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Yasuda I, Saludar NRD, Sayo AR, Suzuki S, Yokoyama A, Ozeki Y, Kobayashi H, Nishiyama A, Matsumoto S, Cox SE, Tanaka T, Yamashita Y. Evaluation of cytokine profiles related to Mycobacterium tuberculosis latent antigens using a whole-blood assay in the Philippines. Front Immunol 2024; 15:1330796. [PMID: 38665909 PMCID: PMC11044679 DOI: 10.3389/fimmu.2024.1330796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction There is no useful method to discriminate between latent tuberculosis infection (LTBI) and active pulmonary tuberculosis (PTB). This study aimed to investigate the potential of cytokine profiles to discriminate between LTBI and active PTB using whole-blood stimulation with Mycobacterium tuberculosis (MTB) antigens, including latency-associated antigens. Materials and methods Patients with active PTB, household contacts of active PTB patients and community exposure subjects were recruited in Manila, the Philippines. Peripheral blood was collected from the participants and used for whole-blood stimulation (WBS) with either the early secretory antigenic target and the 10-kDa culture filtrate protein (ESAT-6/CFP-10), Rv3879c or latency-associated MTB antigens, including mycobacterial DNA-binding protein 1 (MDP-1), α-crystallin (Acr) and heparin-binding hemagglutinin (HBHA). Multiple cytokine concentrations were analyzed using the Bio-Plex™ multiplex cytokine assay. Results A total of 78 participants consisting of 15 active PTB patients, 48 household contacts and 15 community exposure subjects were eligible. The MDP-1-specific IFN-γ level in the active PTB group was significantly lower than that in the household contact group (p < 0.001) and the community exposure group (p < 0.001). The Acr-specific TNF-α and IL-10 levels in the active PTB group were significantly higher than those in the household contact (TNF-α; p = 0.001, IL-10; p = 0.001) and community exposure (TNF-α; p < 0.001, IL-10; p = 0.01) groups. However, there was no significant difference in the ESAT-6/CFP-10-specific IFN-γ levels among the groups. Conclusion The patterns of cytokine profiles induced by latency-associated MTB antigens using WBS have the potential to discriminate between LTBI and active PTB. In particular, combinations of IFN-γ and MDP-1, TNF-α and Acr, and IL-10 and Acr are promising. This study provides the first demonstration of the utility of MDP-1-specific cytokine responses in WBS.
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Affiliation(s)
- Ikkoh Yasuda
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of General Internal Medicine and Clinical Infectious Diseases, Fukushima Medical University, Fukushima, Japan
- Department of General Internal Medicine and Infectious Diseases, Kita-Fukushima Medical Center, Fukushima, Japan
| | | | | | - Shuichi Suzuki
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Akira Yokoyama
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
- Department of Respiratory Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
| | - Haruka Kobayashi
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University Graduate School of Medicine, Niigata, Japan
- Department of Medical Microbiology, Universitas Airlangga, Faculty of Medicine, Surabaya, Indonesia
- Division of Research Aids, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
| | - Sharon E. Cox
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Takeshi Tanaka
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Infectious Diseases, Nagasaki University Hospital, Nagasaki, Japan
- Infection Control and Education Center, Nagasaki University Hospital, Nagasaki, Japan
| | - Yoshiro Yamashita
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Respiratory Medicine, Shunkaikai Inoue Hospital, Nagasaki, Japan
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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] [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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David A, Scott LE, Da Silva P, Mayne E, Stevens WS. Storage of Mycobacterium tuberculosis culture isolates in Microbank TM beads at a South African laboratory. Afr J Lab Med 2023; 12:2172. [PMID: 38023785 PMCID: PMC10646387 DOI: 10.4102/ajlm.v12i1.2172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Mycobacterium tuberculosis complex (MTBC) isolates are typically stored at -70 °C in cryovials containing 1 mL aliquots of a liquid medium, with or without 50% glycerol. Multiple uses of the culture stock may decrease the strain viability while increasing the risk of culture contamination. Small culture aliquots may be more practical; however, storage capacity remains challenging. MicrobankTM beads (25 beads/vial) for the long-term storage of fungal cultures is well documented, but their use for storing MTBC isolates is uninvestigated. Objective The study aimed to determine the feasibility of using MicrobankTM beads for long-term storage of MTBC isolates at a laboratory in South Africa. Methods In February 2020, 20 isolates in liquid culture were stored in MicrobankTM beads, following an in-house developed protocol, at -70 °C. At defined time points (16 months [15 June 2021] and 21 months [18 November 2021]), two beads were retrieved from each storage vial and assessed for viability and level of contamination. Results Stored liquid isolates demonstrated MTBC growth within an average time-to-detection of 18 days following retrieval, even at 21 months post storage. Contaminating organisms were detected in 2 of 80 (2.5%) culture isolates. Conclusion MicrobankTM beads will allow for the reculture of up to 25 culture isolates using a reduced culture volume compared to current storage methods. MicrobankTM beads represent a storage solution for the medium-term storage of MTBC isolates. What this study adds This study evaluated the use of MicrobankTM beads as an alternate method for storing MTBC culture isolates at -70 °C and provided a suitable option for medium-term storage of MTBC.
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Affiliation(s)
- Anura David
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lesley E. Scott
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Pedro Da Silva
- National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
| | - Elizabeth Mayne
- National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
- Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Wendy S. Stevens
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Program, National Health Laboratory Services, Johannesburg, South Africa
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Werbajh S, Larocca L, Carrillo C, Stolowicz F, Ogas L, Pallotto S, Cassará S, Mammana L, Zapiola I, Bouzas MB, Vojnov AA. Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation. Viruses 2023; 15:1910. [PMID: 37766315 PMCID: PMC10537693 DOI: 10.3390/v15091910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas.
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Affiliation(s)
- Santiago Werbajh
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Luciana Larocca
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Carolina Carrillo
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Fabiana Stolowicz
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Lorena Ogas
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Sergio Pallotto
- Laboratorio Pablo Cassará S.R.L. Saladillo 2452, Buenos Aires C1440FFX, Argentina
| | - Solange Cassará
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
| | - Liliana Mammana
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Inés Zapiola
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - María Belén Bouzas
- Sección Virología, Hospital de Enfermedades Infecciosas Francisco Javier Muñiz Uspallata 2272, Buenos Aires C1282AEN, Argentina (I.Z.); (M.B.B.)
| | - Adrian A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET. Saladillo 2468, Buenos Aires C1440FFX, Argentina (C.C.); (S.C.)
- Facultad de Medicina-Universidad del Salvador, Av. Córdoba 1601, Buenos Aires C1055AAG, Argentina
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Mukherjee S, Perveen S, Negi A, Sharma R. Evolution of tuberculosis diagnostics: From molecular strategies to nanodiagnostics. Tuberculosis (Edinb) 2023; 140:102340. [PMID: 37031646 PMCID: PMC10072981 DOI: 10.1016/j.tube.2023.102340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/12/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Tuberculosis has remained a global concern for public health affecting the lives of people for ages. Approximately 10 million people are affected by the disease and 1.5 million succumb to the disease worldwide annually. The COVID-19 pandemic has highlighted the role of early diagnosis to win the battle against such infectious diseases. Thus, advancement in the diagnostic approaches to provide early detection forms the foundation to eradicate and manage contagious diseases like tuberculosis. The conventional diagnostic strategies include microscopic examination, chest X-ray and tuberculin skin test. The limitations associated with sensitivity and specificity of these tests demands for exploring new techniques like probe-based assays, CRISPR-Cas and microRNA detection. The aim of the current review is to envisage the correlation between both the conventional and the newer approaches to enhance the specificity and sensitivity. A significant emphasis has been placed upon nanodiagnostic approaches manipulating quantum dots, magnetic nanoparticles, and biosensors for accurate diagnosis of latent, active and drug-resistant TB. Additionally, we would like to ponder upon a reliable method that is cost-effective, reproducible, require minimal infrastructure and provide point-of-care to the patients.
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Affiliation(s)
| | - Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anjali Negi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Giantini A, Suhaeri M, Kusumaningrum A, Prasetyo DS, Sahar W, Hidayat R, Putra MA, Hermawan. Evaluation of loop-mediated isothermal amplification for detecting COVID-19. JOURNAL OF CLINICAL VIROLOGY PLUS 2023; 3:100132. [PMID: 36594046 PMCID: PMC9798669 DOI: 10.1016/j.jcvp.2022.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/01/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
The emergence of SARS-CoV-2 has caused worldwide pandemic of COVID-19. Infection is difficult to diagnose early as some patients remain asymptomatic and may carry this virus to other people. Currently, qRT-PCR is the widely accepted mode for detection. However, the need for sophisticated instrument and trained personnel may hinder its application, especially in remote and facility-lacking areas. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) may serve as a potential approach for detection of SARS-CoV-2 as the resources needed in its application is far less complex than those of qRT-PCR. Herein, we evaluated RT-LAMP based analytical method (COVIDNow), relative to qRT-PCR, in detecting SARS-CoV-2 by using 63 clinical respiratory samples. Based on our finding, COVIDNow exhibited sensitivity and specificity values of 87.5% and 80.6%, respectively. Taken together, RT-LAMP based detection of SARS-CoV-2 by utilizing COVIDNow might serves as a valuable diagnostic tool in the management of global COVID-19 pandemic condition.
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Affiliation(s)
- Astuti Giantini
- Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia,Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Muhammad Suhaeri
- Unit of Education, Research, and Training, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
| | - Ardiana Kusumaningrum
- Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia,Biomolecular Laboratory, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
| | - Dimas Seto Prasetyo
- Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia,Biomolecular Laboratory, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
| | - Windy Sahar
- Unit of Education, Research, and Training, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
| | - Rakhmad Hidayat
- Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia,Medical Service Unit, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
| | - Muhammad Arza Putra
- Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia,Medical Service Unit, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
| | - Hermawan
- Medical Service Unit, Universitas Indonesia Hospital, Universitas Indonesia, Depok 16424, Indonesia
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Inbaraj LR, Daniel J, Rajendran P, Bhaskar A, Srinivasalu VA, Narayanan MKS, Shewade HD, Kirubakaran R, Scandrett K, Malaisamy M, Takwoingi Y, Padmapriyadarsini C. Truenat MTB assays for pulmonary tuberculosis and rifampicin resistance in adults. THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2023; 2023:CD015543. [PMCID: PMC9837843 DOI: 10.1002/14651858.cd015543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This is a protocol for a Cochrane Review (diagnostic). The objectives are as follows: To determine the diagnostic accuracy of Truenat assays (MTB, MTB Plus, and MTB RIF Dx) for detecting pulmonary tuberculosis and rifampicin resistance in adults with presumptive pulmonary tuberculosis.
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Affiliation(s)
| | - Leeberk Raja Inbaraj
- Department of Clinical ResearchICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Jefferson Daniel
- Department of Pulmonary MedicineChristian Medical CollegeVelloreIndia
| | - Priya Rajendran
- Department of BacteriologyICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Adhin Bhaskar
- Department of BiostatisticsICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Vignes Anand Srinivasalu
- Department of Clinical ResearchICMR - National Institute for Research in TuberculosisChennaiIndia
| | - Mukesh KS Narayanan
- Department of EpidemiologyICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Hemant D Shewade
- Division of Health System ResearchICMR – National Institute of EpidemiologyChennaiIndia
| | - Richard Kirubakaran
- Prof. BV Moses Center for Evidence-Informed Health Care and Health PolicyChristian Medical CollegeVelloreIndia
| | - Katie Scandrett
- Test Evaluation Research Group, Institute of Applied Health ResearchUniversity of BirminghamBirminghamUK
| | - Muniyandi Malaisamy
- Department of Health EconomicsICMR – National Institute for Research in TuberculosisChennaiIndia
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health ResearchUniversity of BirminghamBirminghamUK
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A Comparative Study on Visual Detection of Mycobacterium tuberculosis by Closed Tube Loop-Mediated Isothermal Amplification: Shedding Light on the Use of Eriochrome Black T. Diagnostics (Basel) 2023; 13:diagnostics13010155. [PMID: 36611447 PMCID: PMC9818645 DOI: 10.3390/diagnostics13010155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Loop-mediated isothermal amplification is a promising candidate for the rapid detection of Mycobacterium tuberculosis. However, the high potential for carry-over contamination is the main obstacle to its routine use. Here, a closed tube LAMP was intended for the visual detection of Mtb to compare turbidimetric and two more favorable colorimetric methods using calcein and hydroxy naphthol blue (HNB). Additionally, a less studied dye (i.e., eriochrome black T (EBT)) was optimized in detail in the reaction for the first time. Mtb purified DNA and 30 clinical specimens were used to respectively determine the analytical and diagnostic sensitivities of each method. The turbidimetric method resulted in the best analytical sensitivity (100 fg DNA/reaction), diagnostic sensitivity and specificity (100%), and time-to-positivity of the test (15 min). However, this method is highly prone to subjective error in reading the results. Moreover, HNB-, calcein-, and EBT-LAMP could respectively detect 100 fg, 1 pg, and 1 pg DNA/reaction (the analytical sensitivities) in 30, 15, and 30 min, while the diagnostic sensitivity and specificity were respectively 93.3% and 100% for them all. Interestingly, EBT-LAMP showed the lowest potential for subjective error in reading the results. This report helps judiciously choose the most appropriate visual method, taking a step forward toward the field applicability of LAMP for the detection of Mtb, particularly in resource-limited settings.
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WITHDRAWN: Analysis of the application value of molecular diagnostic technology of mycobacterium tuberculosis. J Clin Tuberc Other Mycobact Dis 2022. [DOI: 10.1016/j.jctube.2022.100330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Guo YL, Wang SS, Jiang GL, Ban WJ, Liu Y. Evaluation of the diagnostic value of loop-mediated isothermal amplification assays targeting three different Mycobacterium tuberculosis genes. J Microbiol Methods 2022; 200:106547. [PMID: 35926680 DOI: 10.1016/j.mimet.2022.106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/16/2022] [Accepted: 07/29/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The aim of the study was to evaluate a loop-mediated isothermal amplification (LAMP) assay for the ability to diagnose tuberculosis directly from clinical samples rapidly. METHODS LAMP assays were performed using previously reported primer sets to amplify three specific Mycobacterium tuberculosis (MTB) gene targets, hspX, gyrB, and IS6110. Quantitated DNA from strain H37Rv were detected for assessment of analytical sensitivity; specificity was evaluated by testing eight species of non-tuberculosis Mycobacterium (NTM) and four unrelated bacterial species. Sputum samples from 68 pulmonary tuberculosis patients and a control group consisting of 45 lung cancer patients and 20 healthy controls were analyzed using LAMP assays, and then compared with smear, culture and quantitative real-time PCR (qRT-PCR) methods. RESULTS All three LAMP assays showed 100% specificity for MTB when tested against NTM and other bacterial species. The gyrB-LAMP assay was able to detect 60 cfu/ml of H37Rv suspension within 1 h, similar to qRT-PCR, but 10 times more sensitive than the hspX-LAMP and IS6110-LAMP assays. In clinical samples, when qRT-PCR was used as the reference method, the sensitivity of the three LAMP assays targeting hspX, gyrB, and IS6110 genes was 94.6, 98.2 and 92.9%, respectively. CONCLUSIONS LAMP is more sensitive than smear microscopy and close to qRT-PCR in sensitivity for the detection of MTB. LAMP has comparable specificity to qRT-PCR but was more rapid and convenient.
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Affiliation(s)
- Yan-Ling Guo
- Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Sai-Sai Wang
- Disease Prevention and Control Department, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China
| | - Guang-Lu Jiang
- National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China
| | - Wu-Juan Ban
- Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Yang Liu
- Disease Prevention and Control Department, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China.
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Rapid and Reliable Detection of SARS-CoV-2 Using Direct RT-LAMP. Diagnostics (Basel) 2022; 12:diagnostics12040828. [PMID: 35453876 PMCID: PMC9029081 DOI: 10.3390/diagnostics12040828] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The global pandemic coronavirus SARS-CoV-2 has a healthcare, social and economic burden. To limit the spread of the virus, the World Health Organization (WHO) urgently called for extensive screening of suspected individuals; thus, a quick, simple, and sensitive diagnostic assay is always in need. Methods: We applied reverse transcription-loop-mediated isothermal amplification (RT-LAMP) for the detection of SARS-CoV-2. The RT-LAMP method was optimized by evaluating two fluorescence amplification mixes and several reaction times, and results were compared to the standard real-time RT-PCR (rtRT-PCR). The assay was validated using 200 nasopharyngeal swabs collected in viral transport media (62 positive for SARS-CoV-2, and 138 negative for SARS-CoV-2 detected by the rtRT-PCR method). The samples were diluted 1:4 in diethylpyrocarbonate (DEPC)-treated water, utilized for RT-LAMP using different singleplex and multiplex sets of LAMP primers (N gene, S gene, and orf1ab gene), and incubated at 65 °C using real-time PCR 7500. Results: Our direct detection with the RT-LAMP protocol showed 100% concordance (sensitivity and specificity) with the standard protocol used for the detection of SARS-CoV-2 nucleic acid. Conclusions: In this study, we set up a rapid, simple, and sensitive RT-LAMP assay for the detection of SARS-CoV-2 in clinical samples. The assay is suitable for point of care detection in public hospitals, medical centers in rural areas, and in transportation hubs.
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Erber AC, Sandler PJ, de Avelar DM, Swoboda I, Cota G, Walochnik J. Diagnosis of visceral and cutaneous leishmaniasis using loop-mediated isothermal amplification (LAMP) protocols: a systematic review and meta-analysis. Parasit Vectors 2022; 15:34. [PMID: 35073980 PMCID: PMC8785018 DOI: 10.1186/s13071-021-05133-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Sensitive, reliable and fast diagnostic tools that are applicable in low-resource settings, at the point of care (PoC), are seen as crucial in the fight against visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Addressing the need for a PoC test, several diagnostic tests, including serological and molecular methods, have been developed and evaluated in the past. One promising molecular method, already implemented for diagnosis of a range of diseases, is the loop-mediated isothermal amplification (LAMP) protocol. In this systematic review and meta-analysis, using a comprehensive search strategy, we focus on studies evaluating the performance of LAMP for the diagnosis of leishmaniasis in humans and other mammals such as dogs, compared with microscopy and/or any other molecular diagnostic method. A meta-analysis, pooling sensitivity and specificity rates and calculating areas under the curve (AUCs) in summary receiver operating characteristic (SROC) plots, was conducted on datasets extracted from studies, grouped by clinical condition and sample type. We found high sensitivity and specificity for LAMP when compared with microscopy and PCR using blood samples, with pooled estimate values of > 90% for all subgroups, corresponding to calculated AUC values > 0.96, except for LAMP compared to microscopy for diagnosis of CL. However, only a limited number of studies were truly comparable. Most of the observed heterogeneity is likely based on true differences between the studies rather than sampling error only. Due to simple readout methods and low laboratory equipment requirements for sample preparation compared to other molecular methods, LAMP is a promising candidate for a molecular (near-)PoC diagnostic method for VL and CL.
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Affiliation(s)
- Astrid Christine Erber
- Department of Epidemiology, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1st floor, 1090, Vienna, Austria. .,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LG, UK.
| | - Peter Julian Sandler
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Daniel Moreira de Avelar
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ines Swoboda
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Gláucia Cota
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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Carboxamide and N-alkylcarboxamide additives can greatly reduce non specific amplification in Loop-Mediated Isothermal Amplification for Foot-and-Mouth disease Virus (FMDV) using Bst 3.0 polymerase. J Virol Methods 2021; 298:114284. [PMID: 34520810 DOI: 10.1016/j.jviromet.2021.114284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/12/2021] [Accepted: 09/10/2021] [Indexed: 11/23/2022]
Abstract
Foot-and-Mouth disease Virus (FMDV) is a highly infectious RNA virus that causes severe economic losses in cloven-hoofed animals. Early detection is needed to control epidemics, and loop-mediated isothermal amplification (LAMP) can be performed using inexpensive and commonly available equipment with a short processing time, but existing assays for FMDV still require an additional reverse transcriptase enzyme to convert RNA to cDNA prior to amplification. We sought to develop a novel RT-LAMP assay for FMDV with carboxamide and N-alkylcarboxamide additives to reduce non-specific amplification in combination with an improved commercially available polymerase (Bst 3.0) with efficient reverse transcriptase activity. SYBR Green I dye was used for sensitive visual detection of amplification products from our LAMP assay within 15 min without the need for a colorimeter. In the presence of a carefully titrated mixture of carboxamide and N-alkylcarboxamide additives, longer reactions of up to 1 h were also possible on both RNA and cDNA without the appearance of non-specific amplification products, thereby increasing the potential robustness of the assay by allowing a greater window of time in which to detect weak positives.
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Comparison of LAMP, GeneXpert, Mycobacterial Culture, Smear Microscopy, TSPOT.TB, TBAg/PHA Ratio for Diagnosis of Pulmonary Tuberculosis. Curr Med Sci 2021; 41:1023-1028. [PMID: 34476662 PMCID: PMC8412392 DOI: 10.1007/s11596-021-2404-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/23/2021] [Indexed: 11/28/2022]
Abstract
Objective To investigate the application value of loop-mediated isothermal amplification (LAMP), GeneXpert, mycobacterial culture, smear microscopy, TSPOT.TB (TSPOT), ratio of TB-specific antigen to phytohemagglutinin (TBAg/PHA ratio) in the detection of mycobacterium tuberculosis in the bronchoalveolar lavage fluid. Methods A retrospective analysis was performed on the patients who underwent bronchoscopy from December 2018 to November 2019 in Tongji Hospital. The patients with positive tuberculosis culture or positive GeneXpert in bronchoalveolar lavage fluid were selected as the case group, and those without tuberculosis served as the control group. The receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of LAMP, GeneXpert, culture, smear microscopy, TSPOT, and TBAg/PHA ratio. Results For the patients with positive cultures as case, the sensitivity of LAMP, GeneXpert, smear microscopy, TSPOT and TBAg/PHA ratio was 73.49%, 89.16%, 25.30%, 80.00%, 33.85%, respectively, the specificity was 99.00%, 100.00%, 99.00%, 86.00%, 100.00%, respectively, the area under the ROC curve (AUC) was 0.849, 0.938, 0.633, 0.830, 0.669, respectively. For the patients with positive GeneXpert as case, the sensitivity of LAMP, mycobacterial culture, smear microscopy, TSPOT and TBAg/PHA ratio was 73.20%, 74.23%, 22.68%, 68.92%, 29.73%, respectively, the specificity was 99.00%, 100.00%, 99.00%, 86.00%, 100.00%, respectively, the AUC was 0.853, 0.878, 0.623, 0.775, 0.649, respectively. Conclusion The sensitivity of GeneXpert was best. The sensitivity and diagnostic value of LAMP were slightly lower than those of GeneXpert, and were similar to tuberculosis culture. The sensitivity of smear microscopy was low. The specificity of TSPOT was low. When TBAg/PHA ratio >0.2 was used as a diagnostic index, the specificity was improved, but the sensitivity was low.
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Akapelwa ML, Kapalamula TF, Ouchi-Aizu Y, Hang'ombe BM, Nishiuchi Y, Gordon SV, Solo ES, Tamaru A, Nishimura T, Hasegawa N, Morimoto K, Fukushima Y, Suzuki Y, Nakajima C. Evaluation of IS1245 LAMP in Mycobacterium avium and the influence of host-related genetic diversity on its application. Diagn Microbiol Infect Dis 2021; 101:115494. [PMID: 34391980 DOI: 10.1016/j.diagmicrobio.2021.115494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
Early detection and treatment are paramount for the timely control of Mycobacterium avium infections. Herein, we designed a LAMP assay targeting a widely used species-specific marker IS1245 for the rapid detection of M. avium and evaluated its applicability using human (n = 137) and pig (n = 91) M. avium isolates from Japan. The developed assay could detect as low as 1 genome copy of M. avium DNA within 30 minutes. All 91 (100%) M. avium isolates from pigs were detected positive while all other tested bacterial species were negative. Interestingly, among the 137 clinical M. avium isolates, 41 (30%) were undetectable with this LAMP assay as they lacked IS1245, the absence of which was revealed by PCR and whole-genome sequencing. These findings highlighted genotypic differences in M. avium strains from humans and pigs in Japan and how this diversity can influence the applicability of a detection tool across different geographic areas and hosts.
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Affiliation(s)
- Mwangala Lonah Akapelwa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Thoko Flav Kapalamula
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Yuki Ouchi-Aizu
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Bernard Mudenda Hang'ombe
- Department of ParaClinicals, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia; Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Aki Tamaru
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | | | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Kozo Morimoto
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan.
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Asdaq SMB, Ikbal AMA, Sahu RK, Bhattacharjee B, Paul T, Deka B, Fattepur S, Widyowati R, Vijaya J, Al mohaini M, Alsalman AJ, Imran M, Nagaraja S, Nair AB, Attimarad M, Venugopala KN. Nanotechnology Integration for SARS-CoV-2 Diagnosis and Treatment: An Approach to Preventing Pandemic. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1841. [PMID: 34361227 PMCID: PMC8308419 DOI: 10.3390/nano11071841] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 outbreak is the COVID-19 disease, which has caused massive health devastation, prompting the World Health Organization to declare a worldwide health emergency. The corona virus infected millions of people worldwide, and many died as a result of a lack of particular medications. The current emergency necessitates extensive therapy in order to stop the spread of the coronavirus. There are various vaccinations available, but no validated COVID-19 treatments. Since its outbreak, many therapeutics have been tested, including the use of repurposed medications, nucleoside inhibitors, protease inhibitors, broad spectrum antivirals, convalescence plasma therapies, immune-modulators, and monoclonal antibodies. However, these approaches have not yielded any outcomes and are mostly used to alleviate symptoms associated with potentially fatal adverse drug reactions. Nanoparticles, on the other hand, may prove to be an effective treatment for COVID-19. They can be designed to boost the efficacy of currently available antiviral medications or to trigger a rapid immune response against COVID-19. In the last decade, there has been significant progress in nanotechnology. This review focuses on the virus's basic structure, pathogenesis, and current treatment options for COVID-19. This study addresses nanotechnology and its applications in diagnosis, prevention, treatment, and targeted vaccine delivery, laying the groundwork for a successful pandemic fight.
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Affiliation(s)
| | - Abu Md Ashif Ikbal
- Department of Pharmacy, Tripura University (A Central University), Suryamaninagar 799022, Tripura (W), India;
| | - Ram Kumar Sahu
- Department of Pharmaceutical Science, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia;
- Department of Pharmaceutical Science, Assam University (A Central University), Silchar 788011, Assam, India
| | - Bedanta Bhattacharjee
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India; (B.B.); (T.P.); (B.D.)
| | - Tirna Paul
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India; (B.B.); (T.P.); (B.D.)
| | - Bhargab Deka
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India; (B.B.); (T.P.); (B.D.)
| | - Santosh Fattepur
- School of Pharmacy, Management and Science University, Seksyen 13, Shah Alam 40100, Selangor, Malaysia
| | - Retno Widyowati
- Department of Pharmaceutical Science, Faculty of Pharmacy, Universitas Airlangga, Surabaya 60115, Indonesia;
| | - Joshi Vijaya
- Department of Pharmaceutics, Government College of Pharmacy, Bangalore 560027, Karnataka, India;
| | - Mohammed Al mohaini
- Basic Sciences Department, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Alahsa 31982, Saudi Arabia;
- King Abdullah International Medical Research Center, Alahsa 31982, Saudi Arabia
| | - Abdulkhaliq J. Alsalman
- Department of Clinical Pharmacy, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia;
| | - Sreeharsha Nagaraja
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; (S.N.); (A.B.N.); (M.A.); (K.N.V.)
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Off Sarjapura Road, Bangalore 560035, India
| | - Anroop B. Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; (S.N.); (A.B.N.); (M.A.); (K.N.V.)
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; (S.N.); (A.B.N.); (M.A.); (K.N.V.)
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Hofuf, Al-Ahsa 31982, Saudi Arabia; (S.N.); (A.B.N.); (M.A.); (K.N.V.)
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
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Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
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Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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Improved Visual Detection of speB Gene in Streptococcus pyogenes Isolates by Real-time Loop-Mediated Isothermal Amplification Turbidimetry Method. Jundishapur J Microbiol 2021. [DOI: 10.5812/jjm.108540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background: Group A Streptococcus (GAS) causes a wide array of clinical manifestations ranging from mild pharyngitis to suppurative and non-suppurative severe debilitating diseases. Hence, a simple, rapid detection method with high sensitivity and specificity is needed. Objectives: This study embarked on the visual detection of the streptococcal pyrogenic exotoxin B (speB) gene by real-time turbidimetry and loop-mediated isothermal amplification (RT-LAMP) methods. The real-time monitoring of the sigmoidal graph generated from a turbidimetry method was incorporated in the assay. Methods: The amplification of the speB gene was virtually observed in real-time monitoring of the graph (sigmoidal curve) generated via a turbidimeter, thus providing a “guide” to accurately estimate the time to positivity for the gene detection. Results: The targeted gene was detected at 15 min but was optimally amplified within 45 min at an isothermal temperature of 63°C with 100% specificity using an established set of primers. The formation of sigmoidal curves was correlated with other visual observations by the naked eye (from orange to green), ultra-violet light (green fluorescence), and agarose gel electrophoresis. The improved detection limit of the real-time RT-LAMP assay was also observed compared to conventional PCR assay (0.001 pg/µL versus 1 ng/µL). Conclusions: The improved visual detection of RT-LAMP assay could provide additional insight for rapid, cost-effective, and reliable identification of GAS via speB gene detection in low or middle-income countries. It could also be a very important tool to improve the healthcare management of patients infected with GAS in the future.
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Wang X, Wang G, Wang Y, Quan S, Qi H, Sun L, Shen C, Huang H, Jiao W, Shen A. Development and Preliminary Application of Multiplex Loop-Mediated Isothermal Amplification Coupled With Lateral Flow Biosensor for Detection of Mycobacterium tuberculosis Complex. Front Cell Infect Microbiol 2021; 11:666492. [PMID: 33987108 PMCID: PMC8110928 DOI: 10.3389/fcimb.2021.666492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to develop a simple and reliable method to detect Mycobacterium tuberculosis complex (MTBC) and verify its clinical application preliminarily. A loop-mediated isothermal amplification method coupled with lateral flow biosensor (LAMP-LFB) assay, was developed and evaluated for detection of MTBC. Two sets of primers, which targeted IS6110 and IS1081 sequences of MTBC, were designed for establishment of multiplex LAMP-LFB assay. The amplicons were labelled with biotin and fluorescein isothiocyanate (FITC) by adding FITC labelled primer and biotin-14-dATP and biotin-14-dCTP and could be visualized using LFB. The optimal reaction conditions of multiplex LAMP-LFB assay confirmed were 66°C for 50 min. The analytical sensitivity of multiplex LAMP-LFB is 10 fg of genomic templates using pure culture, and no cross-reactivity with other common bacteria and non-tuberculous mycobacteria strains was obtained. A total of 143 clinical samples collected from 100 TB patients (62 definite TB cases and 38 probable TB cases) and 43 non-TB patients were used for evaluating the feasibility of multiplex LAMP-LFB assay. The multiplex LAMP-LFB (82.0%, 82/100) showed higher sensitivity than culture (47.0%, 47/100, P < 0.001) and Xpert MTB/RIF (54.0%, 54/100, P < 0.001). Importantly, the multiplex LAMP-LFB assay detected additional 28 probable TB cases, which increased the percentage of definite TB cases from 62.0% (62/100) to 90.0% (90/100). The specificity of multiplex LAMP-LFB assay in patients without TB was 97.7% (42/43). Therefore, multiplex LAMP-LFB assay is a simple, reliable, and sensitive method for MTBC detection, especially in probable TB cases and resource limited settings.
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Affiliation(s)
- Xingyun Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Guirong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yacui Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shuting Quan
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hairong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weiwei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Adong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
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Dixit KK, Ramesh V, Gupta R, Negi NS, Singh R, Salotra P. Real-Time Fluorimetry Loop-Mediated Isothermal Amplification for Diagnosis of Leishmaniasis and as a Tool for Assessment of Cure for Post-Kala-Azar Dermal Leishmaniasis. Am J Trop Med Hyg 2021; 104:2097-2107. [PMID: 33872204 DOI: 10.4269/ajtmh.20-1057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/09/2020] [Indexed: 12/24/2022] Open
Abstract
Despite the dwindling number of visceral leishmaniasis (VL) cases in India, there is an urgent need for early and unequivocal diagnostics for controlling and preventing the reemergence of VL. Post-kala-azar dermal leishmaniasis (PKDL), a dermal sequela of VL, serves as a reservoir of the parasite. Diagnosis of PKDL, especially the macular variant, is challenging and poses impediment toward attainment of VL elimination. In this study, a real-time fluorimetry loop-mediated isothermal amplification (RealAmp) assay has been established for the detection of different clinical manifestations of leishmaniasis. The study included 150 leishmaniasis patients (25 VL, 25 cutaneous leishmaniasis [CL], and 100-PKDL) along with 120 controls. The assay demonstrated sensitivity of 100% (95% CI: 86.68-100) for diagnosis of VL and PKDL (95% CI: 79.61-100) and 96% (95% CI: 86.68-100) for CL with 100% specificity. Moreover, considering the cardinal role of PKDL, diagnosis using minimally invasive slit aspirate was explored, which demonstrated remarkable sensitivity of 96% (95% CI: 87.64-98.47). As a test of cure for PKDL, RealAmp successfully detected parasite in two of posttreatment cases who later reported relapse on follow-up. Also, direct sample lysis using slit aspirate was attempted in a small group that yielded sensitivity of 89% (95% CI: 67.20-96.90). RealAmp depicted excellent diagnostic accuracy in the diagnosis of leishmaniasis in concordance with the established SYBR Green I-based visual loop-mediated isothermal amplification (LAMP) and the reference comparator real-time PCR. The study endorsed the employment of LAMP either as visual-LAMP or RealAmp for an accurate and expeditious diagnosis of PKDL and as a tool for assessment of cure.
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Affiliation(s)
- Keerti Kaumudee Dixit
- 1ICMR-National Institute of Pathology (NIOP), Safdarjung Hospital Campus, New Delhi, India.,2Faculty of Health and Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - V Ramesh
- 3Department of Dermatology and STD, Safdarjung Hospital, Vardhman Mahavir Medical College, New Delhi, India
| | - Ratan Gupta
- 4Department of Paediatrics, Safdarjung Hospital, Vardhman Mahavir Medical College, New Delhi, India
| | - Narendra Singh Negi
- 5Department of Medicine, Safdarjung Hospital, Vardhman Mahavir Medical College, New Delhi, India
| | - Ruchi Singh
- 1ICMR-National Institute of Pathology (NIOP), Safdarjung Hospital Campus, New Delhi, India
| | - Poonam Salotra
- 1ICMR-National Institute of Pathology (NIOP), Safdarjung Hospital Campus, New Delhi, India
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Kitagawa M, Ouhara K, Oka H, Sakamoto S, Yamane Y, Kashiwagi A, Kanamoto R, Miyauchi M, Nagamine K. Selective and easy detection of the Porphyromonas gingivalis fimA type II and IV genes by loop-mediated isothermal amplification. J Microbiol Methods 2021; 185:106228. [PMID: 33878444 DOI: 10.1016/j.mimet.2021.106228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022]
Abstract
Porphyromonas gingivalis fimbrillin (fimA) type II and IV, the definitive factors for periodontitis, are also found to be associated with systemic diseases. To detect the fimA type II and IV genes easily and rapidly, we used the loop-mediated isothermal amplification (LAMP) method. The LAMP method showed high specificity as DNA from the P. gingivalis HW24D1 strain could only be amplified by the type II-specific primers and that from the W83 strain could only be amplified by the type IV-specific primers. Pathogens, namely, Streptococcus sobrinus, S. mutans, and Candida species, lack the type II and IV genes, and hence, were not detected by the LAMP reaction. Both bacterial cells and purified DNA could be used in the LAMP reaction. The LAMP reaction was highly sensitive and both type II and type IV genes could be detected in 1000 DNA molecules. In the bacterial suspensions of HW24D1 and W83 strains, type II and type IV genes, respectively, could be detected in 100 bacterial cells. We examined the type II and type IV genes in the dental plaques from 22 P. gingivalis-positive patients using the LAMP method. Only one person was found to be positive for the type II gene (4.5%). For the type IV gene, 3 positive cases (13.6%) were identified. Moreover, type II and type IV genes could be detected simultaneously using a multiplex amplification primer of fimA type II and type IV, under visible light. Thus, we established a selective and easy method to detect P. gingivalis fimA type II and IV genes using LAMP.
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Affiliation(s)
- Masae Kitagawa
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan.
| | - Kazuhisa Ouhara
- Department of Periodontology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroko Oka
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan; Center for Cause of Death Investigation Research & Education, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Shinichi Sakamoto
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan
| | - Yuka Yamane
- Faculty of Health Sciences, Hiroshima International University, Hiroshima, Japan
| | - Ayaka Kashiwagi
- Faculty of Health Sciences, Hiroshima International University, Hiroshima, Japan
| | - Rinka Kanamoto
- Faculty of Health Sciences, Hiroshima International University, Hiroshima, Japan
| | - Mutusmi Miyauchi
- Department of Oral Maxillofacial Pathobiology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kentaro Nagamine
- Faculty of Health Sciences, Hiroshima International University, Hiroshima, Japan
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Clinical COVID-19 diagnostic methods: Comparison of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and quantitative RT-PCR (qRT-PCR). J Clin Virol 2021; 139:104813. [PMID: 33848785 PMCID: PMC7997201 DOI: 10.1016/j.jcv.2021.104813] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/13/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022]
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic is a major public health concern. Accurate and rapid diagnosis of COVID-19 is critical for disease control. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a nucleic acid amplification assay similar to reverse transcription-polymerase chain reaction (RT-PCR), the former being a simple, low cost, and rapid method. Objectives This study aimed to compare the RT-LAMP assay with RT-PCR using the Loopamp™ SARS-CoV-2 Detection Kit. Study design One hundred and fifty-one nasopharyngeal swab and 88 sputum samples obtained from individuals with suspected or confirmed COVID-19 were examined. Results RT-LAMP had high specificity (98.5 % (95 % CI: 96.9–100 %)), sensitivity (87.0 % (95 % CI: 82.8–91.3 %)), positive predictive value (97.9 % (95 % CI: 96.1–99.7 %)), negative predictive value (90.2 % (95 % CI: 86.4–94.0 %)), and concordance rate (93.3 % (95 % CI: 90.1–96.5 %)). Nasopharyngeal and sputum samples positive in RT-LAMP contained as few as 10.2 and 23.4 copies per 10 μL, respectively. RT-LAMP showed similar performance to RT-PCR for samples with cycle threshold value below 36. Conclusions These results indicate that RT-LAMP is a highly reliable and at least equivalent to RT-PCR in utility, and potentially applicable in settings that are more diverse as a point-of-care tool.
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23
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Development of a loop-mediated isothermal amplification assay based on RoTat1.2 gene for detection of Trypanosoma evansi in domesticated animals. Parasitol Res 2021; 120:1873-1882. [PMID: 33712930 DOI: 10.1007/s00436-021-07118-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 03/04/2021] [Indexed: 01/02/2023]
Abstract
The early containment of trypanosomosis depends on early, sensitive, and accurate diagnosis in endemic areas with low-intensity infections. The study was planned to develop a simple read out loop-mediated isothermal amplification (LAMP) assay targeting a partial RoTat1.2 VSG gene of Trypanosoma evansi with naked eye visualization of LAMP products by adding SYBR® Green I dye. The visual results were further confirmed with those of agarose gel electrophoresis, restriction enzyme digestion of LAMP products with AluI, and sequencing of the PCR products using LAMP outer primers. The LAMP primers did not show cross reactivity and non-specific reactions with regional common hemoparasitic DNA revealing high specificity of the assay. The threshold sensitivity level of the LAMP assay was determined to be 0.003 fg compared to 0.03 fg RoTat1.2 amplified DNA fragments of T. evansi by PCR assay. Moreover, assessment of 500 blood samples collected from unhealthy domestic animals in field suspected for various hemoparasitic infections was carried out for the presence of T. evansi by microscopy, RoTat1.2 VSG PCR, and LAMP assay. LAMP could detect T. evansi in 36 samples, while PCR and microscopy could detect 33 and 12 samples, respectively. All the samples positive by microscopy and PCR were also confirmed positive by the LAMP assay. The current LAMP assay has appealing point of care characteristics to visually monitor the results, lessen the need of post DNA amplification procedure, and enable this method to be applied as a rapid and sensitive molecular diagnostic tool in under resourced laboratories and field setup.
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24
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Tatulli G, Cecere P, Maggioni D, Galimberti A, Pompa PP. A Rapid Colorimetric Assay for On-Site Authentication of Cephalopod Species. BIOSENSORS-BASEL 2020; 10:bios10120190. [PMID: 33255443 PMCID: PMC7760856 DOI: 10.3390/bios10120190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022]
Abstract
A colorimetric assay, exploiting the combination of loop-mediated isothermal amplification (LAMP) with DNA barcoding, was developed to address the authentication of some cephalopod species, a relevant group in the context of seafood traceability, due to the intensive processing from the fishing sites to the shelf. The discriminating strategy relies on accurate design of species-specific LAMP primers within the conventional 5' end of the mitochondrial COI DNA barcode region and allows for the identification of Loligo vulgaris among two closely related and less valuable species. The assay, coupled to rapid genomic DNA extraction, is suitable for large-scale screenings and on-site applications due to its easy procedures, with fast (30 min) and visual readout.
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Affiliation(s)
- Giuseppina Tatulli
- Istituto Italiano di Tecnologia, Nanobiointeractions&Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.T.); (P.C.)
| | - Paola Cecere
- Istituto Italiano di Tecnologia, Nanobiointeractions&Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.T.); (P.C.)
| | - Davide Maggioni
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, P.za Della Scienza 1, 20126 Milan, Italy;
- Marine Research and High Education (MaRHE) Center, University of Milano-Bicocca, Faafu Magoodhoo 12030, Maldives
| | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, 20126 Milan, Italy
- Correspondence: (A.G.); (P.P.P.)
| | - Pier Paolo Pompa
- Istituto Italiano di Tecnologia, Nanobiointeractions&Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.T.); (P.C.)
- Correspondence: (A.G.); (P.P.P.)
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25
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Sreedeep K, Sethi S, Yadav R, Vaidya PC, Angurana SK, Saini A, Mehra N, Singh M. Loop-mediated isothermal amplification (LAMP) in the respiratory specimens for the diagnosis of pediatric pulmonary tuberculosis: A pilot study. J Infect Chemother 2020; 26:823-830. [DOI: 10.1016/j.jiac.2020.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 11/28/2022]
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26
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Xu H, Zhang X, Cai Z, Dong X, Chen G, Li Z, Qiu L, He L, Liang B, Liu X, Liu J. An Isothermal Method for Sensitive Detection of Mycobacterium tuberculosis Complex Using Clustered Regularly Interspaced Short Palindromic Repeats/Cas12a Cis and Trans Cleavage. J Mol Diagn 2020; 22:1020-1029. [PMID: 32470556 DOI: 10.1016/j.jmoldx.2020.04.212] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis is one of the most serious infectious diseases, resulting in death worldwide. Traditional detection methods are not enough to meet the clinical requirements of rapid diagnosis, high specificity, and high sensitivity. Fast, sensitive, and accurate detection of Mycobacterium tuberculosis (MTB) is urgently needed to treat and control tuberculosis disease. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas12a) exhibit strong nonspecific degradation ability of exogenous single-strand nucleic acids (trans cleavage) after specific recognition of target sequence. We purified Cas12a protein and selected a proper guide RNA based on conserved sequences of MTB from designed guide RNA library. Then, we proposed a novel detection method based on recombinase polymerase amplification and CRISPR/Cas12a nuclease system for specific and sensitive detection of MTB DNA. The assay, based on fluorescence detection, showed 4.48 fmol/L of limit of detection and good linear correlation of concentration with fluorescence value (R2 = 0.9775). It also showed good performance in distinguishing other bacteria. Furthermore, its clinical performance was evaluated by 193 samples and showed sensitivity of 99.29% (139/140) and specificity of 100% (53/53) at 99% CI, compared with culture method. Taken together, the CRISPR/Cas12a system showed good specificity, excellent sensitivity, and excellent accuracy for MTB detection, and it meets requirements of MTB detection in clinical samples and has great potential for clinical translation.
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Affiliation(s)
- Haipo Xu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Xiaolong Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Liman Qiu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Lei He
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, People's Republic of China
| | - Bin Liang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China.
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
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27
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Hansen GT. Point-of-Care Testing in Microbiology: A Mechanism for Improving Patient Outcomes. Clin Chem 2020; 66:124-137. [PMID: 31811002 DOI: 10.1373/clinchem.2019.304782] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/15/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND Increasingly, demands for improved health and quality of life conflict with the realities of delivering healthcare in an environment of higher expenditures, adherence to test utilization, and patient-centered experience. Patient-centered care is commonly identified as a goal of healthcare delivery, and yet healthcare systems struggle with delivery of care to patients, often failing to identify the seriously ill and capitalize on the predictive qualities of diagnostic testing. Point-of-care (POC) testing provides access to rapid diagnosis and predictive value key to realizing patient outcomes. An evaluation of cost-effective models and the clinical impact of POC testing for clinical microbiology is needed. CONTENT Accurate and rapid diagnostics have the potential to affect healthcare decisions to a degree well out of proportion to their cost. Contemporary healthcare models increasingly view POC testing as a mechanism for efficient deployment of healthcare. POC testing can deliver rapid diagnosis in environments where testing results can be used to direct management during patient visits and in areas where centralized laboratory testing may limit access to care. Nucleic acid assays, designed for POC testing, can match, or exceed, the sensitivity of conventional laboratory-based testing, eliminating the need for confirmation testing. Here, the goals of POC testing for microbiology, applications, and technologies, as well as outcomes and value propositions, are discussed. SUMMARY The combination of rapid reporting, an increasing array of organisms capable of causing disease, actionable resulting, and improved patient outcomes is key in the evolution of POC testing in clinical microbiology.
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Affiliation(s)
- Glen T Hansen
- Microbiology and Molecular Diagnostics, Hennepin County Medical Center, Department of Infectious Diseases, University of Minnesota School of Medicine, Minneapolis, MN.,Department of Pathology & Laboratory Medicine University of Minnesota, School of Medicine.,Department of Medicine, Infectious Diseases, University of Minnesota School of Medicine, Minneapolis, MN
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28
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Evaluation of Loopamp Assay for the Diagnosis of Pulmonary Tuberculosis in Cambodia. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6828043. [PMID: 32596349 PMCID: PMC7288195 DOI: 10.1155/2020/6828043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/18/2020] [Indexed: 11/18/2022]
Abstract
The Loopamp™ MTBC kit (TB-LAMP) is recommended by WHO for Mycobacterium tuberculosis complex detection in low-income countries with a still low drug-resistant tuberculosis (TB) rate. This study is aimed at testing its feasibility in Cambodia on sputa collected from presumptive tuberculosis patients. 499 samples were tested at a smear microscopy center and 200 at a central-level mycobacteriology laboratory. Using mycobacterial cultures as reference, TB-LAMP results were compared with those of LED fluorescent microscopy (LED-FM) and Xpert® MTB/RIF. At the microscopy center, TB-LAMP sensitivity was higher than that of LED-FM (81.5% [95% CI, 74.5-87.6] versus 69.4% [95% CI, 62.2-76.6]), but lower than that of the Xpert assay (95.5% [95% CI 92.3-98.8]). At the central-level laboratory, TB-LAMP sensitivity (92.8% [95% CI, 87.6-97.9]) was comparable to that of Xpert (90.7% [95% CI, 85.0-96.5]) using stored sample. No significant difference in terms of specificity between TB-LAMP and Xpert assays was observed in both study sites. In conclusion, our data demonstrate that TB-LAMP could be implemented at microscopy centers in Cambodia to detect TB patients. In addition, TB-LAMP can be a better choice to replace smear microscopy for rapid TB diagnosis of new presumptive TB patients, in settings with relative low prevalence of drug-resistant TB and difficulties to implement Xpert assay.
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29
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Huang WE, Lim B, Hsu C, Xiong D, Wu W, Yu Y, Jia H, Wang Y, Zeng Y, Ji M, Chang H, Zhang X, Wang H, Cui Z. RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2. Microb Biotechnol 2020; 13:950-961. [PMID: 32333644 PMCID: PMC7264870 DOI: 10.1111/1751-7915.13586] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
The pandemic coronavirus SARS-CoV-2 in the world has caused a large infected population suffering from COVID-19. To curb the spreading of the virus, WHO urgently demanded an extension of screening and testing; thus, a rapid and simple diagnostic method is needed. We applied a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) to achieve the detection of SARS-CoV-2 in 30 min. We designed four sets of LAMP primers (6 primers in each set), targeting the viral RNA of SARS-CoV-2 in the regions of orf1ab, S gene and N gene. A colorimetric change was used to report the results, which enables the outcome of viral RNA amplification to be read by the naked eye without the need of expensive or dedicated instrument. The sensitivity can be 80 copies of viral RNA per ml in a sample. We validated the RT-LAMP method in a hospital in China, employing 16 clinic samples with 8 positives and 8 negatives. The testing results are consistent with the conventional RT-qPCR. In addition, we also show that one-step process without RNA extraction is feasible to achieve RNA amplification directly from a sample. This rapid, simple and sensitive RT-LAMP method paves a way for a large screening at public domain and hospitals, particularly regional hospitals and medical centres in rural areas.
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Affiliation(s)
- Wei E. Huang
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
- Department of Engineering ScienceUniversity of OxfordParks RoadOX1 3PJOxfordUK
| | - Boon Lim
- Department of Engineering ScienceUniversity of OxfordParks RoadOX1 3PJOxfordUK
| | - Chia‐Chen Hsu
- Department of Engineering ScienceUniversity of OxfordParks RoadOX1 3PJOxfordUK
- Institute of Biomedical EngineeringDepartment of Engineering ScienceUniversity of OxfordOxfordOX3 7DQUK
| | - Dan Xiong
- Medical Laboratory of Shenzhen Luohu People's HospitalShenzhen518001China
| | - Wei Wu
- Medical Laboratory of Shenzhen Luohu People's HospitalShenzhen518001China
| | - Yejiong Yu
- Department of Engineering ScienceUniversity of OxfordParks RoadOX1 3PJOxfordUK
- Institute of Biomedical EngineeringDepartment of Engineering ScienceUniversity of OxfordOxfordOX3 7DQUK
| | - Huidong Jia
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
| | - Yun Wang
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
| | - Yida Zeng
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
| | - Mengmeng Ji
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
| | - Hong Chang
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
| | - Xiuming Zhang
- Medical Laboratory of Shenzhen Luohu People's HospitalShenzhen518001China
| | - Hui Wang
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
| | - Zhanfeng Cui
- Oxford Suzhou Centre for Advanced Research (OSCAR)University of OxfordSuzhou Industrial ParkJiangsuChina
- Department of Engineering ScienceUniversity of OxfordParks RoadOX1 3PJOxfordUK
- Institute of Biomedical EngineeringDepartment of Engineering ScienceUniversity of OxfordOxfordOX3 7DQUK
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30
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Kitagawa M, Nagamine K, Oka H, Ouhara K, Ogawa I, Komatsuzawa H, Kurihara H. Rapid detection of the Streptococcus mutans cnm gene by loop-mediated isothermal amplification. Anal Biochem 2020; 605:113812. [PMID: 32592714 PMCID: PMC7315161 DOI: 10.1016/j.ab.2020.113812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 01/05/2023]
Abstract
This study investigated a method using loop-mediated isothermal amplification (LAMP) for the rapid detection of cnm-positive Streptococcus mutans (S. mutans) associated with cerebral microhemorrhage. LAMP amplified the cnm gene plasmid vector, but not human or microbial genomic DNA. The cnm DNA of the cnm-positive S. mutans strain was detected in saliva without DNA extraction after 1 day of culture. This method resulted in a cnm-positive rate of 26.4% in 102 samples, which was higher than that obtained with conventional PCR. In conclusion, LAMP may be used for the detection of cnm-positive S. mutans in a large number of samples.
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Affiliation(s)
- Masae Kitagawa
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan.
| | - Kentaro Nagamine
- Faculty of Health Sciences, Hiroshima International University, Hiroshima, Japan
| | - Hiroko Oka
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan; Center for Cause of Death Investigation Research & Education, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhisa Ouhara
- Department of Bacteriology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ikuko Ogawa
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hidemi Kurihara
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan; Department of Periodontal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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31
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Kitagawa Y, Orihara Y, Kawamura R, Imai K, Sakai J, Tarumoto N, Matsuoka M, Takeuchi S, Maesaki S, Maeda T. Evaluation of rapid diagnosis of novel coronavirus disease (COVID-19) using loop-mediated isothermal amplification. J Clin Virol 2020; 129:104446. [PMID: 32512376 PMCID: PMC7241399 DOI: 10.1016/j.jcv.2020.104446] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 11/26/2022]
Abstract
With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need for more rapid and simple detection technologies at the forefront of medical care worldwide. In this study, we evaluated the effectiveness of the Loopamp® 2019-SARSCoV-2 Detection Reagent Kit, which uses loop-mediated isothermal amplification (LAMP) technology. In this protocol, cDNA is synthesized from SARS-CoV-2 RNA using reverse transcriptase, followed by DNA amplification under isothermal conditions in one step. The RT-LAMP test kit amplified the targeted RNA of a SARS-CoV-2 isolate with a detection limit of 1.0 × 101 copies/μL, which was comparable to the detection sensitivity of quantitative reverse transcription PCR (RT-qPCR). Comparison with the results of RT-qPCR for 76 nasopharyngeal swab samples from patients with suspected COVID-19 showed a sensitivity of 100 % and a specificity of 97.6 %. In the 24 RNA specimens derived from febrile Japanese patients with or without influenza A, no amplification was observed using RT-LAMP. RT-LAMP could be a simple and easy-to-use diagnostic tool for the detection of SARS-CoV-2.
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Affiliation(s)
- Yutaro Kitagawa
- Department of Clinical Laboratory, Saitama Medical University Hospital, Saitama, Japan
| | - Yuta Orihara
- Department of Clinical Laboratory, Saitama Medical University Hospital, Saitama, Japan
| | - Rieko Kawamura
- Department of Clinical Laboratory, Saitama Medical University Hospital, Saitama, Japan
| | - Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
| | - Masaru Matsuoka
- Department of Clinical Laboratory, Saitama Medical University Hospital, Saitama, Japan
| | - Shinichi Takeuchi
- Department of Clinical Laboratory, Saitama Medical University Hospital, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
| | - Takuya Maeda
- Department of Clinical Laboratory, Saitama Medical University Hospital, Saitama, Japan; Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan.
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32
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Acharya B, Acharya A, Gautam S, Ghimire SP, Mishra G, Parajuli N, Sapkota B. Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis. Mol Biol Rep 2020; 47:4065-4075. [DOI: 10.1007/s11033-020-05413-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/28/2020] [Indexed: 01/02/2023]
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Development and evaluation of a loop-mediated isothermal amplification (LAMP) diagnostic test for detection of whipworm, Trichuris trichiura, in faecal samples. J Helminthol 2020; 94:e142. [PMID: 32238209 DOI: 10.1017/s0022149x2000022x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Whipworm infection or trichuriasis caused by Trichuris trichiura is of major public health concern in sub-Saharan Africa, particularly among pre-school and school-going children. It is among the neglected tropical diseases targeted for elimination through mass drug administration (MDA). One of the outcomes of MDA is a rapid decline in levels of infection intensity, making it difficult to monitor effectiveness of control measures using the conventional Kato-Katz procedure, which relies on the microscopic detection of parasite ova in faecal samples. In the present study, a loop-mediated isothermal amplification (LAMP) test was developed for the detection of T. trichiura infection in faecal samples. LAMP technology offers greater sensitivity and specificity than the microscopy-based tests. A set of four specific primers targeting the internal transcribed spacer 2 region of the ribosomal DNA were designed using Primer Explorer software. DNA was extracted from faecal samples using the alkaline lysis method (HotSHOT) and the LAMP reaction performed at 63°C for 1 h. The amplicons were visualized by both gel electrophoresis and with the naked eye following staining with SYBR green dye. Sensitivity and specificity tests were determined using the standard Kato-Katz diagnostic procedure as a reference test. The developed LAMP assay reliably detected T. trichiura DNA in faecal samples, with a specificity and sensitivity of 88% and 77%, respectively. No cross-reactivity was observed with several common helminth parasites. The developed LAMP assay is an appropriate diagnostic method for the detection of T. trichiura DNA in human faecal samples due to its simplicity, low cost, high sensitivity and specificity.
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Hegazy MK, Awad SI, Saleh NE, Hegazy MM. Loop mediated isothermal amplification (LAMP) of Toxoplasma DNA from dried blood spots. Exp Parasitol 2020; 211:107869. [PMID: 32119931 DOI: 10.1016/j.exppara.2020.107869] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/20/2020] [Accepted: 02/25/2020] [Indexed: 11/23/2022]
Abstract
INTRODUCTION The cosmopolitan protozoan Toxoplasma gondii is a major parasite of warm-blooded animals including man. Early and accurate diagnosis is a must for proper treatment that prevents life threatening sequels. Loop-mediated isothermal amplification (LAMP) is a novel technique that can amplify DNA with high sensitivity and specificity under isothermal conditions. AIM OF THE STUDY To validate a LAMP-specific protocol for detection of Toxoplasma DNA using dried blood spots (DBS) from mice experimentally infected with the cystogenic Toxoplasma ME-49 strain. METHODS In this study, the target DNA fragment was the Toxoplasma 529-bp repeat element that exists in 200-300 copies per T. gondii genome. The sensitivity of both LAMP and conventional PCR techniques was estimated in DBS samples from experimental mice at 1-week and 8-weeks post-infection. RESULTS Out of 20 blood samples gathered on Whatman filter paper from mice at 1-week post-infection, 18 and 16 were positive by LAMP and conventional PCR, respectively. Neither techniques detected parasite DNA in blood at 8th week of infection. CONCLUSION Dried blood spots are easy source of material for molecular studies. LAMP assay proved higher sensitivity than the conventional PCR in detecting parasitemia in early infection with the cystogenic Toxoplasma strain.
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Affiliation(s)
- Mona K Hegazy
- Department of Medical Parasitology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Soha I Awad
- Department of Medical Parasitology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Nora E Saleh
- Department of Medical Parasitology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt.
| | - Mamdouh M Hegazy
- Department of Medical Parasitology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
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Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Klayut W, Nakajima C, Hamada S, Suzuki Y. Comparison of Loop-Mediated Isothermal Amplification, Microscopy, Culture, and PCR for Diagnosis of Pulmonary Tuberculosis. Jpn J Infect Dis 2020; 73:272-277. [PMID: 32115540 DOI: 10.7883/yoken.jjid.2019.335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The diagnosis of tuberculosis (TB) in endemic countries is challenging due to high caseloads and limited resources. A simple and cost-effective diagnostic test for the rapid detection of Mycobacterium tuberculosis (M. tuberculosis) in clinical specimens is crucially needed. We evaluated the performance of an in-house assay based on loop-mediated isothermal amplification (LAMP) targeting the M. tuberculosis 16S ribosomal RNA (rRNA) gene for the diagnosis of TB in Thailand. A total of 252 sputum samples from suspected cases of pulmonary TB were analyzed. The sensitivity of LAMP was 99.04% (103/104; 95% confidence interval [CI]: 94.76-9.98%) and 72.73% (16/22; 95% CI: 49.78-89.27%) for smear-positive and smear-negative samples with TB-culture positivity, respectively. LAMP detected 20.69% (24/116) of TB culture negative samples but all those were positive by conventional polymerase chain reaction (PCR). The sensitivity of LAMP was higher than that of sputum microscopy while the performance of LAMP was similar to PCR. None of the samples positive for non-tuberculous mycobacteria by culture and PCR were positive by LAMP. Compared to TB culture, the positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient of LAMP were 83.22%, 88.33%, and 0.75 respectively. Based on the diagnostic performance, we propose that LAMP would be suitable as a potential diagnostic test for rapid TB diagnosis in resource-limited laboratory settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Wiphat Klayut
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan
| | - Shigeyuki Hamada
- Section of Bacterial Infections, Research Collaboration Center for Emerging and Re-emerging Infectious Diseases, Thailand.,Research Institute for Microbial Diseases, Osaka University, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan
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Li R, Chen J, Zhang X, Cui J, Tao S, Yang L. Mini-Disk Capillary Array Coupling with LAMP for Visual Detection of Multiple Nucleic Acids using Genetically Modified Organism Analysis as an Example. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:899-906. [PMID: 31891505 DOI: 10.1021/acs.jafc.9b06979] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Convenient, portable, and low-cost multiplex nucleic acid testing (NAT) systems are the trends in the fields of food safety, environmental microorganisms, molecular diagnosis, etc. In this study, we developed a novel system for visual monitoring of multiple nucleic acids combining a mini-disk capillary array (diameter = 17 mm, embedded with 6-10 capillaries), visual loop-mediated isothermal amplification (LAMP), and quick DNA extraction called mDC-LAMP. The performance and applicability of mDC-LAMP in testing multiple nucleic acids were evaluated and verified employing genetically modified contents analysis as an example. All of the results confirmed that mDC-LAMP has the advantages of high specificity without any cross contamination, high sensitivity with a limit of detection of 25 copies/reaction, high throughput with flexible channel sensors, easy fabrication, and low costs. We believe that mDC-LAMP is a competitive choice for on-spot monitoring of multiple nucleic acids in terms of the easy fabrication/operation, low costs, and suitable performance presented in the nucleic acids test.
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Affiliation(s)
- Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Jianwei Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xiujie Zhang
- Development Center of Science and Technology , Ministry of Agriculture of People's Republic of China , Beijing 100025 , China
| | - Jingjie Cui
- Institute of Cotton Research , Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology , Anyang 455000 , Henan , China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
- Institute of Cotton Research , Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology , Anyang 455000 , Henan , China
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Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
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Bamber AI, Fitzsimmons K, Cunniffe JG, Beasor CC, Mackintosh CA, Hobbs G. Diagnosis ofClostridium difficile-associated disease: examination of multiple algorithms using toxin EIA, glutamate dehydrogenase EIA and loop-mediated isothermal amplification. Br J Biomed Sci 2019. [DOI: 10.1080/09674845.2012.12069136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- A. I. Bamber
- Medical Microbiology, Wirral University Teaching Hospitals, Clatterbridge Hospital, Bebington, Wirral
| | - K. Fitzsimmons
- Medical Microbiology, Wirral University Teaching Hospitals, Clatterbridge Hospital, Bebington, Wirral
| | - J. G. Cunniffe
- Medical Microbiology, Wirral University Teaching Hospitals, Clatterbridge Hospital, Bebington, Wirral
| | - C. C. Beasor
- Medical Microbiology, Wirral University Teaching Hospitals, Clatterbridge Hospital, Bebington, Wirral
| | - C. A. Mackintosh
- Medical Microbiology, Wirral University Teaching Hospitals, Clatterbridge Hospital, Bebington, Wirral
| | - G. Hobbs
- Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, UK
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Rakotosamimanana N, Lapierre SG, Raharimanga V, Raherison MS, Knoblauch AM, Raherinandrasana AH, Rakotoson A, Rakotonirina J, Rasolofo V. Performance and impact of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® assays on tuberculosis case detection in Madagascar. BMC Infect Dis 2019; 19:542. [PMID: 31221109 PMCID: PMC6585144 DOI: 10.1186/s12879-019-4198-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/16/2019] [Indexed: 12/02/2022] Open
Abstract
Background Tuberculosis rapid molecular assays, including GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit®, are highly sensitive and specific. Such performance does not automatically translate in improved disease control and highly depends on their use, local epidemiology and the diagnostic algorithms they’re implemented within. We evaluate the performance of both assays and assess their impact on additional cases notification when implemented within WHO recommended tuberculosis diagnostic algorithms in Madagascar. Methods Five hundred forty eight presumptive pulmonary tuberculosis patients were prospectively recruited between November 2013 and December 2014 in Antananarivo, Madagascar, a high TB incidence sub-Saharan African urban setting. Both molecular assays were evaluated as first line or add-on testing following negative smear microscopy. Based on locally defined assay performance characteristics we measure the impact of both assays and WHO-recommended diagnostic algorithms on additional tuberculosis case notifications. Results High sensitivity and specificity was confirmed for both GeneXpert MTB/RIF® (86.6% (95% CI 81.1–90.7%) and 97.4% (95% CI 94.9–98.8%)) and Loopamp MTBC Detection Kit® (84.6% (95% CI 78.9–89.0%) and 98.4% (95% CI 96.2–99.4%)). Implementation of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® increased tuberculosis diagnostic algorithms sensitivity from 73.6% (95% CI 67.1–79.3%) up to 88.1% (95% CI 82.8–91.9%). This increase was highest when molecular assays were used as add-on testing following negative smear microscopy. As add-on testing, GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® respectively improved case detection by 23.8 and 21.2% (p < 0.05). Conclusion Including GeneXpert MTB/RIF® or Loopamp MTBC Detection Kit® molecular assays for TB detection on sputum samples from presumptive TB cases can significantly increase case notification in TB diagnostic centers. The TB case detection rate is further increased when those tests are use as second-line follow-on testing following negative smear microscopy results. A country wide scale-up and digital integration of molecular-based TB diagnosis assays shows promises for TB control in Madagascar.
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Affiliation(s)
| | - Simon Grandjean Lapierre
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Immunopathology axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Canada
| | | | - Mamy Serge Raherison
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Service du Laboratoire des Mycobactéries, Ministry of Public Health, Antananarivo, Madagascar
| | - Astrid M Knoblauch
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Epidemiology and Public Health Department, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Andrianantenaina Rakotoson
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Epidemiology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Julio Rakotonirina
- Centre hospitalier universitaire de soins et de santé publique d'Analakely, Analakely, Antananarivo, Madagascar
| | - Voahangy Rasolofo
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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Sharma G, Tewari R, Dhatwalia SK, Yadav R, Behera D, Sethi S. A loop-mediated isothermal amplification assay for the diagnosis of pulmonary tuberculosis. Lett Appl Microbiol 2019; 68:219-225. [PMID: 30636048 DOI: 10.1111/lam.13115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/08/2018] [Accepted: 10/08/2018] [Indexed: 11/28/2022]
Abstract
Quantitated Mycobacterium tuberculosis (M.tb) H37Rv DNA was used to analyse the sensitivity and the specificity was assessed using DNA isolated from the reference strain H37Rv, 12 nontuberculous mycobacterium (NTM) species and five nonmycobacterium species. Furthermore, performance of the assay was evaluated on the sputum samples and compared with smear microscopy, culture and PCR. mpt64 (also called mpb64 or Rv1980c) loop-mediated isothermal amplification (LAMP) successfully detected 1 pg DNA within 40 min and successfully rejected NTMs and other bacterial species tested. It specifically detected all the 119 confirmed TB cases and 100 of the 104 control cases. The resulting sensitivity and specificity of LAMP assay was found to be 100% (95% CI: 96·79-100%) and 96·15% (95% CI; 90·44-98·94%) respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Loop-mediated isothermal amplification (LAMP) is a technique for isothermal DNA amplification suitable for cost-limited settings as it prevents the use of sophisticated instruments. Using mpt64 antigenic protein gene, we developed a LAMP assay especially for organisms of the M. tuberculosis complex. mpt64 LAMP assay showed 100% sensitivity and detected all the bacteriologically and clinically positive TB cases not detected by smear, culture or PCR methods.
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Affiliation(s)
- G Sharma
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | - R Tewari
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | - S K Dhatwalia
- Department of Biophysics, Panjab University, Chandigarh, India
| | - R Yadav
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - D Behera
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - S Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Diagnosis of mycoplasma pneumoniae by loop-mediated isothermal amplification: systematic review and meta-analysis. BMC Infect Dis 2019; 19:173. [PMID: 30782134 PMCID: PMC6379949 DOI: 10.1186/s12879-019-3799-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/08/2019] [Indexed: 01/24/2023] Open
Abstract
Background A novel method, termed loop-mediated isothermal amplification (LAMP), was developed by Notomi et al. (2000). Individually published results have been reported that this technology has been successfully applied to the detection of a variety of pathogens. However, the overall diagnostic accuracy of LAMP for Mycoplasma pneumoniae (MP) remains unclear. A meta-analysis was therefore performed to review the accuracy of LAMP for Mycoplasma pneumoniae. Methods Cochrane Library and PubMed were systematically searched and checked for studies using LAMP for detecting mycoplasma pneumoniae. We used PCR as a reference standard to evaluate the quality of the studies eligible for inclusion in the meta-analysis. Then, the data from the studies were extracted by two independent assessors. Meta-DiSc 1.4 software was utilized to test the heterogeneity of sensitivity (SEN), specificity (SP), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnosis odds ratio (DOR). The pooled analysis results were plotted, and the summary receiver operating characteristic (SROC) curve was plotted by calculating the area under the curve (AUC). Generated pooled summary estimates (95% CIs) were calculated for the overall accuracy, and a bivariate meta-regression model was used for the meta-analysis. Results Seven studies with nine fourfold tables were included in this meta-analysis. The pooled SEN and SPE for diagnosing Mycoplasma pneumoniae were 0.90 (95% CI: 0.87–0.93) and 0.98 (95% CI: 0.96–0.99), respectively. The PLR was 31.25 (95% CI: 14.83–65.87), NLR 0.10 (95% CI: 0.05–0.22), DOR 399.32 (95% CI: 172.01–927.00), and AUC 0.9892. Conclusions In conclusion, compared with PCR, LAMP is a valuable alternative method for Mycoplasma pneumoniae diagnosis in clinic with high sensitivity and specificity. However, more evidence is required to confirm that LAMP can fully replace other methods in the clinical diagnosis of MP.
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Rajput R, Singh P, Sarin R, Sethi P, Sharma S. Diagnostic accuracy of loop-mediated isothermal amplification assay for extra-pulmonary tuberculosis in Indian population. J Microbiol Methods 2019; 158:59-65. [PMID: 30703448 DOI: 10.1016/j.mimet.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Confirmatory diagnosis of extra-pulmonary tuberculosis remains a true challenge owing to difficulty in procuring appropriate specimen, inefficient laboratory methods and paucibacillary nature of infection. These obstructions become all the very difficult in pediatric EPTB cases, due to non-specific clinical signs and symptoms, low sensitivity of smear microscopy and culture, lack of awareness among clinicians, etc. AIM OF THE STUDY: The present study aimed to evaluate the diagnostic accuracy of rapid and cost-effective loop-mediated isothermal amplification (LAMP) assay for EPTB diagnosis in children. METHODS A total of 154 cases were analyzed by EPTB-site smear microscopy, culture, PCRs for IS6110, MPB64 & Pab genes, nested PCR and LAMP assay. Single-gene PCRs were performed by custom-synthesized primers. Nested PCR was performed using the 3B BIOTUB Kit and the LAMP assay was done using the Nu-LAMP TB kit. RESULTS We observed that the molecular tests displayed 4-fold higher positivity rate (minimum 46%) in comparison to the microbiological tests (maximum 11.03%). In contrast to the composite reference standard, LAMP assay was found to be 79.6% sensitive and 78% specific for EPTB diagnosis in childhood cases. CONCLUSIONS Our results indicate that LAMP assay is a promising technique for efficient diagnosis of EPTB in children belonging to resource-limited regions.
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Affiliation(s)
- Roopali Rajput
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Paras Singh
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India.
| | - Rohit Sarin
- Department of TB and Respiratory Diseases and Director, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Prabhpreet Sethi
- Department of TB and Respiratory Diseases, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Sangeeta Sharma
- Department of Paediatrics, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
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Tubalinal GAS, Balbin MM, Villanueva MA, Domingo CYJ, Mingala CN. Evaluation of LAMP for detection and/or screening of Leptospira spp. infection among domestic animals in the Philippines. J Adv Vet Anim Res 2018; 5:459-465. [PMID: 31453158 PMCID: PMC6702914 DOI: 10.5455/javar.2018.e299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/10/2018] [Accepted: 11/07/2018] [Indexed: 01/01/2023] Open
Abstract
Objective: This study assessed the applicability of loop-mediated isothermal amplification (LAMP) for the detection of leptospirosis among domesticated animals and sewage rats. Specifically, it evaluated the ability of LAMP to amplify Leptospira spp. targeting the 16s rRNA gene in boiled urine samples. Materials and methods: A total of 140 samples from different domestic animals were tested for the presence of the antigen. A nested-polymerase chain reaction (nPCR) protocol was used to compare and determine the sensitivity of LAMP in detecting Leptospira spp. The LAMP was also evaluated by comparing its amplification result using agarose gel electrophoresis and color change using dye. Results: Positivity rate of Leptospira spp. antigen was 29.0% (40/140) for LAMP and 9.3% (13/140) for nPCR. Also, LAMP results for gel electrophoresis and dye color change varied in some samples that may be due to the interpretation of the result in dye color change. Conclusion: Overall, LAMP is a rapid, sensitive, and cost-effective diagnostic method compared with nPCR. Also, LAMP has a potential application as pen-side screening, surveillance, and clinical diagnostic kits of infectious diseases without requiring advance equipment and skilled personnel.
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Affiliation(s)
- Gabriel Alexis Sp Tubalinal
- College of Veterinary Science and Medicine, Central Luzon State University, Nueva Ecija, Philippines.,Biosafety and Environment Section, Philippine Carabao Center National Headquarters and Gene Pool, Nueva Ecija, Philippines.,Both authors contributed equally to this work
| | - Michelle M Balbin
- Biosafety and Environment Section, Philippine Carabao Center National Headquarters and Gene Pool, Nueva Ecija, Philippines
| | - Marvin A Villanueva
- Biosafety and Environment Section, Philippine Carabao Center National Headquarters and Gene Pool, Nueva Ecija, Philippines
| | - Clarissa Yvonne J Domingo
- College of Veterinary Science and Medicine, Central Luzon State University, Nueva Ecija, Philippines
| | - Claro N Mingala
- Biosafety and Environment Section, Philippine Carabao Center National Headquarters and Gene Pool, Nueva Ecija, Philippines.,Department of Animal Science, College of Agriculture, Central Luzon State University, Nueva Ecija, Philippines.,Both authors contributed equally to this work
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Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Klayut W, Sangkitporn S, Nakajima C, Hamada S, Suzuki Y. Loop-Mediated Isothermal Amplification for Rapid Identification of Mycobacterium tuberculosis in Comparison with Immunochromatographic SD Bioline MPT64 Rapid ® in a High Burden Setting. Jpn J Infect Dis 2018; 72:112-114. [PMID: 30381677 DOI: 10.7883/yoken.jjid.2018.128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) was assessed for rapid identification of Mycobacterium tuberculosis complex (MTC) in comparison with an immunochromatographic test (ICT) using SD Bioline Ag MPT64 Rapid®. One hundred and fifty-one MGIT cultures positive for acid-fast bacilli were tested for MTC. DNA was extracted from a small portion of culture samples by heat lysis and subjected to LAMP analysis. Of these, 144 were positive and 5 were negative by both tests. One culture that was ICT negative but was LAMP positive was confirmed to have a mutation in the mpt64 gene. The agreement was 98.68% (95% confidence interval [CI]: 94.80-99.77), and the kappa value was 0.83% (95% CI: 0.59-1.00). Good correlation results suggested that LAMP assay is a reliable molecular test for rapid identification of MTC and is practical for use in resource-limited, high burden settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health
| | - Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health
| | - Wiphat Klayut
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health
| | - Somchai Sangkitporn
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health
| | - Chie Nakajima
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University
| | - Shigeyuki Hamada
- Section of Bacterial Infections, Research Collaboration Center for Emerging and Re-emerging Infectious Diseases.,Research Institute for Microbial Diseases, Osaka University
| | - Yasuhiko Suzuki
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University
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Tatipally S, Srikantam A, Kasetty S. Polymerase Chain Reaction (PCR) as a Potential Point of Care Laboratory Test for Leprosy Diagnosis-A Systematic Review. Trop Med Infect Dis 2018; 3:tropicalmed3040107. [PMID: 30275432 PMCID: PMC6306935 DOI: 10.3390/tropicalmed3040107] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022] Open
Abstract
Leprosy is an infectious disease caused by Mycobacterium leprae and mainly affects skin, peripheral nerves, and eyes. Suitable tools for providing bacteriological evidence of leprosy are needed for early case detection and appropriate therapeutic management. Ideally these tools are applicable at all health care levels for the effective control of leprosy. This paper presents a systematic review analysis in order to investigate the performance of polymerase chain reaction (PCR) vis-à-vis slit skin smears (SSS) in various clinical settings and its potential usefulness as a routine lab test for leprosy diagnosis. Records of published journal articles were identified through PubMed database search. Twenty-seven articles were included for the analysis. The evidence from this review analysis suggests that PCR on skin biopsy is the ideal diagnostic test. Nevertheless, PCR on SSS samples also seems to be useful with its practical value for application, even at primary care levels. The review findings also indicated the necessity for improving the sensitivity of PCR and further research on specificity in ruling out other clinical conditions that may mimic leprosy. The M. leprae-specific repetitive element (RLEP) was the most frequently-used marker although its variable performance across the clinical sites and samples are a matter of concern. Undertaking further research studies with large sample numbers and uniform protocols studied simultaneously across multiple clinical sites is recommended to address these issues.
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Affiliation(s)
- Sushma Tatipally
- LEPRA Society, Blue Peter Public Health and Research Centre, Cherlapally, Hyderabad 501301, Telangana, India.
| | - Aparna Srikantam
- LEPRA Society, Blue Peter Public Health and Research Centre, Cherlapally, Hyderabad 501301, Telangana, India.
| | - Sanjay Kasetty
- Formerly at LEPRA Society, Blue Peter Public Health and Research Centre, Cherlapally, Hyderabad 501301, Telangana, India.
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48
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Patil TS, Deshpande AS. Innovative strategies in the diagnosis and treatment of tuberculosis: a patent review (2014–2017). Expert Opin Ther Pat 2018; 28:615-623. [DOI: 10.1080/13543776.2018.1508454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Tulshidas S. Patil
- School of Pharmacy & Technology Management, SVKM’s NMIMS, Shirpur, India
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Kim CK, Cho EA, Shin DM, Choi SW, Shin SY. Comparative Evaluation of the Loop-Mediated Isothermal Amplification Assay for Detecting Pulmonary Tuberculosis. Ann Lab Med 2018; 38:119-124. [PMID: 29214755 PMCID: PMC5736670 DOI: 10.3343/alm.2018.38.2.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/07/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022] Open
Abstract
Background Early detection of tuberculosis (TB) is challenging in resource-poor settings because of limited accessibility to molecular diagnostics. The aim of this study was to evaluate the performance of the loop-mediated isothermal amplification kit (TB-LAMP) for TB diagnosis compared with conventional and molecular tests. Methods A total of 290 consecutive sputum samples were collected from May till September, 2015. All samples were processed using the N-Acetyl-L-cysteine (NALC) NaOH method and tested by smear microscopy, solid and liquid culture, real-time PCR, and TB-LAMP. Results The sensitivity of TB-LAMP for smear-positive and smear-negative samples with culture positivity was 92.0% and 58.8%, respectively. TB-LAMP was positive in 14.9% of TB culture-negative samples; however, all those samples were also positive by real-time PCR. In addition, none of the samples positive for nontuberculous mycobacteria by culture were positive by TB-LAMP. The overall agreement between TB-LAMP and real-time PCR was good; however, the concordance rate was significantly lower for real-time PCR positive samples with Ct values of 30–35. Conclusions TB-LAMP could replace smear microscopy and increase TB diagnostic capacity when Xpert MTB/RIF is not feasible because of poor infrastructure.
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Affiliation(s)
- Chang Ki Kim
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Guri, Korea.
| | - Eun A Cho
- Korean Institute of Tuberculosis, Cheongju, Korea
| | - Dong Mi Shin
- Korean Institute of Tuberculosis, Cheongju, Korea
| | | | - So Youn Shin
- Korean Institute of Tuberculosis, Cheongju, Korea
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Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Assay for Diagnosis of Cutaneous and Visceral Leishmaniasis. J Clin Microbiol 2018; 56:JCM.00386-18. [PMID: 29695527 PMCID: PMC6018344 DOI: 10.1128/jcm.00386-18] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/13/2018] [Indexed: 12/04/2022] Open
Abstract
A novel pan-Leishmania loop-mediated isothermal amplification (LAMP) assay for the diagnosis of cutaneous and visceral leishmaniasis (CL and VL) that can be used in near-patient settings was developed. Primers were designed based on the 18S ribosomal DNA (rDNA) and the conserved region of minicircle kinetoplast DNA (kDNA), selected on the basis of high copy number. LAMP assays were evaluated for CL diagnosis in a prospective cohort trial of 105 patients in southwest Colombia. Lesion swab samples from CL suspects were collected and were tested using the LAMP assay, and the results were compared to those of a composite reference of microscopy and/or culture in order to calculate diagnostic accuracy. LAMP assays were tested on samples (including whole blood, peripheral blood mononuclear cells, and buffy coat) from 50 suspected VL patients from Ethiopia. Diagnostic accuracy was calculated against a reference standard of microscopy of splenic or bone marrow aspirates. To calculate analytical specificity, 100 clinical samples and isolates from fever-causing pathogens, including malaria parasites, arboviruses, and bacteria, were tested. We found that the LAMP assay had a sensitivity of 95% (95% confidence interval [CI], 87.2% to 98.5%) and a specificity of 86% (95% CI, 67.3% to 95.9%) for the diagnosis of CL. With VL suspects, the sensitivity of the LAMP assay was 92% (95% CI, 74.9% to 99.1%) and its specificity was 100% (95% CI, 85.8% to 100%) in whole blood. For CL, the LAMP assay is a sensitive tool for diagnosis and requires less equipment, time, and expertise than alternative CL diagnostics. For VL, the LAMP assay using a minimally invasive sample is more sensitive than the gold standard. Analytical specificity was 100%.
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