Single-tube nested real-time PCR as a new highly sensitive approach to trace hazelnut

Comparison of ordinary reverse transcription real-time polymerase chain reaction (qRT-PCR) with a newly developed one-step single-tube nested real-time RT-PCR (OSN-qRT-PCR) for sensitive detection of SARS-CoV-2 in wastewater

Wastewater monitoring has proven to be an important approach to detecting and controlling the development of the SARS-CoV-2 pandemic. Various tests based on reverse transcription real-time PCR (qRT-PCR) have been developed and used for the detection of SARS-CoV-2 in wastewater samples. In this study, we attempted to increase the sensitivity of qRT-PCR by developing a one-step single-tube nested qRT-PCR assay (OSN-qRT-PCR). Two variants were developed, oriented to nucleocapsid phosphoprotein gene (N) and to spike protein gene (S), respectively. The performance of conventional qRT-PCR assays oriented to these genes with two novel OSN-qRT-PCR assays were firstly optimized using wastewater artificially contaminated with two encapsidated RNA mimic systems harboring a portion either N or S gene (ENRM and ESRM, respectively). The assays were coupled to a polyethylene glycol-based RNA precipitation/extraction method and applied to detect SARS-CoV-2 in wastewater samples from four cities in Slovakia. Both novel OSN-qRT-PCR assays demonstrated higher detection rates than the ordinary qRT-PCR counterparts. The virus levels in the analyzed wastewater samples had a high or very high relation with the numbers of clinical cases in the monitored regions. In fact, correlation with a 3-, 4-, or 5-day temporal offset was revealed. The OSN-qRT-PCR assays demonstrated robustness, mainly in samples with low viral loads.

Quantitative Real-Time PCR for the Detection of Allergenic Species in Foods

Food allergy is an increasing challenge to public health, with widespread global distribution. With no cure for this pathology, the food-allergic individuals are forced to adopt food eviction measurements, relying on label information to avoid consuming the offending foods. To safeguard these individuals, the analytical methods based on real-time PCR approaches are currently faced as excellent tools to verify labeling compliance, aiding industry and regulatory agencies to efficiently manage food allergen control programs. Therefore, this chapter intends to describe a protocol of real-time PCR to analyze allergenic food species. For method development, the main steps to be considered are (i) in silico sequence analysis and primer/hydrolysis probe design, (ii) preparation of calibrators (model foods containing the allergenic ingredient), (iii) efficient DNA extraction from complex food matrices, (iv) amplification by real-time PCR with hydrolysis probe (90-200 bp) targeting a highly specific DNA region (allergen-encoding gene), (v) sequencing PCR products for identity confirmation, and (vi) validation and application to commercial foods. Herein, a real-time PCR approach for the detection and quantification of cashew nut as an allergenic food is described as an example protocol, including all the steps for method development and validation.

Single-tube nested real-time PCR versus normalised real-time PCR for the quantification of allergenic cashew nut in foods: Impact of thermal processing and matrix

In this work, three allergen-encoding genes (Ana o 1, Ana o 2, Ana o 3) were investigated for the detection of cashew nut as an allergenic food. Normalised and single-tube nested real-time PCR approaches targeting the Ana o 2 or Ana o 3 genes are proposed and compared. Normalised real-time PCR detected 10 pg, while single-tube nested real-time PCR achieved 1 pg of cashew nut DNA. Single-tube nested real-time PCR targeting Ana o 3 allowed the best relative sensitivities (10 mg/kg cashew nut in dough/biscuit), being successfully validated regarding precision/accuracy. The normalised real-time PCR did not show acceptable accuracy for both targets. Sensitivity of single-tube nested real-time PCR was affected by the matrix (pasta), but not by thermal processing (dough/biscuit). Herein, two highly sensitive and specific single-tube nested real-time PCR targeting allergen-encoding genes are proposed for the first time as quantitative/validated tools for cashew nut analysis as an allergenic food.

Identification of the hazelnut cultivar in raw kernels and in semi-processed and processed products

The request for an efficient traceability system able to identify hazelnut cultivars along the entire processing chain is becoming a critical point for avoiding fraudulent practices and safeguarding the interests of growers, food processors and consumers. In this study, DNA was extracted from different hazelnut matrices, including plant material (leaf, kernel and kernel episperm), and processed foods (paste, grain, flour and different types of snacks containing hazelnuts). The efficiency of Simple Sequence Repeat (SSR) markers was tested to identify the hazelnut cultivar ‘Tonda Gentile’ in all the supply chain. The analysis at 10 SSR loci was able to verify the presence/absence of the alleles of a declared cultivar contained in these matrices. The SSR analysis of DNA from raw episperm offers the possibility of identifying the mother cultivar and is suggested as an effective way to discover frauds since DNA analysis can be performed on individual kernels. For food matrices containing hazelnuts, the presence of the mother cultivar’s DNA can be assessed based on the identification of its alleles in the sample, although the presence of multiple alleles from the pollenizers makes the interpretation of results more difficult.

Molecularly imprinted polymer as a synthetic antibody for the biorecognition of hazelnut Cor a 14-allergen

Artificial receptors that mimic their natural biological counterparts have several advantages, such as lower production costs and increased shelf-life stability/versatility, while overcoming the ethical issues related to raising antibodies in animals. In this work, the proposed tailor-made molecularly imprinted polymer (MIP)-allergen receptors aimed at substituting or even transcending the performance of biological antibodies. For this purpose, a MIP was proposed as an artificial antibody for the recognition of hazelnut Cor a 14-allergen. The target protein was grafted onto the conducting polypyrrole receptor film using gold screen-printed electrodes (Au-SPE). The electrochemical assessment presented a linear response for the dynamic range of 100 fg mL^-1-1 μg mL^-1 and a LOD of 24.5 fg mL^-1, as determined by square wave voltammetry from the calibration curves prepared with standards diluted in phosphate buffer. Surface plasmon resonance (SPR) was used as a secondary transducer to evaluate the performance of the Cor a 14-MIP sensor, enabling a linear dynamic range of 100 fg mL^-1- 0.1 μg mL^-1 and a LOD of 18.1 fg mL^-1. The selectivity of the tailored-made Cor a 14-MIP was tested against potentially cross-reactive plant/animal species based on the rebinding affinity (Freundlich isotherm-K_F) of homologues/similar proteins, being further compared with custom-made polyclonal anti-Cor a 14 IgG immunosensor. Results evidenced that the MIP mimics the biorecognition of biological antibodies, presenting higher selectivity (only minor cross-reactivity towards walnut and Brazil nut 2S albumins) than the Cor a 14/anti-Cor a 14 IgG immunosensor. The application of electrochemical Cor a 14-MIP sensor to model mixtures of hazelnut in pasta enabled quantifying hazelnut down to 1 mg kg^-1 (corresponding to 0.16 mg kg^-1 of hazelnut protein in the matrix). To the best of our knowledge, Cor a 14-MIP is the first sensor based on an artificial/synthetic biorecognition platform for the specific detection of hazelnut allergens, while presenting high-performance parameters with demonstrated application in food safety management.

Whey allergens: Influence of nonthermal processing treatments and their detection methods

Whey and its components are recognized as value-added ingredients in infant formulas, beverages, sports nutritious foods, and other food products. Whey offers opportunities for the food industrial sector to develop functional foods with potential health benefits due to its unique physiological and functional attributes. Despite all the above importance, the consumption of whey protein (WP) can trigger hypersensitive reactions and is a constant threat for sensitive individuals. Although avoiding such food products is the most successful approach, there is still a chance of incorrect labeling and cross-contamination during food processing. As whey allergens in food products are cross-reactive, the phenomenon of homologous milk proteins of various species may escalate to a more serious problem. In this review, nonthermal processing technologies used to prevent and eliminate WP allergies are presented and discussed in detail. These processing technologies can either enhance or mitigate the impact of potential allergenicity. Therefore, the development of highly precise analytical technologies to detect and quantify the existence of whey allergens is of considerable importance. The present review is an attempt to cover all the updated approaches used for the detection of whey allergens in processed food products. Immunological and DNA-based assays are generally used for detecting allergenic proteins in processed food products. In addition, mass spectrometry is also employed as a preliminary technique for detection. We also highlighted the latest improvements in allergen detection toward biosensing strategies particularly immunosensors and aptasensors.

Persistence of Xanthomonas campestris pv. campestris in Field Soil in Central Europe

Xanthomonas campestris pv. campestris (Xcc) is a bacterium that causes black rot of crucifers. The greatest losses of brassica crop production usually result from seed-borne infection, but carry-over of inoculum in field soil may also be possible. The aim of this study was to monitor persistence of Xcc in field soil in central Europe using a conventional PCR assay with hrpF primers and a two-step nested real-time PCR assay using Zur primers. The work has demonstrated that nested real-time PCR can be used to improve the analytical sensitivity for detection of Xcc in soil compared to conventional PCR, and that Xcc may persist in soil for up to two years following an infected brassica crop in central European climatic conditions.

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry

Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.

Application of real-time PCR for tree nut allergen detection in processed foods

Currently, food allergies are an important health concern worldwide. The presence of undeclared allergenic ingredients or the presence of traces of allergens due to accidental contamination during food processing poses a great health risk to sensitized individuals. Therefore, reliable analytical methods are required to detect and identify allergenic ingredients in food products. Real-time PCR allowed a specific and accurate amplification of allergen sequences. Some processing methods could induce the fragmentation and/or degradation of genomic DNA and some studies have been performed to analyze the effect of processing on the detection of different targets, as thermal treatment, with and without applying pressure. In this review, we give an updated overview of the applications of real-time PCR for the detection of allergens of tree nut in processed food products. The different variables that contribute to the performance of PCR methodology for allergen detection are also review and discussed.

Development of a single-tube nested PCR-lateral flow biosensor assay for rapid and accurate detection of Alternaria panax Whetz

Alternaria panax Whetz causes one of the most commonly occurring and serious diseases in ginseng cultivation, and may cause significant production and economic losses in the ginseng industry. Rapid, early, and accurate identification of Alternaria panax Whetz is an essential prerequisite for the effective prevention and control of further infection spread. In this work, a rapid and accurate molecular diagnostic method, a single-tube nested PCR-lateral flow biosensor assay (STNPCR-LFBA), was developed for rapid identification of Alternaria panax Whetz. The STNPCR-LFBA was 100 times more sensitive than the traditional PCR-LFBA. Besides that, the PCR product was checked by a lateral flow biosensor assay, which provided a basis for the migration of the detection technology to a point-of-care test (POCT) format. STNPCR-LFBA was specific to Alternaria panax Whetz, and no cross-reactions were observed in other non-target samples; the limit of detection was up to 0.01 pg of Alternaria panax Whetz genomic DNA. STNPCR-LFBA could also be used for specific identification of Alternaria panax Whetz in real samples. STNPCR-LFBA is useful for identifying Alternaria panax Whetz due to its rapidity, accuracy, and simple manipulation.

Highly Sensitive Detection of Bovine β-Lactoglobulin with Wide Linear Dynamic Range Based on Platinum Nanoparticles Probe

Cow's milk allergy is one of the most frequent and severe IgE-induced food allergies for children, demanding sensitive analytical methods, and β-lactoglobulin (BLG) can be as an important biomarker for detection of milk protein. In this study, a highly sensitive sandwich enzyme-linked immunosorbent assay (sELISA) based on a specific polyclonal antibody against human IgE linear epitopes of BLG and an anti-BLG polyclonal antibody-platinum nanoparticles probe was described for detection of BLG. This sELISA exhibited an ultrawide linear range of 0.49-1.6 × 10⁴ ng/mL, covering more than four orders of magnitude. The limit of detection was 0.12 ng/mL, which was 16-fold lower than that using traditional sELISA with the same antibodies. Furthermore, the proposed approach showed high recoveries (93.53%-111.95%) and low coefficient of variation (1.49%-12.50%) after analysis of samples fortified with BLG. The presence of allergenic BLG residues also could be detected in partially hydrolyzed infant formulas. These results, in comparison with conventional and commercial BLG detection sELISAs, highlight that this proposed sELISA could be a reliable and user-friendly tool to monitor trace amounts of BLG and its potentially allergenic residues in foods.

Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis

Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb) in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM), but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST), was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC) microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation.

A Rapid Assay to Detect Toxigenic Penicillium spp. Contamination in Wine and Musts

Wine and fermenting musts are grape products widely consumed worldwide. Since the presence of mycotoxin-producing fungi may greatly compromise their quality characteristics and safety, there is an increasing need for relatively rapid "user friendly" quantitative assays to detect fungal contamination both in grapes delivered to wineries and in final products. Although other fungi are most frequently involved in grape deterioration, secondary infections by Penicillium spp. are quite common, especially in cool areas with high humidity and in wines obtained by partially dried grapes. In this work, a single-tube nested real-time PCR approach-successfully applied to hazelnut and peanut allergen detection-was tested for the first time to trace Penicillium spp. in musts and wines. The method consisted of two sets of primers specifically designed to target the β-tubulin gene, to be simultaneously applied with the aim of lowering the detection limit of conventional real-time PCR. The assay was able to detect up to 1 fg of Penicillium DNA. As confirmation, patulin content of representative samples was determined. Most of analyzed wines/musts returned contaminated results at >50 ppb and a 76% accordance with molecular assay was observed. Although further large-scale trials are needed, these results encourage the use of the newly developed method in the pre-screening of fresh and processed grapes for the presence of Penicillium DNA before the evaluation of related toxins.

Development of a rapid and sensitive one-step reverse transcription-nested polymerase chain reaction in a single tube using the droplet-polymerase chain reaction machine

BACKGROUND

Reverse transcription (RT)-nested polymerase chain reaction (PCR) is a time-consuming procedure because it has several handling steps and is associated with the risk of cross-contamination during each step. Therefore, a rapid and sensitive one-step RT-nested PCR was developed that could be performed in a single tube using a droplet-PCR machine.

METHODS

The K562 BCR-ABL mRNA-positive cell line as well as bone marrow aspirates from 5 patients with chronic myelogenous leukemia (CML) and 5 controls without CML were used. We evaluated one-step RT-nested PCR using the droplet-PCR machine.

RESULTS

One-step RT-nested PCR performed in a single tube using the droplet-PCR machine enabled the detection of BCR-ABL mRNA within 40min, which was 10(3)-fold superior to conventional RT nested PCR using three steps in separate tubes. The sensitivity of the one-step RT-nested PCR was 0.001%, with sample reactivity comparable to that of the conventional assay.

CONCLUSIONS

One-step RT-nested PCR was developed using the droplet-PCR machine, which enabled all reactions to be performed in a single tube accurately and rapidly and with high sensitivity. This one-step RT-nested PCR may be applicable to a wide spectrum of genetic tests in clinical laboratories.

Real-time PCR quantification of the plant growth promoting bacteria Herbaspirillum seropedicae strain SmR1 in maize roots

The plant growth promoting bacteria Herbaspirillum seropedicae SmR1 is an endophytic diazotroph found in several economically important crops. Considering that methods to monitor the plant-bacteria interaction are required, our objective was to develop a real-time PCR method for quantification of PGPB H. seropedicae in the rhizosphere of maize seedlings. Primer pairs were designed, and their specificity was verified using DNA from 12 different bacterial species. Ten standard curves of qPCR assay using HERBAS1 primers and tenfold serial dilutions of H. seropedicae SmR1 DNA were performed, and PCR efficiency of 91 % and correlation coefficient of 0.99 were obtained. H. seropedicae SmR1 limit of detection was 10(1) copies (corresponding to 60.3 fg of bacterial DNA). qPCR assay using HERBAS1 was used to detect and quantify H. seropedicae strain SmR1 in inoculated maize roots, cultivated in vitro and in pots, harvested 1, 4, 7, and 10 days after inoculation. The estimated bacterial DNA copy number per gram of root was in the range 10(7)-10(9) for plants grown in vitro and it was around 10(6) for plants grown in pots. Primer pair HERBAS1 was able to quantify H. seropedicae SmR1, and this assay can be useful for monitoring plant-bacteria interaction.

Quantitative detection of soybean in meat products by a TaqMan real-time PCR assay

In the present work, we propose a normalised real-time quantitative PCR assay to determine the addition of soybean to meat products. The method proved to be a powerful tool for the quantification of soybean protein (dry basis) in the range of 0.01% to 6%, being successfully in-house validated. Its application was effective in the analysis of several meat products, indicating 2% of non-compliance with the food allergen labelling legislation, and some inconsistencies when comparing the declared with estimated amounts of soybean. This work highlights the importance of efficient tools to assess labelling statements of meat products, avoiding fraudulent practices.

Analysis to support allergen risk management: Which way to go?

Food allergy represents an important food safety issue because of the potential lethal effects; the only effective treatment is the complete removal of the allergen involved from the diet. However, due to the growing complexity of food formulations and food processing, foods may be unintentionally contaminated via allergen-containing ingredients or cross-contamination. This affects not only consumers' well-being but also food producers and competent authorities involved in inspecting and auditing food companies. To address these issues, the food industry and control agencies rely on available analytical methods to quantify the amount of a particular allergic commodity in a food and thus to decide upon its safety. However, no "gold standard methods" exist for the quantitative detection of food allergens. Nowadays mostly receptor-based methods and in particular commercial kits are used in routine analysis. However, upon evaluation of their performances, commercial assays proved often to be unreliable in processed foods, attributed to the chemical changes in proteins that affect the molecular recognition with the receptor used. Unfortunately, the analytical outcome of other methods, among which are chromatographic combined with mass spectrometric techniques as well as DNA-based methods, seem to be affected in a comparable way by food processing. Several strategies can be employed to improve the quantitative analysis of allergens in foods. Nevertheless, issues related to extractability and matrix effects remain a permanent challenge. In view of the presented results, it is clear that the food industry needs to continue to make extra efforts to provide accurate labeling and to reduce the contamination with allergens to an acceptable level through the use of allergen risk management on a company level, which needs to be supported inevitably by a tailor-validated extraction and detection method.