Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review

Zatti, Matheus Silva; Arantes, Thales Domingos; Theodoro, Raquel Cordeiro

doi:10.1111/myc.13140

Cited by 21 publications

(5 citation statements)

References 103 publications

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“…Additionally, this case has highlighted the necessity for further development of new molecular biology methods in the future. For instance, methods for obtaining high-quality DNA from samples such as pus, specific primers for rapid Cryptococcus typing, and isothermal amplification systems that are both costeffective and faster than real-time quantitative polymerase chain reaction (PCR), among others [18,19] .…”

Section: Discussionmentioning

confidence: 99%

Disseminated Cryptococcosis Involving Skin and Lung in an Immunocompromised Patient After Kidney Transplantation: A Case Report

Shi,

Zhang,

Liu

et al. 2023

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Cryptococcus neoformans can cause detrimental cryptococcosis and other severe complications, especially in immunocompromised populations. Disseminated cryptococcosis in organ transplantation patients is extremely rare and often involves lungs, brains, skin, nails, and other organs. In this paper, we report a rare disseminated cryptococcosis case involving skin and lung that presented with recurrent dark brown abscesses and nodules in an immunocompromised female after kidney transplantation. The K-Set detection result of Cryptococcus capsular polysaccharide in serum is positive. The identification of pus culture by Autof MS 1000 indicates that the patient was infected with Cryptococcus neoformans var. grubii. In addition to treatment using liposomal amphotericin B, fluorocytosine, and fluconazole, local extraction of pus and simultaneous injection of liposomal amphotericin B into skin lesions were performed. This comprehensive treatment method proved effective, as the patient recovered from fever and skin symptoms. The innovative treatment may contribute to helping more disseminated cryptococcosis patients.

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Section: Discussionmentioning

confidence: 99%

Disseminated Cryptococcosis Involving Skin and Lung in an Immunocompromised Patient After Kidney Transplantation: A Case Report

Shi,

Zhang,

Liu

et al. 2023

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“…LAMP is sensitive, inexpensive, equipment-free, convenient to use, and requires at least four primers for recognition of six different regions in the target DNA [ 75 ]. In the field of mycology, based on the gp43 gene, Endo et al, for the first time, developed a LAMP primer set for Paracoccidioides brasiliensis and detected this gene in 22 clinical and seven armadillo-derived isolates [ 76 ].…”

Section: Other Emerging Modalities Of Nucleic-acid-based Molecular Di...mentioning

confidence: 99%

Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future

Gudisa,

Harchand,

Rudramurthy

2024

Diagnostics

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The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.

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“…Fungal infections, conventionally dependent on morphological and physiological clinical tests demanding days to weeks, can be simplified, turned economical, and made rapid using RCA and with improved specificity and robustness, as demonstrated for the 10-plexed detection of pathogenic fungi . PLP-RCA targeting the internal transcribed spacer rDNA of Histoplasma capsulatum , causing a systemic fungal disease called histoplasmosis, enabled the rapid and specific detection of the fungus in clinical samples .…”

Section: Padlock Probes and Rolling Circle Amplification For Pathogen...mentioning

confidence: 99%

Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping

2021

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Metrics & MoreArticle Recommendations CONSPECTUS:The development of robust methods allowing the precise detection of specific nucleic acid sequences is of major societal relevance, paving the way for significant advances in biotechnology and biomedical engineering. These range from a better understanding of human disease at a molecular level, allowing the discovery and development of novel biopharmaceuticals and vaccines, to the improvement of biotechnological processes providing improved food quality and safety, efficient green fuels, and smart textiles. Among these applications, the significance of pathogen diagnostics as the main focus of this Account has become particularly clear during the recent SARS-CoV-2 pandemic. In this context, while RT-PCR is the gold standard method for unambiguous detection of genetic material from pathogens, other isothermal amplification alternatives circumventing rapid heating−cooling cycles up to ∼95 °C are appealing to facilitate the translation of the assay into point-of-care (PoC) analytical platforms. Furthermore, the possibility of routinely multiplexing the detection of tens to hundreds of target sequences with single base pair specificity, currently not met by state-of-the-art methods available in clinical laboratories, would be instrumental along the path to tackle emergent viral variants and antimicrobial resistance genes. Here, we advocate that padlock probes (PLPs), first reported by Nilsson et al. in 1994, coupled with rolling circle amplification (RCA), termed here as PLP-RCA, is an underexploited technology in current arena of isothermal nucleic acid amplification tests (NAATs) providing an unprecedented degree of multiplexing, specificity, versatility, and amenability to integration in miniaturized PoC platforms. Furthermore, the intrinsically digital amplification of PLP-RCA retains spatial information and opens new avenues in the exploration of pathogenesis with spatial multiomics analysis of infected cells and tissue. The Account starts by introducing PLP-RCA in a nutshell focusing individually on the three main assay steps, namely, (1) PLP design and ligation mechanism, (2) RCA after probe ligation, and (3) detection of the RCA products. Each subject is touched upon succinctly but with sufficient detail for the reader to appreciate some assay intricacies and degree of versatility depending on the analytical challenge at hand. After familiarizing the reader with the method, we discuss specific examples of research in our group and others using PLP-RCA for viral, bacterial, and fungal diagnostics in a variety of clinical contexts, including the genotyping of antibiotic resistance genes and viral subtyping. Then, we dissect key developments in the miniaturization and integration of PLP-RCA to minimize user input, maximize analysis throughput, and expedite the time to results, ultimately aiming at PoC applications. These developments include molecular enrichment for maximum sensitivity, spatial arrays to maximize analytical throughput, automation of liquid handlin...

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Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review

Cited by 21 publications

References 103 publications

Disseminated Cryptococcosis Involving Skin and Lung in an Immunocompromised Patient After Kidney Transplantation: A Case Report

Disseminated Cryptococcosis Involving Skin and Lung in an Immunocompromised Patient After Kidney Transplantation: A Case Report

Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future

Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping

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