Detection of Fungi from an Indoor Environment using Loop-mediated Isothermal Amplification (LAMP) Method

Isothermal nucleic acid amplification for monitoring hand-foot-and-mouth disease: current status and future implications

With the global prevalence of the hand-foot-and-mouth disease (HFMD) epidemic, the development of reliable point-of-care testing (POCT) is crucial for the timely identification and prevention of outbreaks. Isothermal nucleic acid amplification techniques (INAATs) have attracted much attention because of their high efficiency for rapid diagnosis. In this work, we systematically summarize the current status of INAATs for HFMD and discuss advantages and drawbacks of various INAATs for HFMD. The INAATs for HFMD detection mainly include loop-mediated isothermal amplification (LAMP), simultaneous amplification and testing (SAT), and recombinase polymerase amplification (RPA). Among them, LAMP has excelled in several diagnostic metrics and has made significant progress in the field of POCT. SAT has been effective in overcoming the problem of RNA degradation. RPA is suited for on-site testing due to its rapid amplification rate and low reaction temperature. In addition, this study explores the potential of INAATs in lateral flow strips (LFS) test and microfluidic devices for HFMD. LFS is typically used for qualitative analysis and supports multiple detection. Microfluidics can integrate necessary processes of sample pre-processing, amplification, and signal output, enabling high-throughput qualitative or quantitative detection and demonstrating the potential of monitoring HFMD. We hope the current work will provide insights into INAATs for monitoring HFMD and serve as a reference for the implementation of on-site EV detection for public health.

In the flow of molecular miniaturized fungal diagnosis

The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.

Monkeypox virus: insights into pathogenesis and laboratory testing methods

The monkeypox virus (MPXV) is a zoonotic pathogen that transmits between monkeys and humans, exhibiting clinical similarities with the smallpox virus. Studies on the immunopathogenesis of MPXV revealed that an initial strong innate immune response is elicited on viral infection that subsequently helps in circumventing the host defense. Once the World Health Organization (WHO) declared it a global public health emergency in July 2022, it became essential to clearly demarcate the MPXV-induced symptoms from other viral infections. We have exhaustively searched the various databases involving Google Scholar, PubMed, and Medline to extract the information comprehensively compiled in this review. The primary focus of this review is to describe the diagnostic methods for MPXV such as polymerase chain reaction (PCR), and serological assays, along with developments in viral isolation, imaging techniques, and next-generation sequencing. These innovative technologies have the potential to greatly enhance the accuracy of diagnostic procedures. Significant discoveries involving MPXV immunopathogenesis have also been highlighted. Overall, this will be a knowledge repertoire that will be crucial for the development of efficient monitoring and control strategies in response to the MPXV infection helping clinicians and researchers in formulating healthcare strategies.

An Integrated and Multi-Target Nucleic Acid Isothermal Analysis System for Rapid Diagnosis of Vulvovaginal Candidiasis

Rapid identification of Candida species is significant for the diagnosis of vulvovaginal candidiasis (VVC). An integrated and multi-target system for the rapid, high-specificity, and high-sensitivity detection of four Candida species was developed. The system consists of a rapid sample processing cassette and a rapid nucleic acid analysis device. The cassette could process the Candida species to release nucleic acids in 15 min. The released nucleic acids were analyzed by the device as fast as within 30 min, using the loop-mediated isothermal amplification method. The four Candida species could be simultaneously identified, with each reaction using only 1.41 µL of reaction mixture, which was low cost. The RPT (rapid sample processing and testing) system could detect the four Candida species with high sensitivity (<2 CFU/reaction) and high specificity. The system also processed and analyzed 32 clinical samples, giving the results with high clinical sensitivity and specificity. Hence, the system was a significant and effective platform for the diagnosis of VVC. Furthermore, the period of validity of the reagents and chips used in the system was >90 days, and the system could also be used for the detection of bacteria.

Development of a Loop-Mediated Isothermal Amplification Method for Rapid and Visual Detection of Monkeypox Virus

Monkeypox virus (MPXV) is a human pathogenic virus that belongs to the genus Orthopoxvirus. In 2022, MPXV caused an unprecedented number of infections in many countries. As it is difficult to distinguish MPXV from other pathogens by its symptoms in the early stage of infection, a rapid and reliable assay for MPXV detection is needed. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay for the specific detection of MPXV and evaluated its application in simulated clinical samples. The A27L-1 and F3L-1 primer sets were identified as the optimal primers, and 63°C was the most appropriate reaction temperature for sequence amplification. The detection limits of the LAMP assay using primer sets A27L-1 and F3L-1 were both 20 copies/reaction mixture, which were >100-fold higher in terms of sensitivity, compared with conventional PCR. The LAMP assay findings were negative for all 21 non-MPXV pathogens, confirming the high specificity of our assay. All three types of simulated clinical samples were clearly identified by our LAMP assay, and the detection limits were consistent with the sensitivity results, indicating efficient clinical sample identification. Our rapid and reliable MPXV LAMP assay could be useful for MPXV detection and on-site diagnosis, especially in primary hospitals and rural areas. IMPORTANCE MPXV outbreaks rapidly grew in the first half of 2022, and this virus has been recognized as an increasing public health threat, particularly in the context of the COVID-19 pandemic. Thus, developing reliable and fast detection methods for MPXV is necessary.

Loop-mediated isothermal amplification for Candida species surveillance in under-resourced setting: a review of evidence

INTRODUCTION

Non-albicans Candida species (NACS) have emerged as a major public health burden although they are still underappreciated. Some NACS have intrinsic antifungal resistance, requiring constant surveillance to improve patient care and thwart outbreaks of recalcitrant candida infections. However, effective Candida species surveillance has relied on PCR-based or other high-end techniques that are largely unaffordable in under-resourced countries. Loop-mediated isothermal amplification (LAMP) has emerged as a potentially effective and affordable technique for infectious disease surveillance, especially in under resourced settings.

AREAS COVERED

We critically reviewed current literature on application of LAMP for Candida species identification in pure fungal isolates, and in clinical and non-clinical samples.

EXPERT OPINION

LAMP has been studied for Candida species identification, including the NACS. Besides a short turnaround time, LAMP has analytical sensitivity and specificity that are not only higher than culture method but also comparable with conventional and quantitative PCR techniques. However, extensive evaluation of LAMP for Candida species detection using various types of clinical and environmental samples are required before deploying the technique for Candida species surveillance.

Recent advances in loop-mediated isothermal amplification (LAMP) for rapid and efficient detection of pathogens

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Significance of LAMP method in rapid disease diagnosis is highlighted.

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Different detection methods for amplicon visualization are explained.

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Advancements in LAMP technique for disease identification are summarized.

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Trends in development of LAMP disease diagnosis are discussed.

Loop-mediated isothermal amplification (LAMP) method has been demonstrated to bea reliable and robust method for detection and identification of viral and microbial pathogens. LAMP method of amplification, coupled with techniques for easy detection of amplicons, makes a simple-to-operate and easy-to-read molecular diagnostic tool for both laboratory and on-field settings. Several LAMP-based diagnostic kits and assays have been developed that are specifically targeted against a variety of pathogens. With the growing needs of the demanding molecular diagnostic industry, many technical advances have been made over the years by combining the basic LAMP principle with several other molecular approaches like real-time detection, multiplex methods, chip-based assays.This has resulted in enhancing thethe sensitivity and accuracy of LAMP for more rigorous and wide-ranging pathogen detection applications. This review summarizes the current developments in LAMP technique and their applicability in present and future disease diagnosis.

The developed molecular biological identification tools for mycetoma causative agents: An update

Mycetoma is a chronic granulomatous inflammatory disease that is caused either by bacteria or fungi. Bacterial mycetoma (actinomycetoma) can be caused by various causative agents of the genera Nocardia, Streptomyces and Actinomadura. On the other hand, fungal mycetoma (eumycetoma) is most commonly caused by causative agents belonging to the genera Madurella, Scedosporium and Falciformispora. Early and accurate diagnosis of the causative organisms can guide proper patient management and treatment. To allow rapid and accurate species identification, different molecular techniques were developed over the past decades. These techniques can be protein based (MALDI-TOF MS) as well as DNA based (Sequencing, PCR and isothermal amplification methods). In this review, we provide an overview of the different molecular techniques currently in use and identify knowledge gaps, which need to be addressed before we can implement molecular diagnostics for mycetoma in different clinical settings.

Development and comparison of loop-mediated isothermal amplification with quantitative PCR for the specific detection of Saprolegnia spp

Saprolegniasis is an important disease in freshwater aquaculture, and is associated with oomycete pathogens in the genus Saprolegnia. Early detection of significant levels of Saprolegnia spp. pathogens would allow informed decisions for treatment which could significantly reduce losses. This study is the first to report the development of loop-mediated isothermal amplification (LAMP) for the detection of Saprolegnia spp. and compares it with quantitative PCR (qPCR). The developed protocols targeted the internal transcribed spacer (ITS) region of ribosomal DNA and the cytochrome C oxidase subunit 1 (CoxI) gene and was shown to be specific only to Saprolegnia genus. This LAMP method can detect as low as 10 fg of S. salmonis DNA while the qPCR method has a detection limit of 2 pg of S. salmonis DNA, indicating the superior sensitivity of LAMP compared to qPCR. When applied to detect the pathogen in water samples, both methods could detect the pathogen when only one zoospore of Saprolegnia was present. We propose LAMP as a quick (about 20–60 minutes) and sensitive molecular diagnostic tool for the detection of Saprolegnia spp. suitable for on-site applications.

A chemiluminescence-based heterogeneous asymmetric recombinase polymerase amplification assay for the molecular detection of mycotoxin producers

The analysis of mold in indoor air is a prominent topic but it is hardly dealt with. The most affected fields of this issue are residential- and occupational safety since mold can have a number of impacts on human health. To date the most used methods for quantification of microorganism contamination in indoor air are culture- or microscopy-based and are not capable of translating the on-site situation to analytical data reliably. Here we present a chemiluminescence-based method to detect mycotoxin producers through isothermal amplification of mycotoxin biosynthesis genes using glass and polycarbonate carriers. In this proof-of-principle study, zearalenone producers were aimed to be detected by heterogeneous asymmetric recombinase polymerase amplification (haRPA). For this, an appropriate lysis method for fungal spores was developed allowing rapid access to DNA. A system calibration with spores of Fusarium culmorum as zearalenone-producing organism resulted in an LOD of 2.7 × 10⁵ spores per ml. The system was shown to be specific for zearalenone producers. This work presents the first application of a heterogeneous isothermal amplification for rapid detection and quantification of mycotoxin producers. In the future, a multiplex detection can be possible by haRPA.

Fungal keratitis: Pathogenesis, diagnosis and prevention

As a kind of serious, potentially sight-threatening corneal infections with poor prognosis, fungal keratitis can bring a heavy economic burden to patients and seriously affect the quality of life, especially those in developing countries where fungal keratitis is more prevalent. Typical clinical features include immune rings, satellite lesions, pseudopods, hypha moss, hypopyon and endothelial plaques. The ideal therapeutic effects could not be achieved by current treatments for many reasons. Therefore, under the current status, understanding the pathogenesis, early diagnosis and prevention strategies might be of great importance. Here, in this review, we discuss the recent progresses that may advance our understanding of pathogenesis, early diagnosis and prevention of fungal keratitis.

Instrument-Free and Visual Detection of Salmonella Based on Magnetic Nanoparticles and an Antibody Probe Immunosensor

Salmonella, a common foodborne pathogen, causes many cases of foodborne illness and poses a threat to public health worldwide. Immunological detection systems can be combined with nanoparticles to develop sensitive and portable detection technologies for timely screening of Salmonella infections. Here, we developed an antibody-probe-based immuno-N-hydroxysuccinimide (NHS) bead (AIB) system to detect Salmonella. After adding the antibody probe, Salmonella accumulated in the samples on the surfaces of the immuno-NHS beads (INBs), forming a sandwich structure (INB–Salmonella–probes). We demonstrated the utility of our AIB diagnostic system for detecting Salmonella in water, milk, and eggs, with a sensitivity of 9 CFU mL⁻¹ in less than 50 min. The AIB diagnostic system exhibits highly specific detection and no cross-reaction with other similar microbial strains. With no specialized equipment or technical requirements, the AIB diagnostic method can be used for visual, rapid, and point-of-care detection of Salmonella.

Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms

Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.