mL) than detection via electrochemical methods (12 CFU/mL) and PCR (6 CFU/mL). Salmonella and E. coli in the Pseudomonadota domain usually have low LODs. LODs are usually lower for detection in fish and eggs. Gold and iron nanoparticles were the most studied in the reported articles for LFIA, and average LODs were 26 CFU/mL and 12 CFU/mL, respectively. The electrochemical method revealed that the average LOD was highest for cyclic voltammetry (CV) at 18 CFU/mL, followed by electrochemical impedance spectroscopy (EIS) at 12 CFU/mL and differential pulse voltammetry (DPV) at 8 CFU/mL. LOD usually decreases when the sample number increases until it remains unchanged. Exponential relations (R2 > 0.95) between LODs of Listeria in milk via LFIA and via the electrochemical method with sample numbers have been obtained. Finally, the review discusses challenges and future perspectives (including the role of nanomaterials/advanced materials) to improve analytical performance for bacterial detection.

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

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

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

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

Supplementary Information

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

Recognition-Activated Primer-Mediated Exponential Rolling Circle Amplification for Signal Probe Production and Ultrasensitive Visual Detection of Ochratoxin A with Nucleic Acid Lateral Flow Strips

We proposed a visual strategy for rapid and ultrasensitive detection of ochratoxin A (OTA) by integration of primer-mediated exponential rolling circle amplification (P-ERCA) with a designed nucleic acid lateral flow strip (LFS). The recognition component was preimmobilized in the tube by hybridization between the immobilized functionalized aptamer and complementary ssDNA. Recognition of OTA induces the release of complementary ssDNA from the tube, which will also act as the primer of the designed P-ERCA. Three nicking sites on the template P-ERCA could contribute to the production of enormous signal probes based on the simultaneous amplification-nicking model, which can be visually measured directly with the constructed nucleic acid LFS. Importantly, the nicked signal probe can also act as the trigger of the new-round RCA, achieving exponential growth of signal probes for measurement and signal enhancement. Taking advantage of the extraordinary amplification efficiency of P-ERCA and the simplicity of LFS, this P-ERCA-LFS method demonstrates ultrasensitive detection of OTA with a visual limit of detection as low as 100 fg/mL for qualitative screening and a limit of detection of 35 fg/mL for semiquantitative analysis. This designed strategy could also be utilized as a universal method for detection of other chemical analytes with the replacement of the aptamer for recognition, and the nucleic acid LFS unit could also be a useful protocol for direct ssDNA analysis.

Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases

Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.

Nested Phosphorothioated Hybrid Primer-Mediated Isothermal Amplification for Specific and Dye-Based Subattomolar Nucleic Acid Detection at Low Temperatures

Developing dye-based isothermal nucleic acid amplification (INAA) at low temperatures such as 37 °C remains a technical challenge. Here, we describe a nested phosphorothioated (PS) hybrid primer-mediated isothermal amplification (NPSA) assay which only utilizes EvaGreen (a DNA-binding dye) to achieve specific and dye-based subattomolar nucleic acid detection at 37 °C. The success of low-temperature NPSA essentially depends on employing Bacillus smithii DNA polymerase, a strand-displacing DNA polymerase with wide range of activation temperature. However, the NPSA's high efficiency entails nested PS-modified hybrid primers and the additives of urea and T4 Gene 32 Protein. To address the inhibition of urea on reverse transcription (RT), one-tube two-stage recombinase-aided RT-NPSA (rRT-NPSA) is established. By targeting human Kirsten rat sarcoma viral (KRAS) oncogene, NPSA (rRT-NPSA) stably detects 0.2 aM of KRAS gene (mRNA) within 90 (60) min. In addition, rRT-NPSA possesses subattomolar sensitivity to detect human ribosomal protein L13 mRNA. The NPSA/rRT-NPSA assays are also validated to obtain consistent results with PCR/RT-PCR methods on qualitatively detecting DNA/mRNA targets extracted from cultured cells and clinical samples. As a dye-based, low-temperature INAA method, NPSA inherently facilitates the development of miniaturized diagnostic biosensors.

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.

Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review

Milk contaminated with trace amounts of foodborne pathogens can considerably threaten food safety and public health. Therefore, rapid and accurate detection techniques for foodborne pathogens in milk are essential. Nucleic acid amplification (NAA)-based strategies are widely used to detect foodborne pathogens in milk. This review article covers the mechanisms of the NAA-based detection of foodborne pathogens in milk, including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and enzyme-free amplification, among others. Key factors affecting detection efficiency and the advantages and disadvantages of the above techniques are analyzed. Potential on-site detection tools based on NAA are outlined. We found that NAA-based strategies were effective in detecting foodborne pathogens in milk. Among them, PCR was the most reliable. LAMP showed high specificity, whereas RPA and RCA were most suitable for on-site and in-situ detection, respectively, and enzyme-free amplification was more economical. However, factors such as sample separation, nucleic acid target conversion, and signal transduction affected efficiency of NAA-based strategies. The lack of simple and effective sample separation methods to reduce the effect of milk matrices on detection efficiency was noteworthy. Further research should focus on simplifying, integrating, and miniaturizing microfluidic on-site detection platforms.

Development of Recombinase-Aided Amplification (RAA)-Exo-Probe and RAA-CRISPR/Cas12a Assays for Rapid Detection of Campylobacter jejuni in Food Samples

Campylobacter jejuni is the major cause of campylobacteriosis, one of the most common foodborne illnesses worldwide. Here, we report the development of RAA-exo-probe and RAA-CRIPSR/Cas12a assays for the detection of C. jejuni in food samples. The two assays were found to be highly specific to C. jejuni and highly sensitive, as they were one log more sensitive compared to the traditional culture method, with detection thresholds of 9 and 5 copies per reaction, respectively. These assays successfully detected C. jejuni in spiked chicken samples and natural meat samples (chicken, beef, mutton, etc.) and were overall less dependent on expensive equipment, only requiring a fluorescent reader. Their ease of use compared to other nucleic acid amplification-based methods indicates that these assays could be adapted for the rapid, routine surveillance of C. jejuni contamination in food samples, particularly for work done in the field or poorly equipped labs.

A field-deployable diagnostic assay for the visual detection of misfolded prions

Diagnostic tools for the detection of protein-misfolding diseases (i.e., proteopathies) are limited. Gold nanoparticles (AuNPs) facilitate sensitive diagnostic techniques via visual color change for the identification of a variety of targets. In parallel, recently developed quaking-induced conversion (QuIC) assays leverage protein-amplification and fluorescent signaling for the accurate detection of misfolded proteins. Here, we combine AuNP and QuIC technologies for the visual detection of amplified misfolded prion proteins from tissues of wild white-tailed deer infected with chronic wasting disease (CWD), a prion disease of cervids. Our newly developed assay, MN-QuIC, enables both naked-eye and light-absorbance measurements for detection of misfolded prions. MN-QuIC leverages basic laboratory equipment that is cost-effective and portable, thus facilitating real-time prion diagnostics across a variety of settings. In addition to laboratory-based tests, we deployed to a rural field-station in southeastern Minnesota and tested for CWD on site. We successfully demonstrated that MN-QuIC is functional in a non-traditional laboratory setting by performing a blinded analysis in the field and correctly identifying all CWD positive and CWD not-detected deer at the field site in 24 h, thus documenting the portability of the assay. White-tailed deer tissues used to validate MN-QuIC included medial retropharyngeal lymph nodes, parotid lymph nodes, and palatine tonsils. Importantly, all of the white-tailed deer (n = 63) were independently tested using ELISA, IHC, and/or RT-QuIC technologies and results secured with MN-QuIC were 95.7% and 100% consistent with these tests for positive and non-detected animals, respectively. We hypothesize that electrostatic forces help govern the AuNP/prion interactions and conclude that MN-QuIC has great potential for sensitive, field-deployable diagnostics for CWD, with future potential diagnostic applications for a variety of proteopathies.

Colorimetric Systems for the Detection of Bacterial Contamination: Strategy and Applications

Bacterial contamination is a public health concern worldwide causing enormous social and economic losses. For early diagnosis and adequate management to prevent or treat pathogen-related illnesses, extensive effort has been put into the development of pathogenic bacterial detection systems. Colorimetric sensing systems have attracted increasing attention due to their simple and single-site operation, rapid signal readout with the naked eye, ability to operate without external instruments, portability, compact design, and low cost. In this article, recent trends and advances in colorimetric systems for the detection and monitoring of bacterial contamination are reviewed. This article focuses on pathogen detection strategies and technologies based on reaction factors that affect the color change for visual readout. Reactions used in each strategy are introduced by dividing them into the following five categories: external pH change-induced pH indicator reactions, intracellular enzyme-catalyzed chromogenic reactions, enzyme-like nanoparticle (NP)-catalyzed substrate reactions, NP aggregation-based reactions, and NP accumulation-based reactions. Some recently developed colorimetric systems are introduced, and their challenges and strategies to improve the sensing performance are discussed.

State of the art: Lateral flow assays toward the point-of-care foodborne pathogenic bacteria detection in food samples

Diverse chemicals and some physical phenomena recently introduced in nanotechnology have enabled scientists to develop useful devices in the field of food sciences. Concerning such developments, detecting foodborne pathogenic bacteria is now an important issue. These kinds of bacteria species have demonstrated severe health effects after consuming foods and high mortality related to acute cases. The most leading path of intoxication and infection has been through food matrices. Hence, quick recognition of foodborne bacteria agents at low concentrations has been required in current diagnostics. Lateral flow assays (LFAs) are one of the urgent and prevalently applied quick recognition methods that have been settled for recognizing diverse types of analytes. Thus, the present review has stressed on latest developments in LFAs-based platforms to detect various foodborne pathogenic bacteria such as Salmonella, Listeria, Escherichia coli, Brucella, Shigella, Staphylococcus aureus, Clostridium botulinum, and Vibrio cholera. Proper prominence has been given on exactly how the labels, detection elements, or procedures have affected recent developments in the evaluation of diverse bacteria using LFAs. Additionally, the modifications in assays specificity and sensitivity consistent with applied food processing techniques have been discussed. Finally, a conclusion has been drawn for highlighting the main challenges confronted through this method and offered a view and insight of thoughts for its further development in the future.

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

The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

Integration of a Thermoelectric Heating Unit with Ionic Wind-Induced Droplet Centrifugation Chip to Develop Miniaturized Concentration Device for Rapid Determination of Salmonella on Food Samples Using Antibody-Functionalized SERS Tags

When a centrifugation-enriched sample of 100 μL containing the surface-enhanced Raman scattering (SERS) tag-bound bacteria (Salmonella in this study) is siphoned onto a glass slide next to an embedded thermoelectric heating chip, such a sessile droplet is quickly evaporated. As the size of the sample droplet is significantly reduced during the heating process, ionic wind streams from a corona discharge needle, stationed above the sample, sweep across the liquid surface to produce centrifugal vortex flow. Tag-bound Salmonella in the sample are then dragged and trapped at the center of droplet bottom. Finally, when the sample is dried, unlike the "coffee ring" effect, the SERS tag-bound Salmonella is concentrated in one small spot to allow sensitive detection of a Raman signal. Compared with our previous electrohydrodynamic concentration device containing only a corona discharge needle, this thermoelectric evaporation-assisted device is more time-effective, with the time of concentrating and drying about 100 μL sample reduced from 2 h to 30 min. Hence, sample throughput can be accelerated with this device for practical use. It is also more sensitive, with SERS detection of a few cells of Salmonella in neat samples achievable. We also evaluated the feasibility of using this device to detect Salmonella in food samples without performing the culturing procedures. Having spiked a few Salmonella cells into ice cubes and lettuce leaves, we use filtration and ultracentrifugation steps to obtain enriched tag-bound Salmonella samples of 200 μL. After loading an aliquot of 100 μL of sample onto this concentration device, the SERS tag signals from samples of 100 g ice cubes containing two Salmonella cells and 20 g lettuce leaf containing 5 Salmonella cells can be successfully detected.

Point-of-Need Diagnostics for Foodborne Pathogen Screening

Foodborne illness is a major public health issue that results in millions of global infections annually. The burden of such illness sits mostly with developing countries, as access to advanced laboratory equipment and skilled lab technicians, as well as consistent power sources, is limited and expensive. Current gold standards in foodborne pathogen screening involve labor-intensive sample enrichment steps, pathogen isolation and purification, and costly readout machinery. Overall, time to detection can take multiple days, excluding the time it takes to ship samples to off-site laboratories. Efforts have been made to simplify the workflow of such tests by integrating multiple steps of foodborne pathogen screening procedures into a singular device, as well as implementing more point-of-need readout methods. In this review, we explore recent advancements in developing point-of-need devices for foodborne pathogen screening. We discuss the detection of surface markers, nucleic acids, and metabolic products using both paper-based and microfluidic devices, focusing primarily on developments that have been made between 2015 and mid-2020.

Lateral flow fluorescent immunoassay based on isothermal amplification for rapid quantitative detection of Salmonella spp

Salmonella spp. are zoonotic pathogens of substantial public health concern. To enable detection in the field or under instrument-free conditions, we developed a rapid and robust lateral flow fluorescent immunoassay based on strand exchange amplification (SEA-LFIA) for the quantitative detection of Salmonella spp. As far as we know, this work is the first report regarding the use of Bst DNA polymerase-assisted SEA for fluorescence sensing to detect Salmonella spp. The SEA method was further confirmed by enzymatic digestion and Sanger dideoxy sequencing. The specificity of SEA-LFIA assay was verified by 89 Salmonella strains (18 Salmonella reference strains and 71 clinical isolates) and 15 non-Salmonella reference strains (different genera). The sensitivity of SEA-LFIA assay was 6 × 10⁰ CFU mL^-1 of Salmonella pure culture or 3 × 10⁴ CFU 25 g^-1 of artificially spiked raw chicken meat. Using this assay, it was found that 37 (16%) of the 236 samples collected were positive, which was consistent with the results of conventional PCR. The cutoff value is 15 and SEA-LFIA assay only takes ∼30 min without high equipment and reagent cost. In addition, the proposed strategy can be easily extended by redesigning the corresponding amplification primers to detect target analytes. In conclusion, the optimized SEA-LFIA assay is an efficient and specific method for the detection of Salmonella spp., and can potentially serve as a new on-site diagnostic tool in life sciences.

Single and multiple detections of foodborne pathogens by gold nanoparticle assays

A late detection of pathogenic microorganisms in food and drinking water has a high potential to cause adverse health impacts in those who have ingested the pathogens. For this reason there is intense interest in developing precise, rapid and sensitive assays that can detect multiple foodborne pathogens. Such assays would be valuable components in the campaign to minimize foodborne illness. Here, we discuss the emerging types of assays based on gold nanoparticles (GNPs) for rapidly diagnosing single or multiple foodborne pathogen infections. Colorimetric and lateral flow assays based on GNPs may be read by the human eye. Refractometric sensors based on a shift in the position of a plasmon resonance absorption peak can be read by the new generation of inexpensive optical spectrometers. Surface-enhanced Raman spectroscopy and the quartz microbalance require slightly more sophisticated equipment but can be very sensitive. A wide range of electrochemical techniques are also under development. Given the range of options provided by GNPs, we confidently expect that some, or all, of these technologies will eventually enter routine use for detecting pathogens in food. This article is categorized under: Diagnostic Tools > Biosensing.

Single enzyme-based stem-loop and linear primers co-mediated exponential amplification of short gene sequences

Isothermal DNA amplification only using a Bacillus stearothermophilus (Bst) DNA polymerase such as loop-mediated isothermal amplification typically entails multiple target sites for primer design and is thereby not suited for the amplification of short gene sequences, for example, the sequences with size below 200 nucleotides (nt). Here we present SLIMP, a novel single enzyme-based isothermal amplification of short gene sequence mediated by both stem-loop and linear primers. In SLIMP, a pair of stem-loop primers and a pair of linear primers are specifically designed to recognize only two target sites. Linear primers in SLIMP are similar as conventional PCR primers, but stem-loop primers are the modified linear primers through attaching a stem-loop structure at their 5'-ends. Attributed to this unique primer design, three basic reaction modes including linear-priming, single stem-loop-priming, and double stem-loop-priming amplifications co-mediate the SLIMP process under the function of Bst DNA polymerase. As a proof-of-concept assay, a synthetic 80 nt sequence from hepatitis B virus S gene was used as the template to develop SLIMP. On performance, SLIMP detection possesses high sensitivity and specificity, good selectivity, and the potential for analysing real sample. Therefore, SLIMP is expected as a novel alternative to amplify short gene sequences using a single enzyme.

Detection of a microbial source tracking marker by isothermal helicase-dependent amplification and a nucleic acid lateral-flow strip test

Over the last decades, various PCR-based methods have been proposed that can identify sources of faecal pollution in environmental waters. These microbial source tracking (MST) methods are powerful tools to manage water quality and support public health risk assessment. However, their application is limited by the lack of specialized equipment and trained personnel in laboratories performing microbiological water quality assessment. Here, we describe a novel molecular method that combines helicase-dependent amplification (HDA) with a strip test for detecting ruminant faecal pollution sources. Unlike quantitative PCR (qPCR), the developed HDA-strip assay only requires a heating block to amplify the ruminant-associated Bacteroidetes 16S rRNA marker (BacR). Following HDA, the reaction mixture can be directly applied onto the test strip, which detects and displays the amplification products by marker-specific hybridization probes via an on-strip colorimetric reaction. The entire assay takes two hours and demands no extensive practical training. Furthermore, the BacR HDA-strip assay achieved comparable results in head-to-head performance tests with the qPCR reference, in which we investigated source-sensitivity and source-specificity, the analytical limit of detection, and the sample limit of detection. Although this approach only yields qualitative results, it can pave a way for future simple-to-use MST screening tools.

Invited review: Advancements in lateral flow immunoassays for screening hazardous substances in milk and milk powder

Dairy-related food safety outbreaks, such as food-borne pathogen contamination, mycotoxin contamination, and veterinary drug contamination, sometimes happen and have been reported all over the world, affecting human health and, in some cases, leading to death. Thus, rapid yet robust detection methods are needed to monitor milk and milk powder for the presence of hazardous substances. The lateral flow immunoassay (LFI) is widely used in onsite testing because of its rapidity, simplicity, and convenience. In this review, we describe some traditional LFI used to detect hazardous substances in milk and milk powder. Furthermore, we discuss recent advances in LFI that aim to improve sensitivity or detection efficiency. These advances include the use of novel label materials, development of signal amplification systems, design of multiplex detection systems, and the use of nucleic acid-based LFI.

Development of rapid dipstick assay for food pathogens, Salmonella, by optimized parameters

Salmonella is among the very important pathogens threating the human and animal health. Rapid and easy detection of these pathogens is crucial. In this context, antibody (Ab) based lateral flow assays (LFAs) which are simple immunochromatographic point of care test kits were developed by gold nanoparticles (GNPs) as labelling agent for Salmonella detection. For that purpose some critical parameters such as reagent concentrations on the capture zones, conjugate concentrations and ideal membrane type needed for LFAs for whole cell detection were tested for naked eye analysis. Therefore, prepared LFAs were applied to the live and heat inactivated cells when they were used alone or included in different bacterial mixtures. Among the test platforms, membrane 180 (M180) was found as an ideal membrane and 36 nm GNPs showed highly good labelling in the developed LFAs. Diluted conjugates and low concentrations of reagents affected the test signal negatively. Salmonella was detected in different bacterial mixtures, selectively in 4-5 min. The best recognized species by used Ab were S. enteritidis and S. infantis. 5 × 105 S. typhimurium cells were also determined as a limit of detection of this study with mentioned parameters.

A one-pot, isothermal DNA sample preparation and amplification platform utilizing aqueous two-phase systems

Infectious diseases remain one of the major causes of death worldwide in developing countries. While screening via conventional polymerase chain reaction (PCR) is the gold standard in laboratory testing, its limited applications at the point-of-care have prompted the development of more portable nucleic acid detection systems. These include isothermal DNA amplification techniques, which are less equipment-intensive than PCR. Unfortunately, these techniques still require extensive sample preparation, limiting user accessibility. In this study, we introduce a novel system that combines thermophilic helicase-dependent amplification (tHDA) with a Triton X-100 micellar aqueous two-phase system (ATPS) to achieve cell lysis, lysate processing, and enhanced nucleic acid amplification in a simple, one-step process. The combined one-pot system was able to amplify and detect a target gene from whole-cell samples containing as low as 10² cfu/mL, and is the first known application of ATPSs to isothermal DNA amplification. This system's ease-of-use and sensitivity underlie its potential as a point-of-care diagnostic platform to detect for infectious diseases. Graphical abstract ᅟ.

Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection

Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed.

Graphical Abstract