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Antonopoulos A, Higgins O, Doyle SR, Bartley D, Morrison A, Shalaby MM, Reboud J, Devaney E, Smith TJ, Laing R, Busin V. Real-time single-base specific detection of the Haemonchus contortus S168T variant associated with levamisole resistance using loop-primer endonuclease cleavage loop-mediated isothermal amplification. Mol Cell Probes 2024; 73:101946. [PMID: 38097144 PMCID: PMC10884526 DOI: 10.1016/j.mcp.2023.101946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/22/2023]
Abstract
Haemonchus contortus is a parasitic haematophagous nematode that primarily affects small ruminants and causes significant economic loss to the global livestock industry. Treatment of haemonchosis typically relies on broad-spectrum anthelmintics, resistance to which is an important cause of treatment failure. Resistance to levamisole remains less widespread than to other major anthelmintic classes, prompting the need for more effective and accurate surveillance to maintain its efficacy. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) is a recently developed diagnostic method that facilitates multiplex target detection with single nucleotide polymorphism (SNP) specificity and portable onsite testing. In this study, we designed a new LEC-LAMP assay and applied it to detect the levamisole resistance marker S168T in H. contortus. We explored multiplexing probes for both the resistant S168T and the susceptible S168 alleles in a single-tube assay. We then included a generic probe to detect the acr-8 gene in the multiplex assay, which could facilitate the quantification of both resistance markers and overall genetic material from H. contortus in a single step. Our results showed promising application of these technologies, demonstrating a proof-of-concept assay which is amenable to detection of resistance alleles within the parasite population, with the potential for multiplex detection, and point-of-care application enabled by lateral flow end-point detection. However, further optimisation and validation is necessary.
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Affiliation(s)
- Alistair Antonopoulos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom; Kreavet, Kruibeke, Belgium.
| | - Owen Higgins
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David Bartley
- Moredun Research Institute, Penicuik, Scotland, United Kingdom
| | - Alison Morrison
- Moredun Research Institute, Penicuik, Scotland, United Kingdom
| | - Maha Mansour Shalaby
- James Watt School of Engineering, University of Glasgow, Glasgow, Scotland, United Kingdom; Food Control Department, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr-El-Sheikh, Egypt
| | - Julien Reboud
- James Watt School of Engineering, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Eileen Devaney
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Terry J Smith
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Roz Laing
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Valentina Busin
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom.
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Insight into molecular diagnosis for antimalarial drug resistance of Plasmodium falciparum parasites: A review. Acta Trop 2023; 241:106870. [PMID: 36849091 DOI: 10.1016/j.actatropica.2023.106870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Malaria is an infectious disease transmitted by the female Anopheles mosquito and poses a severe threat to human health. At present, antimalarial drugs are the primary treatment for malaria. The widespread use of artemisinin-based combination therapies (ACTs) has dramatically reduced the number of malaria-related deaths; however, the emergence of resistance has the potential to reverse this progress. Accurate and timely diagnosis of drug-resistant strains of Plasmodium parasites via detecting molecular markers (such as Pfnhe1, Pfmrp, Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13) is essential for malaria control and elimination. Here, we review the current techniques which commonly used for molecular diagnosis of antimalarial resistance in P. falciparum and discuss their sensitivities and specificities for different drug resistance-associated molecular markers, with the aim of providing insights into possible directions for future precise point-of-care testing (POCT) of antimalarial drug resistance of malaria parasites.
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Zhang J, Chen X, Pan M, Qin Y, Zhao H, Yang Q, Li X, Zeng W, Xiang Z, Wu Y, Duan M, Li X, Wang X, Mazier D, Zhang Y, Zhu W, Sun K, Wu Y, Cui L, Huang Y, Yang Z. Application of a low-cost, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay to detect Plasmodium falciparum imported from Africa. Mol Biochem Parasitol 2022; 252:111529. [PMID: 36374724 PMCID: PMC9890345 DOI: 10.1016/j.molbiopara.2022.111529] [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: 03/22/2022] [Revised: 08/12/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Chinese citizens traveling abroad bring back imported malaria cases to China. Current malaria diagnostic tests, including microscopy and antigen-detecting rapid tests, cannot reliably detect low-density infections. To complement existing diagnostic methods, we aimed to develop a new loop-mediated isothermal amplification (LAMP) assay to detect and identify Plasmodium falciparum in Chinese travelers returning from Africa. METHODS We developed a miniaturized LAMP assay to amplify the actin I gene of P. falciparum. Each reaction consumed only 25% of the reagents used in a conventional LAMP assay and the same amount of DNA templates used in nested PCR. We evaluated this LAMP assay's performance and compared it to microscopy and a nested PCR assay using 466 suspected malaria cases imported from Africa. We assessed the sensitivity of the new LAMP assay using cultured P. falciparum, clinical samples, and a plasmid construct, allowing unprecedented precision when quantifying the limit of detection. RESULTS The new LAMP assay was highly sensitive and detected two more malaria cases than nested PCR. Compared to nested PCR, the sensitivity and specificity of the novel LAMP assay were 100% [95% confidence interval (CI) 98.5-100%] and 99.1% (95% CI 96.7-99.9%), respectively. When evaluated using serial dilutions of the plasmid construct, the detection limit of the new LAMP was as low as 102 copies/μL, 10-fold lower than PCR. The LAMP assay detected 0.01 parasites/μL of blood (equal to 0.04 parasites/μL of DNA) using cultured P. falciparum and 1-7 parasites/μL of blood (4-28 parasites/μL of DNA) in clinical samples, which is as good as or better than previously reported and commercially licensed assays. CONCLUSION The novel LAMP assay based on the P. falciparum actin I gene was specific, sensitive, and cost-effective, as it consumes 1/4 of the reagents in a typical LAMP reaction.
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Affiliation(s)
- Jiaqi Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Zhejiang Provincial Center for Disease Control and Prevention, No.3399 BinSheng Road, Binjiang District, Hangzhou, Zhejiang Province, 310051, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Maohua Pan
- Shanglin County People’s Hospital, Shanglin, Guangxi, 530500, China
| | - Yucheng Qin
- Shanglin County People’s Hospital, Shanglin, Guangxi, 530500, China
| | - Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, Yunnan,China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Dominique Mazier
- Sorbonne Université, INSERM, CNRS, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Paris, France
| | - Yanmei Zhang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Wenya Zhu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Kemin Sun
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Yiman Wu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, MDC84, Tampa, FL 33612, USA
| | - Yaming Huang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, Guangxi, 530021, China,Correspondence:
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan, 650500, China,Correspondence:
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Jang YO, Lee HJ, Koo B, Cha HH, Kwon JS, Kim JY, Kim MG, Kim HS, Kim SH, Shin Y. Rapid COVID-19 Molecular Diagnostic System Using Virus Enrichment Platform. BIOSENSORS-BASEL 2021; 11:bios11100373. [PMID: 34677329 PMCID: PMC8534047 DOI: 10.3390/bios11100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is rapidly spreading and severely straining the capacities of public health communities and systems around the world. Therefore, accurate, rapid, and robust diagnostic tests for COVID-19 are crucial to prevent further spread of the infection, alleviate the burden on healthcare and diagnostic facilities, and ensure timely therapeutic intervention. To date, several detection methods based on nucleic acid amplification have been developed for the rapid and accurate detection of SARS-CoV-2. Despite the myriad of advancements in the detection methods for SARS-CoV-2, rapid sample preparation methods for RNA extraction from viruses have rarely been explored. Here, we report a rapid COVID-19 molecular diagnostic system that combines a self-powered sample preparation assay and loop-mediated isothermal amplification (LAMP) based naked-eye detection method for the rapid and sensitive detection of SARS-CoV-2. The self-powered sample preparation assay with a hydrophilic polyvinylidene fluoride filter and dimethyl pimelimidate can be operated by hand, without the use of any sophisticated instrumentation, similar to the reverse transcription (RT)-LAMP-based lateral flow assay for the naked-eye detection of SARS-CoV-2. The COVID-19 molecular diagnostic system enriches the virus population, extracts and amplifies the target RNA, and detects SARS-CoV-2 within 60 min. We validated the accuracy of the system by using 23 clinical nasopharyngeal specimens. We envision that this proposed system will enable simple, facile, efficient, and inexpensive diagnosis of COVID-19 at home and the clinic as a pre-screening platform to reduce the burden on the medical staff in this pandemic era.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
| | - Hye-Hee Cha
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Ji-Soo Kwon
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea
| | - Hyun Soo Kim
- INFUSIONTECH, 38, Heungan-daero 427 beon-gil, Dongan-gu, Anyang-si 14059, Korea;
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
- Correspondence: (S.-H.K.); (Y.S.)
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Correspondence: (S.-H.K.); (Y.S.)
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5
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Diagnosing the drug resistance signature in Plasmodium falciparum: a review from contemporary methods to novel approaches. J Parasit Dis 2021; 45:869-876. [PMID: 34475670 DOI: 10.1007/s12639-020-01333-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022] Open
Abstract
The genome sequence project of the human malaria parasite Plasmodium falciparum reveal variations in the parasite DNA sequence. Most of these variations are single nucleotide polymorphism (SNP). A high frequency of single nucleotide polymorphism (SNP) in the Plasmodium falciparum population is usually a benchmark for anti-malarial resistance which allows parasites to be elusive to the chemotherapeutic agents, vaccine and vector control strategies, resulting in the leading cause of morbidity and mortality globally. The high density of drug resistance signature markers such as pfcrt,pfmdr1, pfdhps, pfdhfr, pfkelch13, pfatpase6 and pfmrp1 in the genome opens up a scope for the study of the genetic basis of this elusive parasite. The precise and prompt diagnosis of resistance strains of parasite plays vital role in malaria elimination program.This review probably shed light on contemporary SNP diagnostic tools used in molecular surveillance of Plasmodium falciparum drug resistance in terms of mechanism, reaction modalities, and development with their virtues and shortcomings.
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Kassaza K, Long AC, McDaniels JM, Andre M, Fredrickson W, Nyehangane D, Orikiriza P, Operario DJ, Bazira J, Mwanga-Amumpaire JA, Moore CC, Guler JL, Boum Y. Surveillance of Plasmodium falciparum pfcrt haplotypes in southwestern uganda by high-resolution melt analysis. Malar J 2021; 20:114. [PMID: 33632242 PMCID: PMC7908690 DOI: 10.1186/s12936-021-03657-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Chloroquine (CQ) resistance is conferred by mutations in the Plasmodium falciparum CQ resistance transporter (pfcrt). Following CQ withdrawal for anti-malarial treatment, studies across malaria-endemic countries have shown a range of responses. In some areas, CQ sensitive parasites re-emerge, and in others, mutant haplotypes persist. Active surveillance of resistance mutations in clinical parasites is essential to inform treatment regimens; this effort requires fast, reliable, and cost-effective methods that work on a variety of sample types with reagents accessible in malaria-endemic countries. METHODS Quantitative PCR followed by High-Resolution Melt (HRM) analysis was performed in a field setting to assess pfcrt mutations in two groups of clinical samples from Southwestern Uganda. Group 1 samples (119 in total) were collected in 2010 as predominantly Giemsa-stained slides; Group 2 samples (125 in total) were collected in 2015 as blood spots on filter paper. The Rotor-Gene Q instrument was utilized to assess the impact of different PCR-HRM reagent mixes and the detection of mixed haplotypes present in the clinical samples. Finally, the prevalence of the wild type (CVMNK) and resistant pfcrt haplotypes (CVIET and SVMNT) was evaluated in this understudied Southwestern region of Uganda. RESULTS The sample source (i.e. Giemsa-stained slides or blood spots) and type of LCGreen-based reagent mixes did not impact the success of PCR-HRM. The detection limit of 10- 5 ng and the ability to identify mixed haplotypes as low as 10 % was similar to other HRM platforms. The CVIET haplotype predominated in the clinical samples (66 %, 162/244); however, there was a large regional variation between the sample groups (94 % CVIET in Group 1 and 44 % CVIET in Group 2). CONCLUSIONS The HRM-based method exhibits the flexibility required to conduct reliable assessment of resistance alleles from various sample types generated during the clinical management of malaria. Large regional variations in CQ resistance haplotypes across Southwestern Uganda emphasizes the need for continued local parasite genotype assessment to inform anti-malarial treatment policies.
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Affiliation(s)
- Kennedy Kassaza
- Epicentre Mbarara Research Centre, Mbarara, Uganda
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Anna C Long
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Jennifer M McDaniels
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Mharlove Andre
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA
| | - Wasswa Fredrickson
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | | | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Juliet A Mwanga-Amumpaire
- Epicentre Mbarara Research Centre, Mbarara, Uganda
- Department of Pediatrics and Child Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Box 400328, 22904, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22904, USA.
| | - Yap Boum
- Epicentre Mbarara Research Centre, Mbarara, Uganda.
- Department of Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda.
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Khammanee T, Sawangjaroen N, Buncherd H, Tun AW, Thanapongpichat S. A LAMP-SNP Assay Detecting C580Y Mutation in Pfkelch13 Gene from Clinically Dried Blood Spot Samples. THE KOREAN JOURNAL OF PARASITOLOGY 2021; 59:15-22. [PMID: 33684983 PMCID: PMC7939969 DOI: 10.3347/kjp.2021.59.1.15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/19/2021] [Indexed: 11/23/2022]
Abstract
Artemisinin resistance (ART) has been confirmed in Greater Mekong Sub-region countries. Currently, C580Y mutation on Pfkelch13 gene is known as the molecular marker for the detection of ART. Rapid and accurate detection of ART in field study is essential to guide malaria containment and elimination interventions. A simple method for collection of malaria-infected blood is to spot the blood on filter paper and is fast and easy for transportation and storage in the field study. This study aims to evaluate LAMP-SNP assay for C580Y mutation detection by introducing an extra mismatched nucleotide at the 3’ end of the FIP primer. The LAMP-SNP assay was performed in a water bath held at a temperature of 56°C for 45 min. LAMP-SNP products were interpreted by both gel-electrophoresis and HNB-visualized changes in color. The method was then tested with 120 P. falciparum DNA from dried blood spot samples. In comparing the LAMP-SNP assay results with those from DNA sequencing of the clinical samples, the 2 results fully agreed to detect C580Y. The sensitivity and specificity of the LAMP-SNP assay showed 100%. There were no cross-reactions with other Plasmodium species and other Pfkelch13 mutations. The LAMP-SNP assay performed in this study was rapid, reliable, and useful in detecting artemisinin resistance in the field study.
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Affiliation(s)
- Thunchanok Khammanee
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Nongyao Sawangjaroen
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Hansuk Buncherd
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Aung Win Tun
- Faculty of Graduate Studies, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Supinya Thanapongpichat
- Faculty of Medical Technology, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
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Varo R, Balanza N, Mayor A, Bassat Q. Diagnosis of clinical malaria in endemic settings. Expert Rev Anti Infect Ther 2020; 19:79-92. [PMID: 32772759 DOI: 10.1080/14787210.2020.1807940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Malaria continues to be a major global health problem, with over 228 million cases and 405,000 deaths estimated to occur annually. Rapid and accurate diagnosis of malaria is essential to decrease the burden and impact of this disease, particularly in children. We aimed to review the main available techniques for the diagnosis of clinical malaria in endemic settings and explore possible future options to improve its rapid recognition. AREAS COVERED literature relevant to malaria diagnosis was identified through electronic searches in Pubmed, with no language or date restrictions and limited to humans. EXPERT OPINION Light microscopy is still considered the gold standard method for malaria diagnosis and continues to be at the frontline of malaria diagnosis. However, technologies as rapid diagnostic tests, mainly those who detect histidine-rich protein-2, offer an accurate, rapid and affordable alternative for malaria diagnosis in endemic areas. They are now the technique most extended in endemic areas for parasitological confirmation. In these settings, PCR-based assays are usually restricted to research and they are not currently helpful in the management of clinical malaria. Other technologies, such as isothermal methods could be an interesting and alternative approach to PCR in the future.
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Affiliation(s)
- Rosauro Varo
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique
| | - Núria Balanza
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain
| | - Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat De Barcelona , Barcelona, Spain.,Centro De Investigação Em Saúde De Manhiça (CISM) , Maputo, Mozambique.,ICREA, Pg. Lluís Companys 23 , Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan De Deu (University of Barcelona) , Barcelona, Spain.,Consorcio De Investigación Biomédica En Red De Epidemiología Y Salud Publica (CIBERESP) , Madrid, Spain
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9
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Mohon AN, Getie S, Jahan N, Alam MS, Pillai DR. Ultrasensitive loop mediated isothermal amplification (US-LAMP) to detect malaria for elimination. Malar J 2019; 18:350. [PMID: 31619258 PMCID: PMC6796404 DOI: 10.1186/s12936-019-2979-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
Background Malaria elimination requires diagnostic methods able to detect parasite levels well below what is currently possible with microscopy and rapid diagnostic tests. This is particularly true in surveillance of malaria at the population level that includes so-called “asymptomatic” individuals. Methods The development of the first ultrasensitive loop mediated amplification method capable of detecting malaria from both whole blood and dried blood spots (DBS) is described. The 18S rRNA and corresponding genes that remain stable on DBS for up to 5 months are targeted. Results In the case of Plasmodium falciparum, lower limits of detection of 25 parasite/mL and 50–100 parasite/mL from whole blood and DBS were obtained, respectively. A sensitivity of 97.0% (95% CI 82.5–99.8) and specificity of 99.1% (95% CI 97.6–99.7) was obtained for the detection of all species in asymptomatic individuals from Africa and Asia (n = 494). Conclusion This tool is ideally suited for low middle-income countries where malaria is endemic and ultrasensitive surveillance of malaria is highly desirable for elimination.
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Affiliation(s)
- Abu Naser Mohon
- Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada.,Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, 9-3535 Research Road NW, 1 W-416, Calgary, AB, T2L2K8, Canada
| | - Sisay Getie
- Department of Medical Parasitology, School of Biomedical and Laboratory Science, College of Medicine and Health Sciences, University of Gondar, P. O. Box: 196, Gondar, Ethiopia
| | - Nusrat Jahan
- Emerging Infections and Parasitology Laboratory, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh
| | - Mohammad Shafiul Alam
- Emerging Infections and Parasitology Laboratory, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh
| | - Dylan R Pillai
- Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada. .,Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, 9-3535 Research Road NW, 1 W-416, Calgary, AB, T2L2K8, Canada. .,Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada.
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10
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A probe directed recombinase amplification assay for detection of MTHFR A1298C polymorphism associated with congenital heart disease. Biotechniques 2019; 64:211-217. [PMID: 29793361 DOI: 10.2144/btn-2018-2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) play an important role in susceptibility to complex diseases, treatment efficacy and adverse drug responses. Conventional methods to detect SNPs are usually based on PCR or DNA sequencing, which are typically time-consuming and require sophisticated equipment. In this proof-of-concept study, a probe-directed recombinase amplification (PDRA) assay was developed to detect the A1298C polymorphism of 5,10-methylenetetrahydrofolate reductase (MTHFR). The PDRA assay included two real-time reactions to detect the A and C nucleotides of A1298C polymorphism. Each reaction contained only one primer and one probe and was finished at 39°C within 35 min. The results of genotyping of 150 clinical samples using PDRA were completely consistent with those by direct sequencing. Additionally, when the 1000 Genomes Project HCB frequencies were used as the control group, MTHFR A1298C was found to be associated with congenital heart disease. In conclusion, the proposed novel PDRA assay is a valuable tool for the detection of SNPs and demonstrates significant potential to be widely applicable in both research and clinical settings.
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Chahar M, Anvikar A, Valecha N. Development and Evaluation of a Novel HNB Based Isothermal Amplification Assay for Fast Detection of Pyrimethamine Resistance (S108N) in Plasmodium falciparum. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16091635. [PMID: 31083343 PMCID: PMC6539687 DOI: 10.3390/ijerph16091635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 11/16/2022]
Abstract
Sulphadoxine and pyrimethamine (SP) have been used as long-acting partner antimalarial drugs in artemisinin combination therapy (ACT) for falciparum malaria. The emergence and increasing spread of SP resistance in malaria-endemic areas have become a challenge for the control of malaria. Therefore, regular monitoring of the mutation status of partner drugs is important for the better management of drug policy. There are limitations with traditional molecular methods and there is an urgent need for an easy method for diagnosis of drug resistance. In this study we have introduced and developed a novel single nucleotide polymorphism loop-mediated isothermal amplification (SNP-LAMP) approach based on a hydroxynaphthol blue (HNB) indicator for the easier and quicker detection of pyrimethamine resistance in Plasmodium falciparum malaria. To implement this novel approach, many sets of LAMP primers were designed and tested. Finally, one set of forward inner primer M1 (FIPM1) of LAMP primer was selected that specifically distinguishes pyrimethamine-resistant P. falciparum malaria. The LAMP reactions were optimized at 60-66 °C for 45 min. High sensitivity (7 parasites/µL) was observed with 10-4 fold dilutions (<2 ng DNA) of genomic DNA. Moreover, this approach has the potential to be applied even in laboratories unfamiliar with PCR or other molecular methods, and in future, this can be helpful for the better management of anti-malarial policy.
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Affiliation(s)
- Madhvi Chahar
- Division of Epidemiology and Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India.
| | - Anup Anvikar
- Division of Epidemiology and Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India.
| | - Neena Valecha
- Division of Epidemiology and Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India.
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Ido Y, Hashimoto M, Yatsushiro S, Tanaka M, Yokota K, Kajimoto K, Kataoka M. Loop-Mediated Isothermal Amplification In Microchambers On A Cell Microarray Chip For Identification of Plasmodium Species. J Parasitol 2019. [PMID: 30807712 DOI: 10.1645/18-107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Malaria is caused by Plasmodium spp., a parasitic protist that infects erythrocytes. A method that can detect the parasite with high sensitivity and that can identify the parasite species is urgently required for the control of malaria. The cell microarray chip was made using polystyrene with 200 cone-shaped frustum microchambers (800-μm top diameter, 636-μm bottom diameter, and 225 μm deep). Approximately 3,000 erythrocytes could be accommodated in each microchamber with monolayer formation, there being 60,000 erythrocytes in total microchambers on a cell microarray. Plasmodium could be quantitatively detected with high sensitivity with the use of cell microarray chips. Plasmodium parasitizing in erythrocytes was labeled with a cell-permeant fluorescent nucleic acid stain (SYTO 21), which could be detected in erythrocytes in the microchambers. Next, we used loop-mediated isothermal amplification (LAMP) in the microchambers (on-chip LAMP) to identify the parasite species detected in the microchambers. LAMP was performed in the microchambers (in a reaction volume of 0.09 μl) using Plasmodium falciparum-infected erythrocytes as the template and specific primers targeting 18S rRNA. To avoid evaporation of the reaction buffer during heat treatment, mineral oil was overlaid on each microchamber and the cell microarray chips were heated at 63 C for 1 hr. The results of on-chip LAMP were assessed using a portable ultraviolet transilluminator. We showed that this method has the potential for detection of parasites in 600,000 erythrocytes and for identification of the parasite species on a cell microarray chip. In conclusion, the parasites can be detected quantitatively with high sensitivity, and the species can be identified with the use of cell microarray chips.
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Affiliation(s)
- Yusuke Ido
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan.,2 Present address: Institute for Genome Research, Tokushima University, Kuramotocho-3, Tokushima 770-8503, Japan
| | - Muneaki Hashimoto
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan
| | - Shouki Yatsushiro
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan
| | - Masato Tanaka
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan
| | - Kazumichi Yokota
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan
| | - Kazuaki Kajimoto
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan
| | - Masatoshi Kataoka
- 1 Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa 761-0301, Japan
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13
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Molecular assays for antimalarial drug resistance surveillance: A target product profile. PLoS One 2018; 13:e0204347. [PMID: 30235327 PMCID: PMC6147503 DOI: 10.1371/journal.pone.0204347] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/05/2018] [Indexed: 11/25/2022] Open
Abstract
Antimalarial drug resistance is a major constraint for malaria control and elimination efforts. Artemisinin-based combination therapy is now the mainstay for malaria treatment. However, delayed parasite clearance following treatment with artemisinin derivatives has now spread in the Greater Mekong Sub region and may emerge or spread to other malaria endemic regions. This spread is of great concern for malaria control programmes, as no alternatives to artemisinin-based combination therapies are expected to be available in the near future. There is a need to strengthen surveillance systems for early detection and response to the antimalarial drug resistance threat. Current surveillance is mainly done through therapeutic efficacy studies; however these studies are complex and both time- and resource-intensive. For multiple common antimalarials, parasite drug resistance has been correlated with specific genetic mutations, and the molecular markers associated with antimalarial drug resistance offer a simple and powerful tool to monitor the emergence and spread of resistant parasites. Different techniques to analyse molecular markers associated with antimalarial drug resistance are available, each with advantages and disadvantages. However, procedures are not adequately harmonized to facilitate comparisons between sites. Here we describe the target product profiles for tests to analyse molecular markers associated with antimalarial drug resistance, discuss how use of current techniques can be standardised, and identify the requirements for an ideal product that would allow malaria endemic countries to provide useful spatial and temporal information on the spread of resistance.
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Chahar M, Anvikar A, Dixit R, Valecha N. Evaluation of four novel isothermal amplification assays towards simple and rapid genotyping of chloroquine resistant Plasmodium falciparum. Exp Parasitol 2018; 190:1-9. [PMID: 29750967 DOI: 10.1016/j.exppara.2018.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 04/19/2018] [Accepted: 05/06/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Madhvi Chahar
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, India.
| | - Anup Anvikar
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, India
| | - Rajnikant Dixit
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, India
| | - Neena Valecha
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, India
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15
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Hashimoto M, Sakamoto H, Ido Y, Tanaka M, Yatsushiro S, Kajimoto K, Kataoka M. In situ loop-mediated isothermal amplification (LAMP) for identification of Plasmodium species in wide-range thin blood smears. Malar J 2018; 17:235. [PMID: 29914490 PMCID: PMC6006833 DOI: 10.1186/s12936-018-2381-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 06/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Five species of Plasmodium are known to infect humans. For proper treatment of malaria, accurate identification of the parasite species is crucial. The current gold standard for malaria diagnosis is microscopic examination of Giemsa-stained blood smears. Since the parasite species are identified by microscopists who manually search for the parasite-infected red blood cells (RBCs), misdiagnosis due to human error tends to occur in case of low parasitaemia or mixed infection. Then, molecular methods, such as polymerase chain reaction or loop-mediated isothermal amplification (LAMP), are required for conclusive identification of the parasite species. However, since molecular methods are highly sensitive, false-positive results tend to occur due to contamination (carry over) or the target gene products may be detected even after clearance of the parasites from the patient's blood. Therefore, accurate detection of parasites themselves by microscopic examination is essential for the definitive diagnosis. Thus, the method of in situ LAMP for the parasites was developed. RESULTS Red blood cell suspensions, including cultured Plasmodium falciparum, strain 3D7, infected-RBCs, were dispersed on cyclic olefin copolymer (COC) plate surfaces rendered hydrophilic by reactive ion-etching treatment using a SAMCO RIE system (hydrophilic-treated), followed by standing for 10 min to allow the RBCs to settle down on the plate surface. By rinsing the plate with RPMI 1640 medium, monolayers of RBCs formed on almost the entire plate surface. The plate was then dried with a hair drier. The RBCs were fixed with formalin, followed by permeabilization with Triton X-100. Then, amplification of the P. falciparum 18S rRNA gene by the LAMP reaction with digoxigenin (DIG)-labelled dUTP and a specific primer set was performed. Infected RBCs as fluorescence-positive cells with anti-DIG antibodies conjugated with fluorescein using fluorescent microscopy could be detected. CONCLUSIONS The present work shows that the potential of in situ LAMP for the identification of Plasmodium species at the single cell level on hydrophilic-treated COC palates, allowing highly sensitive and accurate malaria diagnosis. The findings will improve the efficacy of the gold standard method for malaria diagnosis.
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Affiliation(s)
- Muneaki Hashimoto
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan.
| | - Hirokazu Sakamoto
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan.,Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yusuke Ido
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan
| | - Masato Tanaka
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan
| | - Shouki Yatsushiro
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan
| | - Kazuaki Kajimoto
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan
| | - Masatoshi Kataoka
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0301, Japan
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16
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Mohon AN, Menard D, Alam MS, Perera K, Pillai DR. A Novel Single-Nucleotide Polymorphism Loop Mediated Isothermal Amplification Assay for Detection of Artemisinin-Resistant Plasmodium falciparum Malaria. Open Forum Infect Dis 2018; 5:ofy011. [PMID: 29707598 PMCID: PMC5912083 DOI: 10.1093/ofid/ofy011] [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: 11/20/2017] [Accepted: 01/08/2018] [Indexed: 01/06/2023] Open
Abstract
Background Artemisinin-resistant malaria (ARM) remains a significant threat to malaria elimination. In the Greater Mekong subregion, the prevalence of ARM in certain regions has reached greater than 90%. Artemisinin-resistant malaria is clinically identified by delayed parasite clearance and has been associated with mutations in the propeller domain of the kelch 13 gene. C580Y is the most prevalent mutation. The detection of ARM currently relies on labor-intensive and time-consuming methods such as clinical phenotyping or in vitro susceptibility testing. Methods We developed a novel single-nucleotide polymorphism loop mediated isothermal amplification (SNP-LAMP) test method for the detection of the C580Y mutation using a novel primer design strategy. Results The SNP-LAMP was 90.0% sensitive (95% confidence interval [CI], 66.9-98.3) and 91.9% specific (95% CI, 82.6-96.7) without knowledge of the parasite load and was 100% sensitive (95% CI, 79.9-100) and 97.3% specific (95% CI, 89.7-99.5) when the parasitemia was within the assay dynamic range. Tests with potential application near-to-patient such as SNP-LAMP may be deployed in low- and middle-income and developed countries. Conclusions Single-nucleotide polymorphism LAMP can serve as a surveillance tool and guide treatment algorithms for ARM in a clinically relevant time frame, prevent unnecessary use of additional drugs that may drive additional resistance, and avoid longer treatment regimens that cause toxicity for the patient.
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Affiliation(s)
- Abu Naser Mohon
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Alberta, Canada
| | - Didier Menard
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France
| | - Mohammad Shafiul Alam
- Parasitology Laboratory, Centre for Vaccine Sciences, International Center for Diarrheal Disease Research, Mohakhali, Bangladesh
| | - Kevin Perera
- Department of Pathology and Laboratory Medicine, University of Calgary, Alberta, Canada.,Department of Biological Sciences, University of Calgary, Alberta, Canada
| | - Dylan R Pillai
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Alberta, Canada.,Department of Medicine, University of Calgary, Alberta, Canada
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17
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Wang H, Zhang X, Xu X, Zhang Q, Wang H, Li D, Kang Z, Wu Z, Tang Y, An Z, Guan M. A portable microfluidic platform for rapid molecular diagnostic testing of patients with myeloproliferative neoplasms. Sci Rep 2017; 7:8596. [PMID: 28819248 PMCID: PMC5561050 DOI: 10.1038/s41598-017-08674-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/12/2017] [Indexed: 11/10/2022] Open
Abstract
The ability to simultaneously detect JAK2 V617F and MPL W515K/L mutations would substantially improve the early diagnosis of myeloproliferative neoplasms (MPNs) and decrease the risk of arterial thrombosis. The goal of this study is to achieve a point of care testing platform for simultaneous analysis of major genetic alterations in MPN. Here, we report a microfluidic platform including a glass capillary containing polypropylene matrix that extracts genomic DNA from a drop of whole blood, a microchip for simultaneous multi-gene mutation screening, and a handheld battery-powered heating device. The µmLchip system was successfully used for point-of-care identification of the JAK2 V617F and MPL W515K/L mutations. The µmLchip assays were then validated by mutation analysis with samples from 100 MPN patients who had previously been analyzed via unlabeled probe melting curve analysis or real-time PCR. The results from the µmLchip were in perfect agreement with those from the other methods, except for one discrepant result that was negative in the unlabeled probe melting curve analysis but positive in the µmLchip. After T-A cloning, sequences of cloned PCR products revealed JAK2 V617F mutation in the sample. The portable microfluidic platform may be very attractive in developing point-of-care diagnostics for MPL W515K/L and JAK2 V617F mutations.
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Affiliation(s)
- Hua Wang
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xinju Zhang
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Xiao Xu
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qunfeng Zhang
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Hengliang Wang
- Deptartment of Physics, Fudan University, Shanghai, 200040, China
| | - Dong Li
- Deptartment of Clinical Laboratory, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Zhihua Kang
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zhiyuan Wu
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Yigui Tang
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zhenhua An
- Deptartment of Physics, Fudan University, Shanghai, 200040, China
| | - Ming Guan
- Deptartment of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China.
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Mwendwa F, Mbae CK, Kinyua J, Mulinge E, Mburugu GN, Njiru ZK. Stem loop-mediated isothermal amplification test: comparative analysis with classical LAMP and PCR in detection of Entamoeba histolytica in Kenya. BMC Res Notes 2017; 10:142. [PMID: 28359328 PMCID: PMC5374617 DOI: 10.1186/s13104-017-2466-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 03/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Entamoeba histolytica, the causative agent for amoebiasis is a considerable burden to population in the developing countries where it accounts for over 50 million infections. The tools for detection of amoebiasis are inadequate and diagnosis relies on microscopy which means a significant percent of cases remain undiagnosed. Moreover, tests formats that can be rapidly applied in rural endemic areas are not available. METHODS In this study, a loop-mediated isothermal test (LAMP) based on 18S small subunit ribosomal RNA gene was designed with extra reaction accelerating primers (stem primers) and compared with the published LAMP and PCR tests in detection of E. histolytica DNA in clinical samples. RESULTS The stem LAMP test indicated shorter time to results by an average 11 min and analytical sensitivity of 10-7 (~30 pg/ml) compared to the standard LAMP and PCR which showed sensitivities levels of 10-5 (~3 ng/ml) and 10-4 (~30 ng/ml) respectively using tenfold serial dilution of DNA. In the analysis of clinical specimens positive for Entamoeba spp. trophozoites and cysts using microscopy, the stem LAMP test detected E. histolytica DNA in 36/126, standard LAMP test 20/126 and PCR 17/126 cases respectively. There was 100% agreement in detection of the stem LAMP test product using fluorescence of SYTO-9 dye in real time machine, through addition of 1/10 dilution of SYBR® Green I and electrophoresis in 2% agarose gel stained with ethidium bromide. CONCLUSION The stem LAMP test developed in this study indicates potential towards detection of E. histolytica.
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Affiliation(s)
- Fridah Mwendwa
- Institute of Tropical Medicine and Infectious Diseases, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000-0200, Nairobi, Kenya.
| | - Cecilia K Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute, P.O Box 19464-00202, Nairobi, Kenya
| | - Johnson Kinyua
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000-0200, Nairobi, Kenya
| | - Erastus Mulinge
- Centre for Microbiology Research, Kenya Medical Research Institute, P.O Box 19464-00202, Nairobi, Kenya
| | | | - Zablon K Njiru
- Meru University of Science and Technology, P. O. Box 972-60200, Meru, Kenya.,School of Health Professions, Mandurah Campus, Murdoch University, Murdoch, WA, 6210, Australia
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