Simple and rapid detection Aspergillus fumigatus by loop-mediated isothermal amplification coupled with lateral flow biosensor assay

Development of a TaqMan probe-based multiplex real-time PCR for the simultaneous detection of four clinically important filamentous fungi

Filamentous fungi present significant health hazards to immunocompromised individuals globally; however, the prompt and precise identification of them during infection remains challenging. In this study, a TaqMan probe-based multiplex real-time PCR (M-qPCR) assay was developed to detect simultaneously the target genes of four important pathogenic filamentous fungi: ANXC4 gene of Aspergillus fumigatus, EF1-α gene of Fusarium spp., mitochondrial rnl gene of Mucorales, and hcp100 gene of Histoplasma capsulatum. In this M-qPCR assay, the limit of detection (LoD) to all four kinds of fungi was 100 copies and the correlation coefficients (R2) were above 0.99. The specificity of this assay is 100%, and the minimum detection limit is 100 copies/reaction. In conclusion, an M-qPCR detection assay was well established with high specificity and sensitivity for rapid and simultaneous detection on four important filamentous fungi in the clinic.

IMPORTANCE

World Health Organization developed the first fungal priority pathogens list (WHO FPPL) in 2022. Aspergillus fumigatus, Mucorales, Fusarium spp., and Histoplasma spp. are the four types of pathogenic fungi with filamentous morphology in the critical priority group and high priority group of WHO FPPL. These four filamentous fungal infections have become more common and severe in immunocompromised patients with the increase in susceptible populations in recent decades, which resulted in a substantial burden on the public health system. However, prompt and precise identification of them during infection remains challenging. Our study established successfully a TaqMan probe-based multiplex real-time qPCR assay for four clinically important filamentous fungi, A. fumigatus, Fusarium spp., Mucorales, and Histoplasma capsulatum, with high sensitivity and specificity, which shows promising potential for prompt and precise diagnosis against fungal infection.

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.

Utility of a loop-mediated isothermal amplification detection kit to diagnose chronic pulmonary aspergillosis

BACKGROUND

Diagnosing chronic pulmonary aspergillosis (CPA) is still challenging, and infection with Aspergillus spp. must be detected early. The aim of this study was to evaluate, for the first time, the usefulness of a new loop-mediated isothermal amplification (LAMP) test kit in diagnosing CPA.

METHODS

This cross-sectional study was performed at the National Hospital Organization Kinki-Chuo Chest Medical Center. We prospectively enrolled patients with and without CPA. The primary outcomes of this study were the sensitivity and specificity of LAMP for the diagnosis of CPA.

RESULTS

In total, 34 patients with CPA and 21 without CPA (the control group) were enrolled between October 2019 and December 2021. Among the 34 patients with CPA, cultures were positive for CPA in 16 and negative for 18. The majority of fungi isolated in sputum were A. fumigatus in 15 specimens; Aspergillus flavus was isolated in 1) LAMP demonstrated 55.9% sensitivity (95% confidence interval [CI] 37.9-72.8) and 100.0% specificity (95% CI 77.2-100.0).

CONCLUSION

LAMP is an acceptable tool for diagnosing CPA, and its application in clinical practice necessitates more studies.

Specific and sensitive loop-mediated isothermal amplification (LAMP) method for Madurella strains, eumycetoma filamentous fungi causative agent

BACKGROUND

Filamentous fungi of the genus Madurella are the primary causative agents of mycetoma, a disease observed in tropical and subtropical regions. Since early diagnostics based on a morphological approach are difficult and have many shortcomings, a molecular diagnostic method suitable for rural settings is required. In this study, we developed the loop-mediated isothermal amplification (LAMP) method to present a foundational technique of the diagnosis of Madurella spp. (M. mycetomatis, M. pseudomycetomatis, M. tropicana, and M. fahalii), the common causative organisms of eumycetoma.

PRINCIPAL FINDINGS

We successfully designed a primer pair targeting the rDNAs of three Madurella spp. excluding M. fahalii, and detected up to 100 fg of genomic DNA extracted from isolates of M. mycetomatis and 1 pg of M. pseudomycetomatis and M. tropicana, within one hour. Second, a primer pair specific to M. mycetomatis, the most common causative species, or M. fahalii, a drug-resistant species, was constructed, and the detection limit of both primer pairs was 1 pg. The designed primers accurately distinguished 16 strains of the genus Madurella from various fungal species known to cause mycetomas.

CONCLUSION

In summary, we established the first model of a LAMP detection method that rapidly and sensitively detects and identifies Madurella isolates for clinical diagnostics. Moreover, the combined designed primer sets could identify mycetoma-causing strains simultaneously.

Diagnostic Efficacy of LAMP Assay for Human Fungal Pathogens: a Systematic Review and Meta-analysis

Purpose

Human fungal infections particularly caused by Candida and Aspergillus have emerged as major public health burden. Long turnaround time and poor sensitivity of the conventional diagnostics are the major impediments for faster diagnosis of human fungal pathogens.

Recent Findings

To overcome these issues, molecular-based diagnostics have been developed. They offer enhanced sensitivity but require sophisticated infrastructure, skilled manpower, and remained expensive. In that context, loop-mediated isothermal amplification (LAMP) assay represents a promising alternative that facilitates visual read outs. However, to eradicate fungal infections, all forms of fungi must be accurately detected. Thus, a need for alternative testing methodologies is imperative that should be rapid, accurate and facilitate widespread adoption. Therefore, the aim of the present study is to conduct a meta-analysis to assess the diagnostic efficiency of LAMP in the detection of a panel of human fungal pathogens following PRISMA guidelines using scientific databases viz. PubMed, Google Scholar, Science Direct, Scopus, BioRxiv, and MedRxiv.

Summary

From various studies reported on the diagnosis of fungi, only 9 articles were identified as eligible to meet the criteria of LAMP based diagnosis. Through this meta-analysis, it was found that most of the studies were conducted in China and Japan with sputum and blood as the most common specimens to be used for LAMP assay. The collected data underlined that ITS gene and fluorescence-based detections ranked as the most used target and method. The pooled sensitivity values of meta-analysis ranged between 0.71 and 1.0 and forest plot and SROC (summary receiver operating characteristic) curve revealed a pooled specificity values between 0.13 and 1.0 with the confidence interval of 95%, respectively. The accuracy and precision rates of eligible studies mostly varied between 70 to 100% and 68 to 100%, respectively. A quality assessment based on QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies) of bias and applicability was conducted which depicted low risk of bias and applicability concerns. Together, LAMP technology could be considered as a feasible alternative to current diagnostics considering high fungal burden for rapid testing in low resource regions.

Approach to the diagnosis of invasive fungal infections of the respiratory tract in the immunocompromised host

PURPOSE OF REVIEW

The burden of invasive fungal infection is increasing worldwide, largely due to a growing population at-risk. Most serious human fungal pathogens enter the host via the respiratory tract. Early identification and treatment of invasive fungal respiratory infections (IFRIs) in the immunocompromised host saves lives. However, their accurate diagnosis is a difficult challenge for clinicians and mortality remains high.

RECENT FINDINGS

This article reviews IFRIs, focussing on host susceptibility factors, clinical presentation, and mycological diagnosis. Several new diagnostic tools are coming of age including molecular diagnostics and point-of-care antigen tests. As diagnosis of IFRI relies heavily on invasive procedures like bronchoalveolar lavage and lung biopsy, several novel noninvasive diagnostic techniques are in development, such as metagenomics, 'volatilomics' and advanced imaging technologies.

SUMMARY

Where IFRI cannot be proven, clinicians must employ a 'weights-of-evidence' approach to evaluate host factors, clinical and mycological data. Implementation studies are needed to understand how new diagnostic tools can be best applied within clinical pathways. Differentiating invasive infection from colonization and identifying antifungal resistance remain key challenges. As our diagnostic arsenal expands, centralized clinical mycology laboratories and efforts to ensure access to new diagnostics in low-resource settings will become increasingly important.

Point-of-Care Testing for the Diagnosis of Fungal Infections

Invasive fungal infections are increasing worldwide due to factors such as climate change and immunomodulating therapies. Unfortunately, the detection of these infections is limited due to the low sensitivity and long periods required for laboratory testing. Point-of-care testing could lead to more rapid diagnosis of these often devasting infections. However, there are currently no true point-of-care tests on the market for the detection of fungi. In this article, the current state of fungal antigen and molecular testing is reviewed, with commentary on the potential for development and use in the point-of-care setting.

Visual closed dumbbell-mediated isothermal amplification (CDA) for on-site detection of Rickettsia raoultii

Spotted fever group (SFG) rickettsioses are important zoonoses, threatening human health seriously and gradually attracting more attention in the world. SFG rickettsiae are classified as neglected pathogens. If these pathogens are detected at all, they are usually recognized very late in the infection through indirect detection of specific antibodies. Previous studies have shown that Rickettsia raoultii (R. raoultii), a member of the SFG rickettsiae, occurs with increasing incidence in remote countries. Therefore, a rapid detection method for R. raoultii is in urgently need. In this study, a R. raoultii diagnosis method by closed dumbbell-mediated isothermal amplification (R-CDA) assay targeting a conserved sequence of the outer membrane protein A (OmpA) gene with high sensitivity and specificity was developed. This assay offered a rapid and simple method for on-site detection of R. raoultii. Firstly, four pairs of R-CDA primers were designed and the optimum primer set was selected to amplify target gene specifically and effectively. Then, a pair of outer primer was designed to accelerate the reaction based on the inner primers to establish the RO-CDA reaction. In addition, the results of real-time amplification curves, melting curves and end-point colorimetric judgements showed that the established visual RO-CDA reaction could accurately detect R. raoultii without cross-reaction with other closely related pathogens. Furthermore, the detection limit of visual RO-CDA assay was 10 copies/μL, which was feasible for on-site detection with merits of easy-operation, rapidity, high sensitivity, and specificity. In conclusion, the developed RO-CDA detection method could be helpful for pathogen screening and epidemic prevention at the point of care.

Spotted fever group (SFG) rickettsioses are important neglected zoonoses throughout the world, with expanding known distribution, among which R. raoultii is an emerging member. As the clinical symptoms of R. raoultii is similar to other diseases, the accurate diagnosis of the pathogen based on the detection of genome plays a vital role in effective treatment and control at low infection levels. Due to the lack of on-site detection technology of Rickettsia raoultii in remote areas, the pathogen can only be treated in the late infection stage with specific clinical symptoms. Closed dumbbell-mediated isothermal amplification (CDA) is a method that rapidly amplifies nucleic acids under isothermal condition, which can help to resolve the problem of point of care detection for R. raoultii. The established R. raoultii detection approach based on CDA was feasible for on-site detection with merits of easy-operation, rapidity, high sensitivity, and specificity. At last, compared with PCR and LAMP, CDA method is simpler and more efficient to detect R. raoultii, which helps to improve the efficiency of detection and strengthen the prevention and control of this neglected but widely distributed disease.

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 Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.