Application of Recombinase Polymerase Amplification with Lateral Flow for a Naked-Eye Detection of Listeria monocytogenes on Food Processing Surfaces

Regenerative Food Innovation: The Role of Agro-Food Chain By-Products and Plant Origin Food to Obtain High-Value-Added Foods

Food losses in the agri-food sector have been estimated as representing between 30 and 80% of overall yield. The agro-food sector has a responsibility to work towards achieving FAO sustainable goals and global initiatives on responding to many issues, including climate pressures from changes we are experiencing globally. Regenerative agriculture has been discussed for many years in terms of improving our land and water. What we now need is a focus on the ability to transform innovation within the food production and process systems to address the needs of society in the fundamental arenas of food, health and wellbeing in a sustainable world. Thus, regenerative food innovation presents an opportunity to evaluate by-products from the agriculture and food industries to utilise these waste streams to minimise the global effects of food waste. The mini-review article aims to illustrate advancements in the valorisation of foods from some of the most recent publications published by peer-reviewed journals during the last 4-5 years. The focus will be applied to plant-based valorised food products and how these can be utilised to improve food nutritional components, texture, sensory and consumer perception to develop the foods for the future.

Application of MinION sequencing as a tool for the rapid detection and characterization of Listeria monocytogenes in smoked salmon

Microbial pathogens may be present in different types of foods, and hence the development of novel methods to assure consumers' safeness is of great interest. Molecular methods are known to provide sensitive and rapid results; however, they are typically targeted approaches. In recent years, the advent of non-targeted approaches based on next-generation sequencing (NGS) has emerged as a rational way to proceed. This technology allows for the detection of several pathogens simultaneously. Furthermore, with the same set of data, it is possible to characterize the microorganisms in terms of serotype, virulence, and/ or resistance genes, among other molecular features. In the current study, a novel method for the detection of Listeria monocytogenes based on the "quasimetagenomics" approach was developed. Different enrichment media and immunomagnetic separation (IMS) strategies were compared to determine the best approach in terms of L. monocytogenes sequences generated from smoked salmon samples. Finally, the data generated were analyzed with a user-friendly workflow that simultaneously provided the species identification, serotype, and antimicrobial resistance genes. The new method was thoroughly evaluated against a culture-based approach, using smoked salmon inoculated with L. monocytogenes as the matrix of choice. The sequencing method reached a very low limit of detection (LOD50, 1.2 CFU/ 25 g) along with high diagnostic sensitivity and specificity (100%), and a perfect correlation with the culture-based method (Cohen's k = 1.00). Overall, the proposed method overcomes all the major limitations reported for the implementation of NGS as a routine food testing technology and paves the way for future developments taking its advantage into consideration.

Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications

Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.

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.

Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens

Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.

Suitability of the MinION long read sequencer for semi-targeted detection of foodborne pathogens

Foodborne pathogens are still a significant source of morbidity and mortality worldwide. In addition to this the current methodologies to track these microorganisms cannot cope with the current intensive production systems, thus novel methods are of outmost importance. DNA-based methods have already demonstrated suitable to address this issue, but most of them are targeted methods such as real-time PCR (qPCR), meaning that one will only find what is looking for, thus taking the risk of missing relevant pathogens in a given sample. To overcome this limitation we have developed an easy-to-implement methodology which enables the detection of several pathogens simultaneously by using long-read Next Generation Sequencing (NGS) with MinION. The method was named "semi-targeted" due to the combination of a non-targeted detection method, NGS, with the usage of selective media in order to partially eliminate non-pathogenic interfering bacteria. To this end, we included an enrichment step for the recovery of different pathogens, namely Salmonella Enteritidis and Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7, after DNA extraction and library preparation, the samples were analyzed with MinION implementing the low-cost Flongle Flow Cells. The methodology was successfully evaluated in spiked milk samples with an excellent agreement with the results obtained by qPCR and culture-based methods. The method can provide accurate results after only 2 h of sequencing. Sample multiplexing, along with the lower cost of the Flongle Flow Cells and the reduced price of the MinION platform, make the assay cost-effective that is of importance for the food industry. Starting the method with a classical microbiological approach, the enrichment, the method is easy to implement in testing laboratories, it provides flexibility in terms of potential pathogens to be detected, and the positive results can be easily confirmed following culture-based, or other type, of confirmation procedures.

A Rapid and Sensitive Europium Nanoparticle-Based Lateral Flow Immunoassay Combined with Recombinase Polymerase Amplification for Simultaneous Detection of Three Food-Borne Pathogens

Food-borne pathogens have become an important public threat to human health. There are many kinds of pathogenic bacteria in food consumed daily. A rapid and sensitive testing method for multiple food-borne pathogens is essential. Europium nanoparticles (EuNPs) are used as fluorescent probes in lateral flow immunoassays (LFIAs) to improve sensitivity. Here, recombinase polymerase amplification (RPA) combined with fluorescent LFIA was established for the simultaneous and quantitative detection of Listeria monocytogenes, Vibrio parahaemolyticus, and Escherichia coliO157:H7. In this work, the entire experimental process could be completed in 20 min at 37 °C. The limits of detection (LODs) of EuNP-based LFIA–RPA were 9.0 colony-forming units (CFU)/mL for Listeria monocytogenes, 7.0 CFU/mL for Vibrio parahaemolyticus, and 4.0 CFU/mL for Escherichia coliO157:H7. No cross-reaction could be observed in 22 bacterial strains. The fluorescent LFIA–RPA assay exhibits high sensitivity and good specificity. Moreover, the average recovery of the three food-borne pathogens spiked in food samples was 90.9–114.2%. The experiments indicate the accuracy and reliability of the multiple fluorescent test strips. Our developed EuNP-based LFIA–RPA assay is a promising analytical tool for the rapid and simultaneous detection of multiple low concentrations of food-borne pathogens.