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Kobayashi T, Tsuyuguchi K, Shimatani Y, Matsuda Y, Kagawa T, Takimoto T, Takeuchi N, Arai T, Inoue Y. Utility of a loop-mediated isothermal amplification detection kit to diagnose chronic pulmonary aspergillosis. J Infect Chemother 2024; 30:7-11. [PMID: 37660734 DOI: 10.1016/j.jiac.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
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.
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Affiliation(s)
- Takehiko Kobayashi
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan; Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan.
| | - Yasuaki Shimatani
- Department of Clinical Microbiology, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Yoshinobu Matsuda
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan; Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Tomoko Kagawa
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Takayuki Takimoto
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Naoko Takeuchi
- Department of Internal Medicine, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Toru Arai
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Sakai City, Osaka, Japan
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Yoshioka I, Mori Y, Fahal AH, Siddig EE, Kaneko S, Yaguchi T. Specific and sensitive loop-mediated isothermal amplification (LAMP) method for Madurella strains, eumycetoma filamentous fungi causative agent. PLoS Negl Trop Dis 2023; 17:e0011644. [PMID: 37721946 PMCID: PMC10538720 DOI: 10.1371/journal.pntd.0011644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
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.
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Affiliation(s)
- Isato Yoshioka
- Medical Mycology Research Center, Chiba University, Chiba, Chiba, Japan
- Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Yugo Mori
- Medical Mycology Research Center, Chiba University, Chiba, Chiba, Japan
| | | | | | - Satoshi Kaneko
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Chiba, Japan
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Bumbrah GS, Jain S, Singh S, Fatima Z, Hameed S. Diagnostic Efficacy of LAMP Assay for Human Fungal Pathogens: a Systematic Review and Meta-analysis. Curr Fungal Infect Rep 2023; 17:1-11. [PMID: 37360855 PMCID: PMC10150145 DOI: 10.1007/s12281-023-00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
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.
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Affiliation(s)
- Gurvinder Singh Bumbrah
- Department of Forensic Sciences, Amity School of Applied Sciences, Amity University Haryana, Gurugram, 122413 Manesar India
| | - Sarika Jain
- Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, 122413 Manesar India
| | - Shweta Singh
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, 122413 Manesar India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, 122413 Manesar India
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, 61922 Saudi Arabia
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, 122413 Manesar India
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Houston H, Wilson AJ, Stone N. Approach to the diagnosis of invasive fungal infections of the respiratory tract in the immunocompromised host. Curr Opin Pulm Med 2023. [PMID: 36917216 DOI: 10.1097/MCP.0000000000000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
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.
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Luethy PM. Point-of-Care Testing for the Diagnosis of Fungal Infections. Clin Lab Med 2023; 43:209-220. [PMID: 37169443 DOI: 10.1016/j.cll.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
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.
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Gui Z, Cai H, Wu L, Miao Q, Yu JF, Cai T, Mao R. Visual closed dumbbell-mediated isothermal amplification (CDA) for on-site detection of Rickettsia raoultii. PLoS Negl Trop Dis 2022; 16:e0010747. [PMID: 36084136 PMCID: PMC9491570 DOI: 10.1371/journal.pntd.0010747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/21/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022] Open
Abstract
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.
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Affiliation(s)
- Zheng Gui
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Hao Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Lin Wu
- Graduate School, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Qing Miao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Jing feng Yu
- Department of Parasitology, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
- * E-mail: (JY); (TC); (RM)
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- * E-mail: (JY); (TC); (RM)
| | - Rui Mao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- * E-mail: (JY); (TC); (RM)
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Garg N, Ahmad FJ, Kar S. Recent advances in loop-mediated isothermal amplification (LAMP) for rapid and efficient detection of pathogens. Current Research in Microbial Sciences 2022; 3:100120. [PMID: 35909594 PMCID: PMC9325740 DOI: 10.1016/j.crmicr.2022.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 11/01/2022] Open
Abstract
Significance of LAMP method in rapid disease diagnosis is highlighted. Different detection methods for amplicon visualization are explained. Advancements in LAMP technique for disease identification are summarized. 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.
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens. Plants (Basel) 2021; 10:plants10112424. [PMID: 34834787 PMCID: PMC8621059 DOI: 10.3390/plants10112424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/27/2023]
Abstract
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.
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