Nucleic acid amplification-based techniques for pathogen detection and identification

Reduction of background-triggered amplification in lesion-induced DNA amplification (LIDA)

Lesion-induced DNA amplification (LIDA) enables isothermal amplification of nucleic acids, and the only enzyme required is T4 DNA ligase. However, the application of LIDA for the amplification of trace amounts of nucleic acids has been hindered by the observed background-triggered amplification in the absence of the initial target due to a pseudo-blunt end ligation reaction of two of the primers. In this work, we have tested three approaches to minimize the background-triggered amplification: increasing and decreasing the concentration of salts such as NaCl and MgCl2, respectively, and increasing the concentration of ATP. All these optimizations sharply decreased the background-triggered amplification. Employing the most favourable buffer condition of 2.5 mM MgCl2 where the target-initiated amplification was least affected while reducing the background-triggered process enabled us to achieve a detection range of 14 nM-140 aM with an approximate limit of detection of 680 aM, which is five orders of magnitude more sensitive than using our standard amplification conditions. This optimization of the salt and co-factor concentrations to decrease the background and enhance the sensitivity of LIDA has demonstrated LIDA's potential for application in clinical diagnostics.

Coenzyme Q10 alleviates AlCl3 and D-galactose induced Alzheimer via modulating oxidative burden and TLR-4/MAPK pathways and regulation microRNA in rat brain

Alzheimer's disease (ad) is the most progressive form of neurodegenerative disease resulting in cognitive and non-cognitive deficits. Coenzyme Q10 (CoQ10) is an anti-inflammatory and anti-oxidative stress supplement that can improve inflammation and oxidative stress associated with ad. This study aimed to explore the protective potential of coenzyme Q10 (CoQ10). It also sought to uncover any synergistic effects when combined with donepezil, an acetylcholinesterase inhibitor, in treating Alzheimer's disease in rats, focusing on the modulation of the TLR-4/MAPK pathway and regulation of microRNA. The experiment involved seventy rats categorized into different groups: control, Reference group (donepezil 10 mg/kg/P.O.), CoQ10 alone (1,200 mg/kg/P.O.), ad-model (D-galactose (120 mg/kg/i.p) + Alcl3 (50 mg/kg/P.O.)), donepezil co-treatment, CoQ10 co-treatment, and CoQ10 + donepezil co-treatment. Behavioral parameter was defined using the Morris-Maze test (MMT) and various assessments, such as GABA, oxidative stress, Aβ1-42, ion homeostasis, toll-like receptor-4 (TLR-4), mitogen-activated protein kinase-1 (MAPK-1), micro-RNA (mir-106b, mir-107, and mir-9) were measured. Immunohistological staining was used to assess structural abnormalities in hippocampus. CoQ10 treatment demonstrated memory improvement, enhanced locomotion, and increased neuronal differentiation, mainly through the activation of the TLR-4/MAPK pathway and regulation of mir-106b, mir-107, and mir-9.

Highlights

Coenzyme Q10 (CoQ10) improved the rats' passive avoidance memory impairment caused by D-gal and AlCl3. ad led to the alteration of the TLR-4/MAPK pathways.CoQ10 as a protective agent, diminishes oxidative burden, improve ion homeostasis.CoQ10 counteracts Alzheimer's disease by enhancing neurotransmitter parameter and regulating the MicroRNA.CoQ10 lowered accumulation of Aβ plaque in the hippocampal neurons of D-Gal and AlCl3-treated rats.One promising therapeutic method was the combination of donepezil and CoQ10 therapy.

Development of a loop-mediated isothermal amplification assay for detecting Porphyromonas endodontalis

Context

Loop-mediated isothermal amplification (LAMP) may be used in the future to detect infecting microorganisms. LAMP assays exist for the endodontic pathogens Enterococcus faecalis and Fusobacterium nucleatum, but not yet for Porphyromonas endodontalis.

Aim

To develop a LAMP assay for detecting P. endodontalis.

Settings and Design

It was an in vitro benchtop study.

Subjects and Methods

The National Center for Biotechnology Information GenBank Basic Local Alignment Search Tool was used to identify a segment of the dipeptidyl peptidase 11 (DPP11) gene unique to P. endodontalis. A primer design tool was used to generate six primers required for developing the LAMP assay. WarmStart Colorimetric LAMP 2X Master Mix was used to evaluate the LAMP assay, using purified P. endodontalis DNA as a control.

Statistical Analysis Used

Statistical parameters for sensitivity and specificity.

Results

The assay was performed in triplicate on pure DNA from P. endodontalis and P. gingivalis and on the DNA that was extracted from P. endodontalis, P. gingivalis, F. nucleatum, and E. faecalis cells and diluted two-fold from 1/2 to 1/256. Assays for the diluted samples were performed in triplicate, and the contingency tables indicated the LAMP assay to be 82% sensitive and 90% specific for P. endodontalis.

Conclusions

LAMP assay could be a highly sensitive and specific chairside detection method for P. endodontalis.

Strategies for diagnosing Nosema bombycis (Microsporidia: Nosematidae); the agent of pebrine disease

Pebrine disease, caused by Nosema bombycis (N. bombycis), is the most important pathogen known to the silk industry. Historical evidence from several countries shows that the outbreaks of pebrine disease have largely caused the decline of the sericulture industry. Prevention is the first line to combat pebrine as a deadly disease in silkworm; however, no effective treatment has yet been presented to treat the disease. Many different methods have been used for detection of pebrine disease agent. This review focuses on the explanation and comparison of these methods, and describes their advantages and/or disadvantages. Also, it highlights the ongoing advances in diagnostic methods for N. bombycis that could enable efforts to halt this microsporidia infection. The detection methods are categorized as microscopic, immunological and nucleic acid-based approaches, each with priorities over the other methods; however, the suitability of each method depends on the available equipment in the laboratory, the mass of infection, and the speed and sensitivity of detection. The accessibility and economic efficiency are compared as well as the speed and the sensitivity for each method. Although, the light microscopy is the most common method for detection of N. bombycis, qPCR is the most preferred method for large data based on speed and sensitivity as well as early detection ability.

A colorimetric loop-mediated isothermal amplification assay (c-LAMP) for rapid detection of Pythium insidiosum

Pythiosis, caused by Pythium insidiosum, is a severe infectious disease affecting humans and animals worldwide. There is an urgent need for a simple and rapid detection method for pythiosis, especially in remote areas where this disease is prevalent. To address this, a colorimetric loop-mediated isothermal amplification assay (c-LAMP) using hydroxynaphthol blue dye as a color indicator has been developed. This method utilized a one-step closed-tube system under a single temperature reaction to detect P. insidiosum, minimizing DNA carry-over contamination and eliminating the need for expensive tools. The test result can be easily read through the color change from violet (negative) to sky blue (positive). When tested with DNA samples from P. insidiosum (n = 51) and other fungi (n = 70), c-LAMP showed a detection sensitivity, specificity, and accuracy of 100.0 %, 95.7 %, and 97.5 %, respectively. The assay detection limit was 1 x 10-5 ng of DNA template, 10,000 times lower than the reference multiplex PCR assay (m-PCR). c-LAMP also showed a faster assay turnaround time, taking only 65 min, as opposed to the 180 min required for m-PCR. This newly established c-LAMP is rapid, cost-effective, and efficient, making it a promising tool for detecting P. insidiosum in resource-limited laboratories.

Optimizing the nested PCR method for Decapod iridescent virus 1 (DIV1) targeting ATPase gene by reselecting the inner primers

DIV1 has the characteristics of fast transmission and a broad host range. Its infection leads to a high mortality rate, posing a serious threat to the global crustacean aquaculture industry. In order to increase the accuracy of DIV1 detection and reduce the difficulty of result interpretation, this study modified the original nested PCR method targeting the DIV1 ATPase gene. The internal primers for the nested PCR were redesigned to produce a 338 bp amplification product in the second step PCR, effectively distinguishing the target band from primer dimers. The newly established nested PCR method exhibits strong specificity and high sensitivity, with a detection limit as low as 1.37 × 101 copies/reaction. The developed nested PCR assay provides new technical support for the accurate detection of DIV1 in global crustacean aquaculture.

Bacteriophage λ exonuclease and a 5'-phosphorylated DNA guide allow PAM-independent targeting of double-stranded nucleic acids

Sequence-specific recognition of double-stranded nucleic acids is essential for molecular diagnostics and in situ imaging. Clustered regularly interspaced short palindromic repeats and Cas systems rely on protospacer-adjacent motif (PAM)-dependent double-stranded DNA (dsDNA) recognition, limiting the range of targetable sequences and leading to undesired off-target effects. Using single-molecule fluorescence resonance energy transfer analysis, we discover the enzymatic activity of bacteriophage λ exonuclease (λExo). We show binding of 5'-phosphorylated single-stranded DNA (pDNA) to complementary regions on dsDNA and DNA-RNA duplexes, without the need for a PAM-like motif. Upon binding, the λExo-pDNA system catalytically digests the pDNA into nucleotides in the presence of Mg2+. This process is sensitive to mismatches within a wide range of the pDNA-binding region, resulting in exceptional sequence specificity and reduced off-target effects in various applications. The absence of a requirement for a specific motif such as a PAM sequence greatly broadens the range of targets. We demonstrate that the λExo-pDNA system is a versatile tool for molecular diagnostics, DNA computing and gene imaging applications.

Early detection of tuberculosis: a systematic review

Tuberculosis remains a significant global health challenge. Tuberculosis affects millions of individuals worldwide. Early detection of tuberculosis plays a relevant role in the management of treatment of tuberculosis. This systematic review will analyze the findings of several published studies on the topic of the early detection of tuberculosis. This systematic review highlights their methodologies and limitations as well as their contributions to our understanding of this pressing issue. Early detection of tuberculosis can be achieved through tuberculosis screening for contacts. Comprehensive health education for household contacts can be used as early detection. The in-house deep learning models can be used in the X-ray used for automatic detection of tuberculosis. Interferon gamma release assay, routine passive and active case detection, portable X-ray and nucleic acid amplification testing, and highly sensitive enzyme-linked immunosorbent assay tests play critical roles in improving tuberculosis detection.

Synergistic effect of spermidine and ciprofloxacin against Alzheimer's disease in male rat via ferroptosis modulation

Alzheimer's disease (AD) is a prevalent form of neurodegenerative disease with a complex pathophysiology that remains not fully understood, and the exact mechanism of neurodegeneration is uncertain. Ferroptosis has been linked to the progression of degenerative diseases observed in AD models. The present study is designed to investigate the protective effects of spermidine, a potent antioxidant and iron chelator, and its synergistic interactions with ciprofloxacin, another iron chelator, in modulating ferroptosis and mitigating AD progression in rats. This study investigated AD-related biomarkers like neurotoxic amyloid beta (Aβ), arginase I, and serotonin. Spermidine demonstrated an anti-ferroptotic effect in the AD model, evident from the modulation of ferroptosis parameters such as hippocampus iron levels, reduced protein expression of transferrin receptor 1 (TFR1), and arachidonate 15-lipoxygenase (ALOX15). Additionally, the administration of spermidine led to a significant increase in protein expression of phosphorylated nuclear factor erythroid 2-related factor 2 (p-Nrf2) and upregulation of Cystine/glutamate transporter (SLC7A11) gene expression. Moreover, spermidine notably decreased p53 protein levels, acrolein, and gene expression of spermidine/spermine N1-acetyltransferase 1 (SAT1). Overall, our findings suggest that spermidine and/or ciprofloxacin may offer potential benefits against AD by modulating ferroptosis. Furthermore, spermidine enhanced the antioxidant efficacy of ciprofloxacin and reduced its toxic effects.

The synergistic effect of nanocurcumin and donepezil on Alzheimer's via PI3K/AKT/GSK-3β pathway modulating

Alzheimer's disease (AD) hallmarks include amyloid-βeta (Aβ) and tau proteins aggregates, neurite degeneration, microglial activation with cognitive impairment. Phosphatidylinositol-3-kinase/protein kinase B/Glycogen synthase kinase-3-beta (PI3K/AKT/GSK-3) pathway is essential for neuroprotection, cell survival and proliferation by blocking apoptosis. This study aimed to assess protective role of nanocurcumin (NCMN) as strong antioxidant and anti-inflammatory agent with elucidating its synergistic effects with Donepezil as acetylcholinesterase inhibitor on AD in rats via modulating PI3K/AKT/GSK-3β pathway. The experiment was performed on 70 male Wistar albino rats divided into seven groups (control, NCMN, Donepezil, AD-model, Donepezil co-treatment, NCMN only co-treatment, and NCMN+Donepezil combined treatment). Behavioral and biochemical investigations as cholinesterase activity, oxidative stress (malondialdehyde, reduced glutathione, nitric oxide, superoxidedismutase, and catalase), tumor necrosis factor-alpha, Tau, β-site amyloid precursor protein cleaving enzyme-1 (BACE-1), Phosphatase and tensin homolog (Pten), mitogen-activated protein kinase-1 (MAPK-1), Glycogen synthase kinase-3-beta (GSK-3β) and toll-like receptor-4 were evaluated. Treatment with NCMN improved memory, locomotion, neuronal differentiation by activating PI3K/AKT/GSK-3β pathway. These results were confirmed by histological studies in hippocampus.

A novel sensitive hexaplex high-resolution melt assay for identification of five human Plasmodium species plus internal control

BACKGROUND

The diagnosis of malaria infection in humans remains challenging, further complicated by mixed Plasmodium species infections, potentially altering disease severity and morbidity. To facilitate appropriate control measures and treatment, rapid, sensitive, and specific detection assays, including those for the second minor species, would be required. This study aimed to develop a multiplex high-resolution melting (hexaplex PCR-HRM) assay with seven distinct peaks corresponding to five Plasmodium species of the Plasmodium genus, and an internal control to limit false negatives providing quality assurance testing results.

METHODS

Five species-specific primers for human malaria species were designed targeting on the Plasmodium 18 small subunit ribosomal RNA (18S rRNA) and mitochondrial genes. The hexaplex PCR-HRM was developed for the simultaneous and rapid detection and differentiation of five human Plasmodium spp. The limit of detection (LoD), sensitivity, and specificity of the assay were evaluated. Artificial mixing was used to assess the ability to determine the second minor species. Furthermore, a hexaplex PCR-HRM assay was used to identify 120 Plasmodium-infected clinical isolates from Kanchanaburi, Western Thailand, where malaria is endemic.

RESULTS

The hexaplex PCR-HRM assay detected the targeted genome of five Plasmodium species at levels as low as 2.354-3.316 copies/uL with 91.76 % sensitivity and 98.04 % specificity. In artificial mixing, the assay could detect minority parasite species at 0.001 % of the predominant parasite population. Plasmodium vivax infections (99 %) accounted for the majority of malaria cases in Kanchanaburi, Thailand.

CONCLUSIONS

The developed hexaplex PCR-HRM assay we present in this study is a novel approach for multiplexing the Plasmodium genus and detecting five Plasmodium species with the advantage of detecting second minority parasite species. The developed one-step assay without any nesting protocols would reduce the risks of cross-contamination. Moreover, it also provides a simple, sensitive, specific, and low-cost approach for optional molecular detection of malaria.

CRISPR/Cas12a-assisted visible fluorescence for pseudo dual nucleic acid detection based on an integrated chip

BACKGROUND

A false negative result is one of the major problems in nucleic acid detection. Failure to screen positive samples for pathogens or viruses poses a risk to public health. This situation will lead to more serious consequences for infectious pathogens or viruses. At present, the common solution is to introduce exogenous or endogenous internal control. Because it amplifies and is detected separately from the target gene, it cannot avoid false negative results caused by DNA extraction failure or reagent inactivation. There is an urgent need for a simple and reliable method to solve the false negative problem of nucleic acid detection.

RESULTS

We established a chip and an on-chip detection method for the integrated detection of target genes and internal control using the CRISPR system in LAMP amplification products. The chip is processed from a low-cost PMMA board and has three chambers and some channels. After adding the sample, the chip only needs to be rotated twice, and the sample enters three chambers successively depending on its gravity for dual LAMP reaction and CRISPR detections. With a portable LED blue light exciter, visual fluorescence detection is realized. Whether the detection result is positive, negative, or invalid can be determined according to the fluorescence in the CRISPR chamber for target gene and CRISPR chamber for internal control. In this study, the detection of Salmonella enterica in Fenneropenaeus chinensis was taken as an example. The results showed good specificity and sensitivity. It could detect as low as 15 copies/μL of Salmonella enterica.

SIGNIFICANCE

The on-chip detection solves the problem of aerosol contamination and false negative results. It has the advantages of high sensitivity, high specificity, high accuracy, and low cost. This research will advance the development of nucleic acid detection technology, providing a new and reliable strategy for POCT detection of pathogenic bacteria and viruses.

Utilizing Electrochemical Biosensors as an Innovative Platform for the Rapid and On-Site Detection of Animal Viruses

Animal viruses are a significant threat to animal health and are easily spread across the globe with the rise of globalization. The limitations in diagnosing and treating animal virus infections have made the transmission of diseases and animal deaths unpredictable. Therefore, early diagnosis of animal virus infections is crucial to prevent the spread of diseases and reduce economic losses. To address the need for rapid diagnosis, electrochemical sensors have emerged as promising tools. Electrochemical methods present numerous benefits, including heightened sensitivity and selectivity, affordability, ease of use, portability, and rapid analysis, making them suitable for real-time virus detection. This paper focuses on the construction of electrochemical biosensors, as well as promising biosensor models, and expounds its advantages in virus detection, which is a promising research direction.

Scope of Onsite, Portable Prevention Diagnostic Strategies for Alternaria Infections in Medicinal Plants

Medicinal plants are constantly challenged by different biotic inconveniences, which not only cause yield and economic losses but also affect the quality of products derived from them. Among them, Alternaria pathogens are one of the harmful fungal pathogens in medicinal plants across the globe. Therefore, a fast and accurate detection method in the early stage is needed to avoid significant economic losses. Although traditional methods are available to detect Alternaria, they are more time-consuming and costly and need good expertise. Nevertheless, numerous biochemical- and molecular-based techniques are available for the detection of plant diseases, but their efficacy is constrained by differences in their accuracy, specificity, sensitivity, dependability, and speed in addition to being unsuitable for direct on-field studies. Considering the effect of Alternaria on medicinal plants, the development of novel and early detection measures is required to detect causal Alternaria species accurately, sensitively, and rapidly that can be further applied in fields to speed up the advancement process in detection strategies. In this regard, nanotechnology can be employed to develop portable biosensors suitable for early and correct pathogenic disease detection on the field. It also provides an efficient future scope to convert innovative nanoparticle-derived fabricated biomolecules and biosensor approaches in the diagnostics of disease-causing pathogens in important medicinal plants. In this review, we summarize the traditional methods, including immunological and molecular methods, utilized in plant-disease diagnostics. We also brief advanced automobile and efficient sensing technologies for diagnostics. Here we are proposing an idea with a focus on the development of electrochemical and/or colorimetric properties-based nano-biosensors that could be useful in the early detection of Alternaria and other plant pathogens in important medicinal plants. In addition, we discuss challenges faced during the fabrication of biosensors and new capabilities of the technology that provide information regarding disease management strategies.

Rolling Circle Amplification on a Bead: Improving the Detection Time for a Magnetic Bioassay

Detection of pathogens has become increasingly important, especially in the face of outbreaks and epidemics all over the world. Nucleic acid detection techniques provide a solid base to detect and identify pathogens. In recent years, magnetic sensors and magnetic labels have become of more interest due to their simplicity of use, low cost, and versatility. In this work, we have used the isothermal DNA amplification technique of rolling circle amplification (RCA) in combination with oligo-functionalized magnetic nanoparticles. Detection of RCA products takes place through specific binding between magnetic nanoparticles and RCA products. Upon binding, the relaxation frequency of the nanoparticle changes. This change was measured using an AC susceptometer. We showcase that the RCA time can be reduced for a quicker assay when performing the RCA on the surface of micrometer-sized beads, which consequently increases the hydrodynamic volume of the RCA products. This, in turn, increases the Brownian relaxation frequency shift of the nanoparticles upon binding. We performed optimization work to determine the ideal quantity of micrometer-sized particles, oligo-functionalized nanoparticles, and the amplification time of the RCA. We show that the detection of 0.75 fmol of preamplification synthetic target is possible with only 20 min of amplification time. Finally, we showcase the high specificity of the assay, as the functionalized nanoparticles are unable to bind to amplified DNA that does not match their labels. Overall, this paves the way for a simple bioassay that can be used without expensive laboratory equipment for detection of pathogens in outbreak settings and clinics around the world.

Immunological Studies to Understand Hybrid/Recombinant Variants of SARS-CoV-2

The zoonotic SARS-CoV-2 virus was present before the onset of the pandemic. It undergoes evolution, adaptation, and selection to develop variants that gain high transmission rates and virulence, resulting in the pandemic. Structurally, the spike protein of the virus is required for binding to ACE2 receptors of the host cells. The gene coding for the spike is known to have a high propensity of mutations, as a result generating numerous variants. The variants can be generated by random point mutations or recombination during replication. However, SARS-CoV-2 can also produce hybrid variants on co-infection of the host by two distinct lineages of the virus. The genomic sequences of the two variants undergo recombination to produce the hybrid variants. Additionally, these sub-variants also contain numerous mutations from both the parent variants, as well as some novel mutations unique to the hybrids. The hybrid variants (XD, XE, and XF) can be identified through numerous techniques, such as peak PCR, NAAT, and hybrid capture SARS-CoV-2 NGS (next generation sequencing) assay, etc., but the most accurate approach is genome sequencing. There are numerous immunological diagnostic assays, such as ELISA, chemiluminescence immunoassay, flow-cytometry-based approaches, electrochemiluminescence immunoassays, neutralization assays, etc., that are also designed and developed to provide an understanding of the hybrid variants, their pathogenesis, and other reactions. The objective of our study is to comprehensively analyze the variants of SARS-CoV-2, especially the hybrid variants. We have also discussed the techniques available for the identification of hybrids, as well as the immunological assays and studies for analyzing the hybrid variants.

Nucleic Acid-Based Detection of Pythium insidiosum: A Systematic Review

Pythiosis, a life-threatening infectious condition caused by Pythium insidiosum, has been increasingly reported in humans and animals worldwide. Antifungal drugs usually fail to control the pathogen. The surgical removal of an infected organ is the treatment of choice. Many affected patients die due to advanced infection. A timely and accurate diagnosis could lead to a better prognosis in pythiosis patients and save their lives. Although a standard culture method is available in microbiological laboratories, it is time-consuming, laborious, and insensitive for P. insidiosum identification. Immunological assays have been developed to improve the diagnosis of pythiosis. However, immunological methods are commercially unavailable and primarily detect anti-P. insidiosum antibodies, which constitute indirect evidence of pythiosis, making it challenging to differentiate a past from a recent infection. Moreover, such immunological tests cannot diagnose patients with a local infection, such as in the eye. Nucleic acid-based tests (NATs) are efficient for the direct and rapid detection of P. insidiosum DNA in trace-amount or culture-negative specimens. The reagents and equipment required for NATs are usually available in molecular diagnostic laboratories. Herein, we provide a systematic review to comprehensively present the principal and clinical usages, advantages, and limitations of such NATs in the detection of P. insidiosum. Various NATs have been established to detect P. insidiosum, which can be classified into amplification-based (i.e., PCR assays, isothermal tests, and next-generation sequencing methods) and non-amplification-based (i.e., DNA hybridization) techniques. This concise review on NATs constitutes an up-to-date reference with which healthcare professionals can learn about and decide upon which detection method is suitable for their respective laboratory environments.

Paper-Based Electrochemical Biosensors for Food Safety Analysis

Nowadays, foodborne pathogens and other food contaminants are among the major contributors to human illnesses and even deaths worldwide. There is a growing need for improvements in food safety globally. However, it is a challenge to detect and identify these harmful analytes in a rapid, sensitive, portable, and user-friendly manner. Recently, researchers have paid attention to the development of paper-based electrochemical biosensors due to their features and promising potential for food safety analysis. The use of paper in electrochemical biosensors offers several advantages such as device miniaturization, low sample consumption, inexpensive mass production, capillary force-driven fluid flow, and capability to store reagents within the pores of the paper substrate. Various paper-based electrochemical biosensors have been developed to enable the detection of foodborne pathogens and other contaminants that pose health hazards to humans. In this review, we discussed several aspects of the biosensors including different device designs (e.g., 2D and 3D devices), fabrication techniques, and electrode modification approaches that are often optimized to generate measurable signals for sensitive detection of analytes. The utilization of different nanomaterials for the modification of electrode surface to improve the detection of analytes via enzyme-, antigen/antibody-, DNA-, aptamer-, and cell-based bioassays is also described. Next, we discussed the current applications of the sensors to detect food contaminants such as foodborne pathogens, pesticides, veterinary drug residues, allergens, and heavy metals. Most of the electrochemical paper analytical devices (e-PADs) reviewed are small and portable, and therefore are suitable for field applications. Lastly, e-PADs are an excellent platform for food safety analysis owing to their user-friendliness, low cost, sensitivity, and a high potential for customization to meet certain analytical needs.

Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection

The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has severely impacted human health and the health management system globally. The ongoing pandemic has required the development of more effective diagnostic strategies for restricting deadly disease. For appropriate disease management, accurate and rapid screening and isolation of the affected population is an efficient means of containment and the decimation of the disease. Therefore, considerable efforts are being directed toward the development of rapid and robust diagnostic techniques for respiratory infections, including SARS-CoV-2. In this article, we have summarized the origin, transmission, and various diagnostic techniques utilized for the detection of the SARS-CoV-2 virus. These higher-end techniques can also detect the virus copy number in asymptomatic samples. Furthermore, emerging rapid, cost-effective, and point-of-care diagnostic devices capable of large-scale population screening for COVID-19 are discussed. Finally, some breakthrough developments based on spectroscopic diagnosis that could revolutionize the field of rapid diagnosis are discussed.

Recent Advances in Signal Amplification to Improve Electrochemical Biosensing for Infectious Diseases

The field of infectious disease diagnostics is burdened by inequality in access to healthcare resources. In particular, “point-of-care” (POC) diagnostics that can be utilized in non-laboratory, sub-optimal environments are appealing for disease control with limited resources. Electrochemical biosensors, which combine biorecognition elements with electrochemical readout to enable sensitive and specific sensing using inexpensive, simple equipment, are a major area of research for the development of POC diagnostics. To improve the limit of detection (LOD) and selectivity, signal amplification strategies have been applied towards these sensors. In this perspective, we review recent advances in electrochemical biosensor signal amplification strategies for infectious disease diagnostics, specifically biosensors for nucleic acids and pathogenic microbes. We classify these strategies into target-based amplification and signal-based amplification. Target-based amplification strategies improve the LOD by increasing the number of detectable analytes, while signal-based amplification strategies increase the detectable signal by modifying the transducer system and keep the number of targets static. Finally, we argue that signal amplification strategies should be designed with application location and disease target in mind, and that the resources required to produce and operate the sensor should reflect its proposed application, especially when the platform is designed to be utilized in low-resource settings. We anticipate that, based on current technologies to diagnose infectious diseases, incorporating signal-based amplification strategies will enable electrochemical POC devices to be deployed for illnesses in a wide variety of settings.

Immunocapture Magnetic Beads Enhanced the LAMP-CRISPR/Cas12a Method for the Sensitive, Specific, and Visual Detection of Campylobacter jejuni

Campylobacter jejuni is one of the most important causes of food-borne infectious disease, and poses challenges to food safety and public health. Establishing a rapid, accurate, sensitive, and simple detection method for C. jejuni enables early diagnosis, early intervention, and prevention of pathogen transmission. In this study, an immunocapture magnetic bead (ICB)-enhanced loop-mediated isothermal amplification (LAMP) CRISPR/Cas12a method (ICB-LAMP-CRISPR/Cas12a) was developed for the rapid and visual detection of C. jejuni. Using the ICB-LAMP-CRISPR/Cas12a method, C. jejuni was first captured by ICB, and the bacterial genomic DNA was then released by heating and used in the LAMP reaction. After the LAMP reaction, LAMP products were mixed and detected by the CRISPR/Cas12a cleavage mixture. This ICB-LAMP-CRISPR/Cas12a method could detect a minimum of 8 CFU/mL of C. jejuni within 70 min. Additionally, the method was performed in a closed tube in addition to ICB capture, which eliminates the need to separate preamplification and transfer of amplified products to avoid aerosol pollution. The ICB-LAMP-CRISPR/Cas12a method was further validated by testing 31 C. jejuni-positive fecal samples from different layer farms. This method is an all-in-one, simple, rapid, ultrasensitive, ultraspecific, visual detection method for instrument-free diagnosis of C. jejuni, and has wide application potential in future work.

Application and evaluation of nucleic acid sequence-based amplification, PCR and cryptococcal antigen test for diagnosis of cryptococcosis

Background

Cryptococcosis is a major opportunistic invasive mycosis in immunocompromised patients, but it is also increasingly seen in immunocompetent patients. In the early stages of cryptococcosis, limitations of the detection method may hinder the diagnosis. A molecular diagnostic technique based on nucleic acid sequence-based amplification (NASBA) method was developed to fulfil the need for efficient diagnosis of cryptococcosis.

Methods

We compared the diagnostic performance of NASBA, PCR and cryptococcal antigen (CrAg) test (colloidal gold method) in clinical samples from 25 cryptococcosis patients (including 8 cryptococcal meningoencephalitis and 17 pulmonary cryptococcosis) who were categorized as proven cases (n = 10) and probable cases (n = 15) according to the revised EORTC/MSG definitions. 10 patients with non-Cryptococcus infection and 30 healthy individuals were categorized as control group.

Results

The lowest detection limit of NASBA was 10 CFU/mL, and RNA of non-target bacteria or fungi was not amplified. The sensitivity of NASBA, PCR and colloidal gold method was 92.00% (95% CI 72.50–98.60%), 64.00% (95% CI 42.62–81.29%), 100.00% (95% CI 83.42–100.00%), and the specificity was 95.00% (95% CI 81.79–99.13%), 80.00% (95% CI 63.86–90.39%) and 82.50% (95% CI 66.64–92.11%) respectively. The highest specificity (97.50%), accuracy (95.38%) and k value (0.90) were achieved when both NASBA and colloidal gold results were positive.

Conclusions

NASBA is a new alternative detection method for cryptococcosis which is both accurate and rapid without expensive equipment and specialised personnel. It may be used as a tool for confirming current infection as well as monitoring the effectiveness of antifungal treatment. The use of NASBA to detect Cryptococcus RNA in blood samples is of great significance for the diagnosis of pulmonary cryptococcosis. The combination of NASBA and colloidal gold can improve the diagnostic accuracy of cryptococcosis.

Annealed ZnO/Al2O3 Core-Shell Nanowire as a Platform to Capture RNA in Blood Plasma

RNA analytical platforms gained extensive attention recently for RNA-based molecular analysis. However, the major challenge for analyzing RNAs is their low concentration in blood plasma samples, hindering the use of RNAs for diagnostics. Platforms that can enrich RNAs are essential to enhance molecular detection. Here, we developed the annealed ZnO/Al₂O₃ core-shell nanowire device as a platform to capture RNAs. We showed that the annealed ZnO/Al₂O₃ core-shell nanowire could capture RNAs with high efficiency compared to that of other circulating nucleic acids, including genomic DNA (gDNA) and cell-free DNA (cfDNA). Moreover, the nanowire was considered to be biocompatible with blood plasma samples due to the crystalline structure of the Al₂O₃ shell which serves as a protective layer to prevent nanowire degradation. Our developed device has the potential to be a platform for RNA-based extraction and detection.

Current methods for the detection of antimalarial drug resistance in Plasmodium parasites infecting humans

Malaria is the world's deadliest parasitic disease. Great progress has been made in the fight against malaria over the past two decades, but this has recently begun to plateau, in part due to the global development of antimalarial drug resistance. The ability to track drug resistance is necessary to achieve progress in treatment, disease surveillance and epidemiology, which has prompted the development of advanced diagnostic methods. These new methods provide unprecedented access to information that can help to guide public health policies. Development of new technologies increases the potential for high throughput and reduced costs of diagnostic tests; improving the accessibility of tools to investigate the forces driving disease dynamics and, ultimately, clinical outcomes for malaria patients and public health. This literature review provides a summary of the methods currently available for the detection of antimalarial drug resistance from the examination of patients' blood samples. While no single method is perfect for every application, many of the newly developed methods give promise for more reliable and efficient characterisation of Plasmodium resistance in a range of settings. By exploiting the strengths of the tools available, we can develop a deeper understanding of the evolutionary and spatiotemporal dynamics of this disease. This will translate into more effective disease control, better-informed policy, and more timely and successful treatment for malaria patients.

Beneficial consequences of probiotic on mitochondrial hippocampus in Alzheimer's disease

BACKGROUND

Alzheimer's (AD) is one of the most common neurodegenerative diseases, causing dementia and brain cells death.

OBJECTIVES

This study aimed to assess the ameliorating effect of Acidophilus probiotic against AD induced in rats by d-galactose and AlCl₃ injection via evaluating mitochondrial parameter changes in hippocampus.

METHODS

This study was carried out on rats were classified into five groups; G1 (control group), G2 (probiotic group), G3 (AD group), G4 (co-treated group) and G5 (post-treated group). By the end of the experiment, some different neurotransmitters, oxidative stress biomarkers, zinc, blood glucose, Na⁺K^-ATPase subunit alpha 1 (ATP1A1), and gene expression of mitochondrial membrane potential (MMP) were measured.

RESULTS

Significant changes in neurotransmitters, antioxidants levels and decreased ATP1A1 activity and gene expression of MMP in the hippocampus in G3 were detected if compared to control. Best improvement in G5 than G4 group was observed. These results were confirmed by histological and immunohistochemical studies in hippocampus.

CONCLUSIONS

Acidophilus probiotic was able to alleviate learning and memory associated injuries in AD by reducing mitochondrial dysfunction induced by d-galactose and AlCl₃. This may be associated with its antioxidant properties.

Development and comparison of qPCR and qLAMP for rapid detection of the decapod iridescent virus 1 (DIV1)

Decapod iridescent virus 1 (DIV1) is a new virus discovered in recent years that infects farmed shrimp. DIV1 is highly infectious and causes substantial economic loss to the aquaculture industry of China. To prevent and control the spread and outbreak of DIV1 in a timely manner, it is necessary to establish an efficient method for DIV1 diagnosis. In this study, quantitative real-time polymerase chain reaction (qPCR) and quantitative real-time loop-mediated isothermal amplification (qLAMP) detection methods were established based on the specific sequence of the viral ATPase gene. The results indicated that the minimum detection limits of qPCR and qLAMP were 1.9 × 10¹ copies/μL and 1.9 × 10² copies/μL, respectively; the designed primer had good specificity for DIV1 and did not react with 13 other viruses, including white spot syndrome virus (WSSV), Enterocytozoon hepatopenaei (EHP), acute hepatopancreatic necrosis disease (AHPND), infectious hypodermal and haematopoietic necrosis virus (IHHNV), etc. A total of 43 clinical samples suspected of DIV1 infection were diagnosed by qPCR and qLAMP. Our qPCR demonstrated results consistent with a qPCR assay published previously, and the diagnostic sensitivity (DSe) and diagnostic specificity (DSp) of qLAMP were 85.71% and 100%, respectively. This result indicates that qPCR and qLAMP have good accuracy in the detection of DIVI in clinical samples. As established in this study, qPCR and qLAMP combined with a comprehensive comparative analysis can provide effective new solutions for the detection of DIV1.

Nucleic Acid-Based Sensing Techniques for Diagnostics and Surveillance of Influenza

Influenza virus poses a threat to global health by causing seasonal outbreaks as well as three pandemics in the 20th century. In humans, disease is primarily caused by influenza A and B viruses, while influenza C virus causes mild disease mostly in children. Influenza D is an emerging virus found in cattle and pigs. To mitigate the morbidity and mortality associated with influenza, rapid and accurate diagnostic tests need to be deployed. However, the high genetic diversity displayed by influenza viruses presents a challenge to the development of a robust diagnostic test. Nucleic acid-based tests are more accurate than rapid antigen tests for influenza and are therefore better candidates to be used in both diagnostic and surveillance applications. Here, we review various nucleic acid-based techniques that have been applied towards the detection of influenza viruses in order to evaluate their utility as both diagnostic and surveillance tools. We discuss both traditional as well as novel methods to detect influenza viruses by covering techniques that require nucleic acid amplification or direct detection of viral RNA as well as comparing advantages and limitations for each method. There has been substantial progress in the development of nucleic acid-based sensing techniques for the detection of influenza virus. However, there is still an urgent need for a rapid and reliable influenza diagnostic test that can be used at point-of-care in order to enhance responsiveness to both seasonal and pandemic influenza outbreaks.

Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection

Polymerase chain reaction (PCR) is by far the most commonly used method of nucleic acid amplification and has likewise been employed for a plethora of diagnostic purposes. Nonetheless, multiplexed PCR-based detection schemes have hitherto been largely limited by technical challenges associated with nonspecific interactions and other limitations inherent to traditional fluorescence-based assays. Here, we describe a novel strategy for multiplexed PCR-based analysis called Ligation-eNabled fluorescence-Coding PCR (LiNC PCR) that exponentially enhances the multiplexing capability of standard fluorescence-based PCR assays. The technique relies upon a simple, preliminary ligation reaction in which target DNA sequences are converted to PCR template molecules with distinct endpoint fluorescence signatures. Universal TaqMan probes are used to create target-specific multicolor fluorescence signals that can be readily decoded to identify amplified targets of interest. We demonstrate the LiNC PCR technique by implementing a two-color-based assay for detection of 10 ovarian cancer epigenetic biomarkers at analytical sensitivities as low as 60 template molecules with no detectable target cross-talk. Overall, LiNC PCR provides a simple and inexpensive method for achieving high-dimensional multiplexing that can be implemented in manifold molecular diagnostic applications.

Alzheimer's disease improved through the activity of mitochondrial chain complexes and their gene expression in rats by boswellic acid

The foremost neurodegenerative disease is Alzheimer's (AD), which is characterized as a gradual decrease in memory, cognitive function, and also personal changes occurred. This study aims to assess the role of boswellic bioactive component in control Alzheimer's disease through enhancing mitochondrial electron transport chain complexes in the rat model. Rats were divided into five equal groups: the control group (G1), boswellic acid control group (G2), AD disease group (G3), boswellic acid -pre-treated group (G4) and boswellic acid-treated group (G5). At the end of the experiment, blood glucose level, tau protein, different neurochemicals parameters (dopamine, acetylcholine), L-malondialdehyde (MDA) levels, and superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) activities was determined. Also, GLUT2 and mitochondrial electron transport chain complexes were evaluated. As a result, an increase in hippocampus glucose, tau protein expression, MDA and GLUT2 in the AD group (G3) compared to control groups (G1 and G2) has been recorded. These parameters were declined after pre (G4) and treated (G5) by boswellic acid. The neurochemicals, antioxidants parameters, four mitochondrial chain complexes activities and their gene expression in the hippocampus of the AD group were decreased compared to the control groups (G1 and G2). In contrast, pre and treated groups by boswellic acid (G4 and G5, respectively) have shown an increase in antioxidants parameters, and the activities of four mitochondrial complexes, with the best improvement in the pre-treated group (G4), then treated group (G5). In conclusion; the boswellic acid improved the antioxidant and mitochondrial complexes in Alzheimer's disease.

Development of Diagnostic Tests for Detection of SARS-CoV-2

One of the most effective ways to prevent the spread of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is to develop accurate and rapid diagnostic tests. There are a number of molecular, serological, and imaging methods that are used to diagnose this infection in hospitals and clinical settings. The purpose of this review paper is to present the available approaches for detecting SARS-CoV-2 and address the advantages and limitations of each detection method. This work includes studies from recent literature publications along with information from the manufacturer's manuals of commercially available SARS-CoV-2 diagnostic products. Furthermore, supplementary information from the Food & Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and World Health Organization (WHO) is cited. The viral components targeted for virus detection, the principles of each diagnostic technique, and the detection efficiency of each approach are discussed. The potential of using diagnostic tests that were originally developed for previous epidemic viruses is also presented.

Multiplex Detection of Salmonella spp., E. coli O157 and L. monocytogenes by qPCR Melt Curve Analysis in Spiked Infant Formula

Food poisoning continue to be a threat in the food industry showing a need to improve the detection of the pathogen responsible for the hospitalization cases and death. DNA-based techniques represent a real advantage and allow the detection of several targets at the same time, reducing cost and time of analysis. The development of new methodology using SYBR Green qPCR for the detection of L. monocytogenes, Salmonella spp. and E. coli O157 simultaneously was developed and a non-competitive internal amplification control (NC-IAC) was implemented to detect reaction inhibition. The formulation and supplementation of the enrichment medium was also optimized to allow the growth of all pathogens. The limit of detection (LoD) 95% obtained was <1 CFU/25 g for E. coli O157, and 2 CFU/25 g for Salmonella spp. and L. monocytogenes and regarding the multiplex detection a LoD 95% of 1.7 CFU/25 g was observed. The specificity, relative sensitivity and accuracy of full methodology were 100% and the use of the NC-IAC allowed the reliability of the results without interfering with the sensitivity of the methodology. The described study proved to obtain results comparable to those of probe-based qPCR, and more economically than classical high resolution melting qPCR, being both important aspects for its implementation in the food industry.

Paper-based microfluidics for rapid diagnostics and drug delivery

Paper is a common material that is promising for constructing microfluidic chips (lab-on-a-paper) for diagnostics and drug delivery for biomedical applications. In the past decade, extensive research on paper-based microfluidics has accumulated a large number of scientific publications in the fields of biomedical diagnosis, food safety, environmental health, drug screening and delivery. This review focuses on the recent progress on paper-based microfluidic technology with an emphasis on the design, optimization and application of the technology platform, in particular for medical diagnostics and drug delivery. Novel advances have concentrated on engineering paper devices for point-of-care (POC) diagnostics, which could be integrated with nucleic acid-based tests and isothermal amplification experiments, enabling rapid sample-to-answer assays for field testing. Among the isothermal amplification experiments, loop-mediated isothermal amplification (LAMP), an extremely sensitive nucleic acid test, specifically identifies ultralow concentrations of DNA/RNA from practical samples for diagnosing diseases. We thus mainly focus on the paper device-based LAMP assay for the rapid infectious disease diagnosis, foodborne pathogen analysis, veterinary diagnosis, plant diagnosis, and environmental public health evaluation. We also outlined progress on paper microfluidic devices for drug delivery. The paper concludes with a discussion on the challenges of this technology and our insights into how to advance science and technology towards the development of fully functional paper devices in diagnostics and drug delivery.

Simple microfluidic device for detecting the negative dielectrophoresis of DNA labeled microbeads

We propose a new microfluidic device that can be used to determine the change in the negative dielectrophoresis (n-DEP) of dielectric microbeads when a small amount of DNA is attached to them. We previously proposed a DNA detection method based on changes in the DEP of microbeads induced by the attachment of DNA. When target DNA is attached to the microbeads having n-DEP property, the DEP changes from negative to positive. This occurs because electric charges of the DNA increase the surface conductance of the microbeads. Thus, only the DNA-labeled microbeads are attracted to a microelectrode by positive DEP. The trapped DNA-labeled microbeads can be counted by dielectrophoretic impedance measurements. A large amount of DNA (approximately 10⁵ DNA molecules) is required to change the DEP from negative to positive. Even though this method can be combined with DNA amplification, reducing the amount of DNA required can help us to shorten the reaction time. In this study, we aimed to detect DNA less than 10⁵ DNA molecules by determining the change in the n-DEP change. To achieve this, we proposed a simple microfluidic device consisting of a single microchannel and a single pair of microelectrodes. Numerical simulations revealed that the device can identify the slight change in the n-DEP of the microbeads corresponding to the attachment of a small amount of DNA. In practical experiments, the fabricated device distinguished 10-1000 DNA molecules per microbead. This method represents a fast and easy method of DNA detection when combined with DNA amplification techniques.

Dual-Priming Isothermal Amplification (DAMP) for Highly Sensitive and Specific Molecular Detection with Ultralow Nonspecific Signals

Nucleic acid amplification tests have been widely used in clinical diagnostics, food safety monitoring, and molecular biology. Loop-mediated isothermal amplification (LAMP) is a prevailing nucleic acid isothermal amplification method. It has become a powerful alternative to conventional polymerase chain reaction (PCR) for pathogen detection because of its simplicity, rapidity, and high sensitivity. However, the current LAMP methods, especially LAMP with two loop primers, suffer from undesired nonspecific amplification with strong background signals due to the increasing target sites. This nonspecific amplification substantially reduced the reliability of LAMP and limited its applications in clinical diagnostics. Here, we report a "dual-priming" ("self-priming" and "pairing-priming") isothermal amplification (DAMP) assay for rapid nucleic acid detection with ultralow nonspecific signals. This method takes advantage of the "dual-priming" strand extension strategy by adding two pairing-competition primers and designing unique inner primers, enabling highly sensitive and specific molecular detection. As an application demonstration, the DAMP assay was used to detect HIV-1 DNA/RNA and Escherichia coli DNA, showing equal or better sensitivity with shorter detection time compared to conventional LAMP and PCR methods. More importantly, the DAMP assay showed ultralow background signals without false positive signals even after a 2 h incubation. Such a simple, reliable, sensitive, and specific DAMP assay can be well suited for rapid nucleic acid detection as point-of-care testing, particularly in resource-limited settings.

Dark-Field Microscopic Detection of Bacteria using Bacteriophage-Immobilized SiO2@AuNP Core-Shell Nanoparticles

To replace molecular biological and immunological methods, biosensors have recently been developed for the rapid and sensitive detection of bacteria. Among a wide variety of biological materials, bacteriophages have received increasing attention as promising alternatives to antibodies in biosensor applications. Thus, we herein present a rapid and highly selective detection method for pathogenic bacteria, which combines dark-field light scattering imaging with a plasmonic biosensor system. The plasmonic biosensor system employs bacteriophages as the biorecognition element and the aggregation-induced light scattering signal of gold nanoparticle-assembled silica nanospheres as a signal transducer. Using Staphylococcus aureus strain SA27 as a model analyte, we demonstrated that the plasmonic biosensor system detects S. aureus in the presence of excess Escherichia coli in a highly selective manner. After the sample and the S. aureus phage S13'-conjugated plasmon scattering probe were mixed, S. aureus detection was completed within 15-20 min with a detection limit of 8 × 10⁴ colony forming units per milliliter.

Ratiometric Fluorescence Coding for Multiplex Nucleic Acid Amplification Testing

Although nucleic acid amplification testing (NAAT) has become the cornerstone for molecular diagnosis of diseases, expanding the multiplexed detection capacity of NAAT remains an important objective. To this end, encoding each nucleic acid target with a specific fluorescently labeled probe has been the most mature approach for multiplexed detection. Unfortunately, the number of targets that can be differentiated via this one-target-one-fluorophore multiplexed detection approach is restricted by spectral overlaps between fluorophores. In response, we present herein a new multiplexed detection approach termed ratiometric fluorescence coding, in which we encode each nucleic acid target with a specific ratio between two standard fluorophores. In ratiometric fluorescence coding, we employ the padlock probe chemistry to encode each nucleic acid target with a specific number of binding sites for two probes labeled with different fluorophores. Coupling the padlock probes with either rolling circle amplification (RCA) or hyperbranched rolling circle amplification (HRCA), we transform each nucleic acid target into a specific template that allows hybridization with the fluorescently labeled probes at predesigned ratios, thereby achieving multiplexed detection. For demonstration, we detected DNA targets from six infectious diseases and demonstrated the potential for further expanding the multiplexing capability of our approach. With further development, ratiometric fluorescence coding has the potential to enable highly multiplexed detection of nucleic acid targets and facilitate molecular diagnosis of diseases.

Handheld isothermal amplification and electrochemical detection of DNA in resource-limited settings

This paper demonstrates a new method for electrochemical detection of specific sequences of DNA present in trace amounts in serum or blood. This method is designed for use at the point-of-care (particularly in resource-limited settings). By combining recombinase polymerase amplification (RPA)- an isothermal alternative to the polymerase chain reaction - with an electroactive mediator, this electrochemical methodology enables accurate detection of DNA in the field using a low-cost, portable electrochemical analyzer (specifically designed for this type of analysis). This handheld device has four attributes: (1) It uses disposable, paper-based strips that incorporate screen-printed carbon electrodes; (2) It accomplishes thermoregulation with ±0.1 °C temperature accuracy; (3) It enables electrochemical detection using a variety of pulse sequences, including square-wave and cyclic voltammetry, and coulometry; (4) It is operationally simple to use. Detection of genomic DNA from Mycobacterium smegmatis (a surrogate for M. tuberculosis-the main cause of tuberculosis), and from M. tuberculosis itself down to ∼0.040 ng/μL provides a proof-of-concept for the applicability of this method of screening for disease using molecular diagnostics. With minor modifications to the reagents, this method will also enable field monitoring of food and water quality.

Culture-Independent Diagnostics for Health Security

The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop.

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

From research lab to standard environmental analysis tool: Will NASBA make the leap?

Nucleic acid sequence-based amplification (NASBA) is a sensitive and efficient molecular tool for amplification of RNA and has been widely adopted in clinical diagnostics. Monitoring of water and other environmental samples demands sensitive techniques, as potential pathogens may be in low concentrations and require only a few infectious units to infect their host. NASBA has qualities that should be advantageous for analysis of environmental samples, such as short reaction times, high sensitivity, and not readily affected by inhibitory substances that are often abundant in environmental samples. NASBA is well suited for incorporation into lab-on-a-chip (LOC) devices, as part of analysis systems that can be taken into the field for on-site screening. In this review, we explore advantages and drawbacks of NASBA as a tool for environmental analyses, and try to answer the question of whether it will be a recognised technique in the same manner as in clinical diagnostics.

Fungal disease detection in plants: Traditional assays, novel diagnostic techniques and biosensors

Fungal diseases in commercially important plants results in a significant reduction in both quality and yield, often leading to the loss of an entire plant. In order to minimize the losses, it is essential to detect and identify the pathogens at an early stage. Early detection and accurate identification of pathogens can control the spread of infection. The present article provides a comprehensive overview of conventional methods, current trends and advances in fungal pathogen detection with an emphasis on biosensors. Traditional techniques are the "gold standard" in fungal detection which relies on symptoms, culture-based, morphological observation and biochemical identifications. In recent times, with the advancement of biotechnology, molecular and immunological approaches have revolutionized fungal disease detection. But the drawback lies in the fact that these methods require specific and expensive equipments. Thus, there is an urgent need for rapid, reliable, sensitive, cost effective and easy to use diagnostic methods for fungal pathogen detection. Biosensors would become a promising and attractive alternative, but they still have to be subjected to some modifications, improvements and proper validation for on-field use.

Deploying aptameric sensing technology for rapid pandemic monitoring

The genome of virulent strains may possess the ability to mutate by means of antigenic shift and/or antigenic drift as well as being resistant to antibiotics with time. The outbreak and spread of these virulent diseases including avian influenza (H1N1), severe acute respiratory syndrome (SARS-Corona virus), cholera (Vibrio cholera), tuberculosis (Mycobacterium tuberculosis), Ebola hemorrhagic fever (Ebola Virus) and AIDS (HIV-1) necessitate urgent attention to develop diagnostic protocols and assays for rapid detection and screening. Rapid and accurate detection of first cases with certainty will contribute significantly in preventing disease transmission and escalation to pandemic levels. As a result, there is a need to develop technologies that can meet the heavy demand of an all-embedded, inexpensive, specific and fast biosensing for the detection and screening of pathogens in active or latent forms to offer quick diagnosis and early treatments in order to avoid disease aggravation and unnecessary late treatment costs. Nucleic acid aptamers are short, single-stranded RNA or DNA sequences that can selectively bind to specific cellular and biomolecular targets. Aptamers, as new-age bioaffinity probes, have the necessary biophysical characteristics for improved pathogen detection. This article seeks to review global pandemic situations in relation to advances in pathogen detection systems. It particularly discusses aptameric biosensing and establishes application opportunities for effective pandemic monitoring. Insights into the application of continuous polymeric supports as the synthetic base for aptamer coupling to provide the needed convective mass transport for rapid screening is also presented.

Novel quantitative TaqMan® MGB real-time PCR for sensitive detection of Vibrio aestuarianus in Crassostrea gigas

Validation of a novel quantitative real-time PCR using TaqMan® minor groove binder (MGB) chemistry is described for sensitive and rapid detection of Vibrio aestuarianus, an increasingly important pathogen of Pacific cupped oyster Crassostrea gigas aquaculture. Primers and TaqMan® MGB hydrolysis probe were designed to specifically amplify a 58bp DNA fragment of the V. aestuarianus dnaJ gene. Real-time PCR selectivity was empirically tested using DNA extracted from isolates of V. aestuarianus and a selection of different aquatic bacterial species, including other Vibrio spp. Theoretical selectivity was assessed through sequence comparison using the NCBI BLAST similarity tool. Quantitative PCR plasmid standards were generated to test assay linearity, amplification efficiency and the limit of quantitation (LOQ), according to International Organisation for Standardisation ISO 16140 validation recommendations. LOQ ranged between 5 and 10 PCR copies, although the detection range extended beyond this with reduced precision. Applied performance was tested using C. gigas samples taken from a selection of Irish aquaculture sites. Increasing levels of V. aestuarianus, accompanied by the development of tissue pathology in examined oysters, were found at 1 site that was sampled repeatedly in 2013. Rapid, sensitive and reproducible detections of V. aestuarianus from C. gigas tissue samples were attained during this validation study with a small sample size, and a practical application for disease management is described.

Sensitive and direct electrochemical detection of double-stranded DNA utilizing alkaline phosphatase-labelled zinc finger proteins

Direct detection of double-stranded DNA (dsDNA) using zinc finger proteins (ZFPs) is of great importance in biomedical applications such as identifying pathogens and circulating DNAs. However, its sensitivity is still not sufficiently high because limited signalling labels can be conjugated or fused. Herein, we report sensitive and direct detection of dsDNA using (i) alkaline phosphatase (ALP) as a fast catalytic label conjugated to ZFPs along with (ii) electrochemical measurement of an ALP product (l-ascorbic acid) at the indium-tin oxide electrode with a high signal-to-background ratio. ALP is simply conjugated to a ZFP through lysine residues in a ZFP purification tag, a maltose binding protein (MBP). Sandwich-type electrochemical detection of dsDNA allows a detection limit of ca. 100 fM without using DNA amplification.

Colorimetric biosensing of pathogens using gold nanoparticles

Rapid detection of pathogens is crucial to minimize adverse health impacts of nosocomial, foodborne, and waterborne diseases. Gold nanoparticles are extremely successful at detecting pathogens due to their ability to provide a simple and rapid color change when their environment is altered. Here, we review general strategies of implementing gold nanoparticles in colorimetric biosensors. First, we highlight how gold nanoparticles have improved conventional genomic analysis methods by lowering detection limits while reducing assay times. Then, we focus on emerging point-of-care technologies that aim at pathogen detection using simpler assays. These advances will facilitate the implementation of gold nanoparticle-based biosensors in diverse environments throughout the world and help prevent the spread of infectious diseases.

Specific PCR and real-time PCR assays for detection and quantitation of 'Candidatus Phytoplasma phoenicium'

Almond witches' broom (AlmWB) is a fast-spreading lethal disease of almond, peach and nectarine associated with 'Candidatus Phytoplasma phoenicium'. The development of PCR and quantitative real-time PCR (qPCR) assays for the sensitive and specific detection of the phytoplasma is of prime importance for early detection of 'Ca. P. phoenicium' and for epidemiological studies. The developed qPCR assay herein uses a TaqMan(®) probe labeled with Black Hole Quencher Plus. The specificity of the PCR and that of the qPCR detection protocols were tested on 17 phytoplasma isolates belonging to 11 phytoplasma 16S rRNA groups, on samples of almond, peach, nectarine, native plants and insects infected or uninfected with the phytoplasma. The developed assays showed high specificity against 'Ca. P. phoenicium' and no cross-reactivity against any other phytoplasma, plant or insect tested. The sensitivity of the developed PCR and qPCR assays was similar to the conventional nested PCR protocol using universal primers. The qPCR assay was further validated by quantitating AlmWB phytoplasma in different hosts, plant parts and potential insect vectors. The highest titers of 'Ca. P. phoenicium' were detected in the phloem tissues of stems and roots of almond and nectarine trees, where they averaged from 10(5) to 10(6) genomic units per nanogram of host DNA (GU/ng of DNA). The newly developed PCR and qPCR protocols are reliable, specific and sensitive methods that are easily applicable to high-throughput diagnosis of AlmWB in plants and insects and can be used for surveys of potential vectors and alternative hosts.