Development of isothermal amplification methods for rapid and sensitive detection of heat-labile enterotoxin producing Escherichia coli

Isothermal amplification technology (IAT) for rapid diagnosis of Rickettsioses: scope, overview, existing evidence, and the way forward

Rickettsioses, a category of zoonosis primarily caused by Rickettsia and Orientia, is a huge cause of public health concern worldwide. Diseases like murine typhus, scrub typhus, Mediterranean spotted fever and rocky mountain spotted fever are major contributors of Rickettsioses globally, with peculiar distributions in south-east Asia, Africa, Arabia and the Americas. With the innovations in molecular diagnostics, Isothermal Amplification Technology is gaining popularity for its fidelity, rapidity and cost-effectiveness. Compared to commercial assays, they are easily adaptable for point-of-care (PoC) settings. Due to nonspecific presentation as an acute undifferentiated febrile illness, diagnosis of Rickettsioses poses a great challenge. Certain isothermal amplification assays have proven to be highly efficient in diagnosing vector borne diseases like dengue, malaria, and chikungunya. The purpose of this review is to provide readers the current advancements, scope, challenges, and future prospects of isothermal amplification technologies in the detection of zoonotic pathogens like Rickettsia and Orientia.

Lateral Flow Assay for Hepatitis B Detection: A Review of Current and New Assays

From acute to chronic hepatitis, cirrhosis, and hepatocellular cancer, hepatitis B infection causes a broad spectrum of liver diseases. Molecular and serological tests have been used to diagnose hepatitis B-related illnesses. Due to technology limitations, it is challenging to identify hepatitis B infection cases at an early stage, particularly in a low- and middle-income country with constrained resources. Generally, the gold-standard methods to detect hepatitis B virus (HBV) infection requires dedicated personnel, bulky, expensive equipment and reagents, and long processing times which delay the diagnosis of HBV. Thus, lateral flow assay (LFA), which is inexpensive, straightforward, portable, and operates reliably, has dominated point-of-care diagnostics. LFA consists of four parts: a sample pad where samples are dropped; a conjugate pad where labeled tags and biomarker components are combined; a nitrocellulose membrane with test and control lines for target DNA-probe DNA hybridization or antigen-antibody interaction; and a wicking pad where waste is stored. By modifying the pre-treatment during the sample preparation process or enhancing the signal of the biomarker probes on the membrane pad, the accuracy of the LFA for qualitative and quantitative analysis can be improved. In this review, we assembled the most recent developments in LFA technologies for the progress of hepatitis B infection detection. Prospects for ongoing development in this area are also covered.

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.

Development of a simple, rapid, and sensitive diagnostic assay for enterotoxigenic E. coli and Shigella spp applicable to endemic countries

Enterotoxigenic E. coli (ETEC) and Shigella spp (Shigella) are complex pathogens. The diagnostic assays currently used to detect these pathogens are elaborate or complicated, which make them difficult to apply in resource poor settings where these diseases are endemic. The culture methods used to detect Shigella are not sensitive, and the methods used to detect ETEC are only available in a few research labs. To address this gap, we developed a rapid and simple diagnostic assay–"Rapid LAMP based Diagnostic Test (RLDT)." The six minutes sample preparation method directly from the fecal samples with lyophilized reaction strips and using established Loop-mediated Isothermal Amplification (LAMP) platform, ETEC [heat labile toxin (LT) and heat stable toxins (STh, and STp) genes] and Shigella (ipaH gene) detection was made simple, rapid (<50 minutes), and inexpensive. This assay is cold chain and electricity free. Moreover, RLDT requires minimal equipment. To avoid any end user’s bias, a battery-operated, handheld reader was used to read the RLDT results. The results can be read as positive/negative or as real time amplification depending on the end user’s need. The performance specifications of the RLDT assay, including analytical sensitivity and specificity, were evaluated using fecal samples spiked with ETEC and Shigella strains. The limit of detection was ~10⁵ CFU/gm of stool for LT, STh, and STp and ~10⁴ CFU/gm of stool for the ipaH gene, which corresponds to about 23 CFU and 1 CFU respectively for ETEC and Shigella per 25uL reaction within 40 minutes. The RLDT assay from stool collection to result is simple, and rapid and at the same time sufficiently sensitive. RLDT has the potential to be applied in resource poor endemic settings for the rapid diagnosis of ETEC and Shigella.

Enterotoxigenic E. coli and Shigella are the leading causes of moderate to severe diarrhea in the low-and middle-income countries (LMICs). A critical constraint to determine the ETEC and Shigella disease burden at the country or sub-national level, is the complex diagnostic methods currently required for detecting these pathogens. These methods are neither sufficiently sensitive nor standardized and are not feasible in the resource poor settings where these infections occur most commonly. We developed a simple and rapid diagnostic assay called "Rapid Loop-mediated isothermal amplification based Diagnostic Test (RLDT)" for the detection of these pathogens in low-resource settings. Using RLDT, ETEC and Shigella were detected directly from the stool, in less than 1 hour with minimal hands-on time. The assay does not require maintaining a cold chain and is electricity-free. Being rapid, simple, and sensitive, RLDT can be scaled up and is appropriate to apply in the LMICs where ETEC and Shigella diarrhea are endemic.

Ultra-specific nucleic acid testing by target-activated nucleases

Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.

A novel label-free electrochemical immunesensor for ultrasensitive detection of LT toxin using prussian blue@gold nanoparticles composite as a signal amplification

In the current study, a novel electrochemical label-free immunosensor is proposed for sensitive detection of heat-labile enterotoxin (LT) from Escherichia coli. Firstly, a glassy carbon electrode (GCE) was modified by a mixture containing reduced graphene oxide/room temperature ionic liquid (rGO/RTIL) composite. Then, simultaneous electrodeposition of prussian blue and gold nanoparticles led to formation of prussian blue@gold nanoparticles (PB@GNPs) composite on the electrode surface. The modified electrode was characterized by field emission scanning electron microscopy (FE-SEM), energy dispersive spectroscopy (EDS), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques. After immobilization of anti-LT and blocking the unreacted sites with BSA (bovine serum albumin), the analytical performance of the proposed immunosensor was evaluated under optimal conditions (i.e. optimal pH, incubation time and temperature of incubation). Square wave voltammetry (SWV) was used to determine different concentrations of the LT antigen. The linear dynamic range of the proposed immunosensor was from 0.01 to 50 µg/mL and the detection limit of the immunosensor was found to be 0.0023 µg/mL. An acceptable selectivity in the real sample, long-term stability and goodreproducibility made the fabricated immunosensor a good candidate for detecting LT.

SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases

Infectious diseases are one of the most intimidating threats to human race, responsible for an immense burden of disabilities and deaths. Rapid diagnosis and treatment of infectious diseases offers a better understanding of their pathogenesis. According to the World Health Organization, the ideal approach for detecting foreign pathogens should be rapid, specific, sensitive, instrument-free, and cost-effective. Nucleic acid pathogen detection methods, typically PCR, have numerous limitations, such as highly sophisticated equipment requirements, reagents, and trained personnel relying on well-established laboratories, besides being time-consuming. Thus, there is a crucial need to develop novel nucleic acid detection tools that are rapid, specific, sensitive, and cost-effective, particularly ones that can be used for versatile point-of-care diagnostic applications. Two new methods exploit unpredicted in vitro properties of CRISPR-Cas effectors, turning activated nucleases into basic amplifiers of a specific nucleic acid binding event. These effectors can be attached to a diversity of reporters and utilized in tandem with isothermal amplification approaches to create sensitive identification in multiple deployable field formats. Although still in their beginning, SHERLOCK and DETECTR technologies are potential methods for rapid detection and identification of infectious diseases, with ultrasensitive tests that do not require complicated processing. This review describes SHERLOCK and DETECTR technologies and assesses their properties, functions, and prospective to become the ultimate diagnostic tools for diagnosing infectious diseases and curbing disease outbreaks.

Rapid Detection of Hepatitis B Virus in Blood Samples Using a Combination of Polymerase Spiral Reaction With Nanoparticles Lateral-Flow Biosensor

A rapid, highly sensitive, and robust diagnostic technique for point-of-care (PoC) testing can be developed using the combination of the nanoparticle-based lateral flow biosensors (LFB) and isothermal nucleic acid amplification technology. Here, we developed a polymerase spiral reaction (PSR) containing FITC-labeled DNA probes coupled with the nanoparticle-based LFB assay (PSR-LFB) to detect the amplified products to detect HBV visually. Under the optimized conditions, the PSR assay involved incubation of the reaction mixture for 20 min at 63°C, followed by visual detection of positive amplicons using LFB, which would generate a red test line based on the biotin/streptavidin interaction and immunoreactions, within 5 min. A cross-reactivity test revealed that the developed PSR-LFB assay showed good specificity for HBV and could distinguish HBV from other pathogenic microorganisms. For the analytical sensitivity, the limit of detection (LoD) of PSR-LFB assay was recorded as 5.4 copies/mL of HBV genomic DNA, which was ten-times more sensitive than qPCR and loop-mediated isothermal amplification (LAMP). Additionally, all the HBV-positive (29/82) samples, identified using ELISA, were also successfully detected by the PSR-LFB assay. We found that the true positive rate of the PSR-LFB assay was higher than that of qPCR (100 vs. 89.66%, respectively), as well as the LAMP assay (100 vs. 96.55%, respectively). Furthermore, the integrated procedure could be completed in 60 min, including the processing of the blood samples (30 min), an isothermal reaction (20 min), and result visualization (5 min). Thus, this PSR-LFB assay could be a potentially useful technique for PoC diagnosis of HBV in resource-limited countries.

Establishment and application of isothermal amplification techniques for the detection of heat-stable I enterotoxin of enterotoxigenic Escherichia coli

The aim of this study was to establish isothermal multiple self-matching initiated amplification (IMSA) and cross-priming amplification (CPA) methods to detect heat-stable I enterotoxin (STa)-producing enterotoxigenic Escherichia coli (ETEC). To avoid cross-contamination of aerosols, a closed independent isothermal amplification tube (IAT) was used to perform the assays. Optimal amplification conditions for IMSA and CPA were selected for specificity and sensitivity, respectively, and for clinical relevance. Both IMSA and CPA assays could specifically recognize all 3-STa positive strains in which they fluoresced green under UV light, but not in the 11 non-STa strains. The results of the sensitivity analysis indicated that the detection limit of the IMSA assay was 1.5 ×102 CFU, comparable to real-time PCR, but 10-fold more sensitive than CPA and LAMP. Further evaluation of the detection methods of swine diarrhea samples demonstrated that both could successfully identify the DNA of STa-producing ETEC in clinical specimens, consistent with LAMP and qPCR methods. The results demonstrated that the IMSA and CPA methods had high specificity and sensitivity with rapid detection of ETEC, so having great potential in clinical applications.

Rapid and Sensitive Detection of Hepatitis C Virus in Clinical Blood Samples Using Reverse Transcriptase Polymerase Spiral Reaction

This study established a new polymerase spiral reaction (PSR) that combines with reverse transcription reactions for HCV detection targeting 5'UTR gene. To avoid cross-contamination of aerosols, an isothermal amplification tube (IAT), as a separate containment control, was used to judge the result. After optimizing the RT-PSR reaction system, its effectiveness and specificity were tested against 15 different virus strains which included 8 that were HCV positive and 7 as non-HCV controls. The results showed that the RT-PSR assay effectively detected all 8 HCV strains, and no false positives were found among the 7 non-HCV strains. The detection limit of our RT-PSR assay is comparable to the real-time RT-PCR, but is more sensitive than the RT-LAMP. The established RT-PSR assay was further evaluated for detection of HCV in clinical blood samples, and the resulting 80.25% detection rate demonstrated better or similar effectiveness compared to the RT-LAMP (79.63%) and real-time RT-PCR (80.25%). Overall, the results showed that the RT-PSR assay offers high specificity and sensitivity for HCV detection with great potential for screening HCV in clinical blood samples.