Ensuring accuracy in the development and application of nucleic acid amplification tests (NAATs) for infectious disease

Diagnostic tests were heralded as crucial during the Coronavirus disease (COVID-19) pandemic with most of the key methods using bioanalytical approaches that detected larger molecules (RNA, protein antigens or antibodies) rather than conventional clinical biochemical techniques. Nucleic Acid Amplification Tests (NAATs), like the Polymerase Chain Reaction (PCR), and other molecular methods, like sequencing (that often work in combination with NAATs), were essential to the diagnosis and management during COVID-19. This was exemplified both early in the pandemic but also later on, following the emergence of new genetic SARS-CoV-2 variants. The 100 day mission to respond to future pandemic threats highlights the need for effective diagnostics, therapeutics and vaccines. Of the three, diagnostics represents the first opportunity to manage infectious diseases while also being the most poorly supported in terms of the infrastructure needed to demonstrate effectiveness. Where performance targets exist, they are not well served by consensus on how to demonstrate they are being met; this includes analytical factors such as limit of detection (LOD) false positive results as well as how to approach clinical evaluation. The selection of gold standards or use of epidemiological factors such as predictive value, reference ranges or clinical thresholds are seldom correctly considered. The attention placed on molecular diagnostic tests during COVID-19 illustrates important considerations and assumptions on the use of these methods for infectious disease diagnosis and beyond. In this manuscript, we discuss state-of-the-art approaches to diagnostic evaluation and explore how they may be better tailored to diagnostic techniques like NAATs to maximise the impact of these highly versatile bioanalytical tools, both generally and during future outbreaks.

Double-Tube Multiplex TaqMan Real-Time PCR for the Detection of Eight Animal-Derived Dairy Ingredients

Milk and dairy products represent important sources of nutrition in our daily lives. The identification of species within dairy products holds importance for monitoring food adulteration and ensuring traceability. This study presented a method that integrated double-tube and duplex real-time polymerase chain reaction (PCR) with multiplex TaqMan probes to enable the high-throughput detection of animal-derived ingredients in milk and dairy products. The detection system utilized one pair of universal primers, two pairs of specific primers, and eight animal-derived specific probes for cow, buffalo, goat, sheep, camel, yak, horse, and donkey. These components were optimized within a double-tube and four-probe PCR multiplex system. The developed double-tube detection system could simultaneously identify the above eight targets with a detection limit of 10-0.1 pg/μL. Validation using simulated adulterated milk samples demonstrated a detection limit of 0.1%. The primary advantage of this method lies in the simplification of the multiplex quantitative real-time PCR (qPCR) system through the use of universal primers. This method provides an efficient approach for detecting ingredients in dairy products, providing powerful technical support for market supervision.

Meat Authenticity Made Easy: DNA Extraction-Free Rapid Onsite Detection of Duck and Pork Ingredients in Beef and Lamb Using Dual-Recombinase-Aided Amplification and Multiplex Lateral Flow Strips

Meat adulteration is a major global concern that poses a threat to public health and consumer rights. However, current detection techniques, such as quantitative polymerase chain reaction (qPCR) and gas chromatography-mass spectrometry, are time-consuming and require sophisticated equipment. In this study, we developed a rapid onsite identification method for animal-derived ingredients by utilizing a fast nucleic acid lysis buffer to expedite the release of sample nucleic acids and combined it with dual-recombinase-aided amplification (dual-RAA) technology and visual multiplex lateral flow strips (MLFSs). Our method successfully detected duck- and bovine-derived, porcine- and bovine-derived, duck- and ovine-derived, and porcine- and ovine-derived meat in a rapid 20 min onsite detection assay, with a detection limit of 101 copies/50 μL reaction system for target genes. Moreover, our method accurately detected adulterated meat with proportions as low as 1:999. These findings have significant implications for food safety and the protection of consumer rights.

Design, Fabrication, and Applications of SERS Substrates for Food Safety Detection: Review

Sustainable and safe food is an important issue worldwide, and it depends on cost-effective analysis tools with good sensitivity and reality. However, traditional standard chemical methods of food safety detection, such as high-performance liquid chromatography (HPLC), gas chromatography (GC), and tandem mass spectrometry (MS), have the disadvantages of high cost and long testing time. Those disadvantages have prevented people from obtaining sufficient risk information to confirm the safety of their products. In addition, food safety testing, such as the bioassay method, often results in false positives or false negatives due to little rigor preprocessing of samples. So far, food safety analysis currently relies on the enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), HPLC, GC, UV-visible spectrophotometry, and MS, all of which require significant time to train qualified food safety testing laboratory operators. These factors have hindered the development of rapid food safety monitoring systems, especially in remote areas or areas with a relative lack of testing resources. Surface-enhanced Raman spectroscopy (SERS) has emerged as one of the tools of choice for food safety testing that can overcome these dilemmas over the past decades. SERS offers advantages over chromatographic mass spectrometry analysis due to its portability, non-destructive nature, and lower cost implications. However, as it currently stands, Raman spectroscopy is a supplemental tool in chemical analysis, reinforcing and enhancing the completeness and coverage of the food safety analysis system. SERS combines portability with non-destructive and cheaper detection costs to gain an advantage over chromatographic mass spectrometry analysis. SERS has encountered many challenges in moving toward regulatory applications in food safety, such as quantitative accuracy, poor reproducibility, and instability of large molecule detection. As a result, the reality of SERS, as a screening tool for regulatory announcements worldwide, is still uncommon. In this review article, we have compiled the current designs and fabrications of SERS substrates for food safety detection to unify all the requirements and the opportunities to overcome these challenges. This review is expected to improve the interest in the sensing field of SERS and facilitate the SERS applications in food safety detection in the future.

Sulfated fucan could serve as a species marker of sea cucumber with endo-1,3-fucanase as the essential tool

In the past few decades, sulfated fucan from sea cucumber had attracted considerable interest owing to its abundant physiological activities. Nevertheless, its potential for species discrimination had not been investigated. Herein, particular attention was given to sea cucumber Apostichopus japonicus, Acaudina molpadioides, Holothuria hilla, Holothuria tubulosa, Isostichopus badionotus and Thelenota ananas to examine the feasibility of sulfated fucan as a species marker of sea cucumber. The enzymatic fingerprint suggested that sulfated fucan exhibited significant interspecific discrepancy and intraspecific stability, which revealed that sulfated fucan could serve as the species marker of sea cucumber, by utilizing the overexpressed endo-1,3-fucanase Fun168A and the ultra-performance liquid chromatography-high resolution mass spectrum. Moreover, oligosaccharide profile of sulfated fucan was determined. The oligosaccharide profile combined with hierarchical clustering analysis and principal components analysis further confirmed that sulfated fucan could serve as a marker with a satisfying performance. Besides, load factor analysis showed that the minor structure of sulfated fucan also contributed to the sea cucumber discrimination, besides the major structure. The overexpressed fucanase played an indispensable role in the discrimination, due to its specificity and high activity. The study would lead to a new strategy for species discrimination of sea cucumber based on sulfated fucan.

A next-generation sequencing approach for the detection of mixed species in canned tuna

Tuna cans are relevant seafood products for which mixtures of different tuna species are not allowed according to European regulations. In order to support the prevention of food fraud and mislabelling, a next-generation sequencing methodology based on mitochondrial cytochrome b and control region markers has been tested. Analyses of defined mixtures of DNA, fresh tissue and canned tissue revealed a qualitative and, to some extent, semiquantitative identification of tuna species. While the choice of the bioinformatic pipeline had no influence in the results (p = 0.71), quantitative differences occurred depending on the treatment of the sample, marker, species, and mixture (p < 0.01). The results revealed that matrix-specific calibrators or normalization models should also be used in NGS. The method represents an important step towards a semiquantitative method for routine control of this analytically challenging food matrix. Tests of commercial samples uncovered mixed species in some cans, being not in compliance with EU regulations.

An Overview on the Application of Chemometrics Tools in Food Authenticity and Traceability

The use of advanced chemometrics tools in food authenticity research is crucial for managing the huge amount of data that is generated by applying state-of-the-art analytical methods such as chromatographic, spectroscopic, and non-targeted fingerprinting approaches. Thus, this review article provides description, classification, and comparison of the most important statistical techniques that are commonly employed in food authentication and traceability, including methods for exploratory data analysis, discrimination, and classification, as well as for regression and prediction. This literature revision is not intended to be exhaustive, but rather to provide a general overview to non-expert readers in the use of chemometrics in food science. Overall, the available literature suggests that the selection of the most appropriate statistical technique is dependent on the characteristics of the data matrix, but combining complementary tools is usually needed for properly handling data complexity. In that way, chemometrics has become a powerful ally in facilitating the detection of frauds and ensuring the authenticity and traceability of foods.

Metrological framework to support accurate, reliable, and reproducible nucleic acid measurements

Nucleic acid analysis is used in many areas of life sciences such as medicine, food safety, and environmental monitoring. Accurate, reliable measurements of nucleic acids are crucial for maximum impact, yet users are often unaware of the global metrological infrastructure that exists to support these measurements. In this work, we describe international efforts to improve nucleic acid analysis, with a focus on the Nucleic Acid Analysis Working Group (NAWG) of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM). The NAWG is an international group dedicated to improving the global comparability of nucleic acid measurements; its primary focus is to support the development and maintenance of measurement capabilities and the dissemination of measurement services from its members: the National Metrology Institutes (NMIs) and Designated Institutes (DIs). These NMIs and DIs provide DNA and RNA measurement services developed in response to the needs of their stakeholders. The NAWG members have conducted cutting edge work over the last 20 years, demonstrating the ability to support the reliability, comparability, and traceability of nucleic acid measurement results in a variety of sectors.

Development of a Duck Genomic Reference Material by Digital PCR Platforms for the Detection of Meat Adulteration

Low-cost meat, such as duck, is frequently used to adulterate more expensive foods like lamb or beef in many countries. However, the lack of DNA-based reference materials has limited the quality control and detection of adulterants. Here, we report the development and validation of duck genomic DNA certified reference materials (CRMs) through the detection of the duck interleukin 2 (IL2) gene by digital PCR (dPCR) for the identification of duck meat in food products. The certified value of IL2 in CRMs was 5.78 ± 0.51 × 10³ copies/μL with extended uncertainty (coverage factor k = 2) based on IL2 quantification by eight independent collaborating laboratories. Quantification of the mitochondrial gene cytb revealed a concentration of 2.0 × 10⁶ copies/μL, as an information value. The CRMs were also used to determine the limit of detection (LOD) for six commercial testing kits, which confirmed that these kits meet or exceed their claimed sensitivity and are reliable for duck detection.

A review of Fourier Transform Infrared (FTIR) spectroscopy used in food adulteration and authenticity investigations

The increasing demand for food and the globalisation of the supply chain have resulted in a rise in food fraud, and recent high profile cases, such as the Chinese milk scandal in 2008 and the EU horsemeat scandal in 2013 have emphasised the vulnerability of the food supply system to adulteration and authenticity frauds. Fourier Transform Infrared (FTIR) spectroscopy is routinely used in cases of suspected food fraud as it offers a rapid, easy and reliable detection method for these investigations. In this review, we first present a brief summary of the concepts of food adulteration and authenticity as well as a discussion of the current legislation regarding these crimes. Thereafter, we give an extensive overview of FTIR as an analytical technique and the different foods where FTIR analysis has been employed for food fraud investigations as well as the subsequent multivariate data analyses that have been applied successfully to investigate the case of adulteration or authenticity. Finally, we give a critical discussion of the applications and limitations of FTIR, either as a standalone technique or incorporated in a test battery, in the fight against food fraud.

Exploring DNA quantity and quality from raw materials to botanical extracts

OBJECTIVES

The aim of this study was to explore the variability in DNA quality and quantity along a gradient of industrial processing of botanical ingredients from raw materials to extracts.

METHODS

A data matrix was assembled for 1242 botanical ingredient samples along a gradient of industrial processing commonly used in the Natural Health Product (NHP) industry. Multivariate statistics was used to explore dependant variables for quality and quantity. The success of attaining a positive DNA test result along a gradient of industrial processing was compared among four biotechnologies: DNA barcoding, NGS, Sanger sequencing and qPCR.

RESULTS

There was considerable variance in DNA quality and quantity among the samples, which could be interpreted along a gradient from raw materials with greater quantities (50-120 ng/μL) of DNA and longer DNA (400-500bp) sequences to extracts, which were characterized by lower quantities (0.1-10.0 ng/μL) and short fragments (50-150bp).

CONCLUSIONS

Targeted molecular diagnostic tests for species identity can be used in the NHP industry for raw and processed samples. Non-targeted tests or the use of NGS for any identity test needs considerable research and development and must be validated before it can be used in commercial operations as these methods are subject to considerable risk of false negative and positive results. Proper use of these tools can be used to ensure ingredient authenticity, and to avert adulteration, and contamination with plants that are a health concern. Lastly these tools can be used to prevent the exploitation of rare herbal species and the harvesting of native biodiversity for commercial purposes.

A rapid and reliable multiplex PCR assay for simultaneous detection of fourteen animal species in two tubes

A simple and rapid method for animal species identification to prevent food adulteration based on mitochondrial DNA using two independent multiplex polymerase chain reactions (PCRs) and microchip electrophoresis was developed. This method was designed to identify fourteen domestic animals (Group I: cattle, donkey, dog, fox, raccoon-dog, deer and horse; Group II: pig, sheep, goat, chicken, duck, cat and mouse) simultaneously using ten pairs of primers and three of which were degenerate primers. Sequences for species-specific primers were generated based on mitochondrial genes, including 12S rRNA, 16S rRNA, ND2 and CO I. This method was validated in terms of the specificity, sensitivity and practicability, and the developed multiplex PCR method was able to correctly identify animal species of raw meats and processed meat products. The detection limits of two multiplex PCRs were 0.02 ng DNA for animal species in Group I and 0.2 ng DNA for Group II, respectively.

Food Tracking Perspective: DNA Metabarcoding to Identify Plant Composition in Complex and Processed Food Products

One of the main goals of the quality control evaluation is to identify contaminants in raw material, or contamination after a food is processed and before it is placed on the market. During the treatment processes, contamination, both accidental and economically motivated, can generate incongruence between declared and real composition. In our study, we evaluated if DNA metabarcoding is a suitable tool for unveiling the composition of processed food, when it contains small trace amounts. We tested this method on different types of commercial plant products by using tnrL marker and we applied amplicon-based high-throughput sequencing techniques to identify plant components in different food products. Our results showed that DNA metabarcoding can be an effective approach for food traceability in different type of processed food. Indeed, the vast majority of our samples, we identified the species composition as the labels reported. Although some critical issues still exist, mostly deriving from the starting composition (i.e., variable complexity in taxa composition) of the sample itself and the different processing level (i.e., high or low DNA degradation), our data confirmed the potential of the DNA metabarcoding approach also in quantitative analyses for food composition quality control.

Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing

Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, real-time (SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan (JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing (CCS) reads belonging to the ITS2 and psbA-trnH regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.

Detection and dissemination of Toxoplasma gondii in experimentally infected calves, a single test does not tell the whole story

Background

Although the detection of Toxoplasma gondii in bovine tissues is rare, beef might be an important source of human infection. The use of molecular techniques, such as magnetic capture qPCR (MC-qPCR), in combination with the gold standard method for isolating the parasite (mouse bioassay), may increase the sensitivity of T. gondii detection in infected cattle. The risk of transmission of the parasite to humans from undercooked/raw beef is not fully known and further knowledge about the predilection sites of T. gondii within cattle is needed. In the current study, six Holstein Friesian calves (Bos taurus) were experimentally infected with 10⁶ T. gondii oocysts of the M4 strain and, following euthanasia (42 dpi), pooled tissues were tested for presence of the parasite by mouse bioassay and MC-qPCR.

Results

Toxoplasma gondii was detected by both MC-qPCR and mouse bioassay from distinct pools (100 g) of tissues comprising: liver, tongue, heart, diaphragm, semitendinosus (hindlimb), longissimus dorsi muscle (sirloin) and psoas major muscle (fillet). When a selection of individual tissues which had been used for mouse bioassay were examined by MC-qPCR, parasite DNA could only be detected from two animals, despite all calves showing seroconversion after infection.

Conclusions

It is apparent that one individual test will not provide an answer as to whether a calf harbours T. gondii tissue cysts. Although the calves received a known number of infectious oocysts and highly sensitive methods for the detection of the parasite within bovine tissues were applied (mouse bioassay and MC-qPCR), the results confirm previous studies which report low presence of viable T. gondii in cattle and no clear predilection site within bovine tissues.

Rapid Detection and Identification of Mycotoxigenic Fungi and Mycotoxins in Stored Wheat Grain

This study aimed to assess the occurrence of toxigenic fungi and mycotoxin contamination in stored wheat grains by using advanced molecular and analytical techniques. A multiplex polymerase chain reaction (PCR) strategy was established for rapid identification of mycotoxigenic fungi, and an improved analytical method was developed for simultaneous multi-mycotoxin determination in wheat grains by liquid chromatography-tandem mass spectrometry (LC/MS/MS) without the need for any clean-up. The optimized multiplex PCR method was highly specific in detecting fungal species containing species-specific and mycotoxin metabolic pathway genes. The method was applied for evaluation of 34 wheat grain samples collected from storage warehouses for the presence of mycotoxin-producing fungi, and a few samples were found positive for Fusarium and Aspergillus species. Further chemical analysis revealed that 17 samples contained mycotoxins above the level of detection, but only six samples were found to be contaminated over the EU regulatory limits with at least one mycotoxin. Aflatoxin B₁, fumonisins, and deoxynivalenol were the most common toxins found in these samples. The results showed a strong correlation between the presence of mycotoxin biosynthesis genes as analyzed by multiplex PCR and mycotoxin detection by LC/MS/MS. The present findings indicate that a combined approach might provide rapid, accurate, and sensitive detection of mycotoxigenic species and mycotoxins in wheat grains.

Electrochemical detection of magnetically-entrapped DNA sequences from complex samples by multiplexed enzymatic labelling: Application to a transgenic food/feed quantitative survey

Monitoring of genetically modified organisms in food and feed demands molecular techniques that deliver accurate quantitative results. Electrochemical DNA detection has been widely described in this field, yet most reports convey qualitative data and application in processed food and feed samples is limited. Herein, the applicability of an electrochemical multiplex assay for DNA quantification in complex samples is assessed. The method consists of the simultaneous magnetic entrapment via sandwich hybridisation of two DNA sequences (event-specific and taxon-specific) onto the surface of magnetic microparticles, followed by bienzymatic labelling. As proof-of-concept, we report its application in a transgenic food/feed survey where relative quantification (two-target approach) of Roundup Ready Soybean® (RRS) was performed in food and feed. Quantitative coupling to end-point PCR was performed and calibration was achieved from 22 and 243 DNA copies spanning two orders of magnitude for the event and taxon-specific sequences, respectively. We collected a total of 33 soybean-containing samples acquired in local supermarkets, four out of which were found to contain undeclared presence of genetically modified soybean. A real-time PCR method was used to verify these findings. High correlation was found between results, indicating the suitability of the proposed multiplex method for food and feed monitoring.

Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material

Digital PCR has become the emerging technique for the sequence-specific detection and quantification of nucleic acids for various applications. During the past years, numerous reports on the development of new digital PCR methods have been published. Maturation of these developments into reliable analytical methods suitable for diagnostic or other routine testing purposes requires their validation for the intended use. Here, the results of an in-house validation of a droplet digital PCR method are presented. This method is intended for the quantification of the absolute copy number concentration of a purified linearized plasmid in solution with a nucleic acid background. It has been investigated which factors within the measurement process have a significant effect on the measurement results, and the contribution to the overall measurement uncertainty has been estimated. A comprehensive overview is provided on all the aspects that should be investigated when performing an in-house method validation of a digital PCR method.