Ratoon Stunting Disease of Sugarcane: A Review Emphasizing Detection Strategies and Challenges

Sugarcane (Saccharum hybrid) is an important cash crop grown in tropical and subtropical countries. Ratoon stunting disease (RSD), caused by a xylem-inhabiting bacterium, Leifsonia xyli subsp. xyli (Lxx) is one of the most economically significant diseases globally. RSD results in severe yield losses because its highly contagious nature and lack of visually identifiable symptoms make it harder to devise an effective management strategy. The efficacy of current management practices is hindered by implementation difficulties caused by lack of resources, high cost, and difficulties in monitoring. Rapid detection of the causal pathogen in vegetative planting material is crucial for sugarcane growers to manage this disease. Several microscopic, serological, and molecular-based methods have been developed and used for detecting the RSD pathogen. Although these methods have been used across the sugarcane industry worldwide to diagnose Lxx, some lack reliability or specificity, are expensive and time-consuming to apply, and most of all, are not suitable for on-farm diagnosis. In recent decades, there has been significant progress in the development of integrated isothermal amplification-based microdevices for accurate human and plant pathogen detection. There is a significant opportunity to develop a novel diagnostic method that integrates nanobiosensing with isothermal amplification within a microdevice format for accurate Lxx detection. In this review, we summarize (i) the historical background and current knowledge of sugarcane ratoon stunting disease, including some aspects related to transmission, pathosystem, and management practices; and (ii) the drawbacks of current diagnostic methods and the potential for application of advanced diagnostics to improve disease management.

Current and emerging trends in techniques for plant pathogen detection

Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.

Point-of-Care DNA Amplification for Disease Diagnosis and Management

Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.

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.

Development of a loop-mediated isothermal amplification method for the rapid detection of Venturia carpophila on peach

BACKGROUND

Peach scab, caused by Venturia carpophila, can significantly reduce both the yield and quality of peach fruit. It is difficult to distinguish peach scab from other peach diseases such as black spot and bacterial spot. An efficient assay is needed to identify V. carpophila in order to develop scientific management strategies.

RESULTS

A set of loop-mediated isothermal amplification (LAMP) primers was designed based on the internal transcribed spacer (rDNA-ITS) sequence to detect V. carpophila. Compared with the conventional polymerase chain reaction (PCR) method, the LAMP method not only exhibited higher sensitivity and specificity in the detection of V. carpophila, but also required simpler equipment and less operational time. The minimum detectable concentration of V. carpophila genomic DNA with the LAMP method was 56.6 fg μl^-1 , which was 100 times lower than with the conventional PCR method. When eight fungal species including V. carpophila (23 isolates from 14 provinces) and one bacterial species were used with LAMP detection, only V. carpophila showed a color change, from brown to yellowish green, and ladder-like bands in electrophoresis, indicating successful amplification. Moreover, when crude DNAs of peach fruit samples were used in LAMP detection, amplification was observed only from diseased fruits, and not from healthy fruits and the negative control.

CONCLUSION

The LAMP assay shows simplicity, rapidity, high sensitivity and specificity, and will be useful in distinguishing scab caused by Venturia carpophila from other diseases with similar symptoms. © 2020 Society of Chemical Industry.

Simplified formats of modern biosensors: 60 years of using immunochromatographic test systems in laboratory diagnostics

Immunochromatographic test systems known to foreign laboratory diagnostic experts as lateral flow immunoassay (LFIA) are simplified tape formats of modern biosensors. For 60 years, they have been widely used for the rapid detection of target molecules (ligands) in biosubstrates and the diagnosis of many diseases and conditions. The growing popularity of these test systems for providing medical care or diagnostics in developing countries, medical facilities, in emergency situations, as well as for individual home use by patients while monitoring their health are the main factors contributing to the continuous development and improvement of these methods, the emergence of a new generation of formats. The attractiveness and popularity of these fast, easy-to-use, inexpensive and portable diagnostic tools is associated primarily with their high analytical sensitivity and specificity, as well as the ease of interpretation of the results. These qualities have passed the test of time, and today LFIA test systems are fully consistent with the modern world concept of «point-of-care testing», finding wide application not only in medicine, but also in ecology, veterinary medicine, and agriculture. This review will highlight the modern principles of designing the most widely used formats of immunochromatographic test systems for clinical laboratory diagnostics, summarize the main advantages and disadvantages of the method, as well as current achievements and prospects of LFIA technology. Modern innovations aimed at improving the analytical characteristics of LFIA technology are interesting, promising and can bring additional benefits to immunochromatographic platforms that have gained popularity and attractiveness for six decades.

Six decades of lateral flow immunoassay: from determining metabolic markers to diagnosing COVID-19

Technologies based on lateral flow immunoassay (LFIA), known in some countries of the world as immunochromatographic tests, have been successfully used for the last six decades in diagnostics of many diseases and conditions as they allow rapid detection of molecular ligands in biosubstrates. The popularity of these diagnostic platforms is constantly increasing in healthcare facilities, particularly those facing limited budgets and time, as well as in household use for individual health monitoring. The advantages of these low-cost devices over modern laboratory-based analyzers come from their availability, opportunity of rapid detection, and ease of use. The attractiveness of these portable diagnostic tools is associated primarily with their high analytical sensitivity and specificity, as well as with the easy visual readout of results. These qualities explain the growing popularity of LFIA in developing countries, when applied at small hospitals, in emergency situations where screening and monitoring health condition is crucially important, and as well as for self-testing of patients. These tools have passed the test of time, and now LFIA test systems are fully consistent with the world's modern concept of ‘point-of-care testing’, finding a wide range of applications not only in human medicine, but also in ecology, veterinary medicine, and agriculture. The extensive opportunities provided by LFIA contribute to the continuous development and improvement of this technology and to the creation of new-generation formats. This review will highlight the modern principles of design of the most widely used formats of test-systems for clinical laboratory diagnostics, summarize the main advantages and disadvantages of the method, as well as the current achievements and prospects of the LFIA technology. The latest innovations are aimed at improving the analytical performance of LFIA platforms for the diagnosis of bacterial and viral infections, including COVID-19.

Development of lateral flow assay combined with recombinase polymerase amplification for highly sensitive detection of Dickeya solani

Dickeya solani, one of the most significant bacterial pathogens, infects potato plants, resulting in severe economic damage. In this study, a lateral flow assay (LFA) combined with isothermal DNA amplification was developed for rapid, specific, and sensitive diagnosis of the potato blackleg disease caused by D. solani. Recombinase polymerase amplification (RPA) was chosen for this purpose. Five primer pairs specific to different regions of the D. solani genome were designed and screened. A primer pair providing correct recognition of the target sequence was aligned with the SOL-C region specific to D. solani and flanked by fluorescein (forward primer) and biotin (reverse primer). Lateral flow test strips were constructed to detect DNA amplicons. The RPA-LFA demonstrated a detection limit equal to 14,000 D. solani colony-forming units per gram of potato tuber. This assay provided sensitivity corresponding to the polymerase chain reaction (PCR) but was implemented at a fixed temperature (39 °C) over 30 min. No unspecific reactions with Pectobacterium, Clavibacter, and other Dickeya species were observed. Detection of latent infection of D. solani in the potato tubers by the developed RPA-LFA was verified by PCR. The obtained results confirmed that RPA-LFA has great potential for highly sensitive detection of latent infection.