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Milani A, Panozzo S, Grazia TM, Scarabel L. Development of a rapid detection assay for acetolactate synthase inhibitors resistance in three Amaranthus weed species through loop-mediated isothermal amplification. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5522-5532. [PMID: 38358049 DOI: 10.1002/jsfa.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND The early detection of herbicide resistance in weeds is a key factor to avoid herbicide waste and improve agriculture sustainability. The present study aimed to develop and validate an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for the quick on-site detection of the resistance-endowing point mutation Trp-574-Leu in the acetolactate synthase (ALS) gene in three widely diffused Amaranthus weed species: Amaranthus retroflexus, Amaranthus hybridus and Amaranthus tuberculatus. RESULTS The AS-LAMP protocol was developed on wild-type and ALS-mutant plants of the three species and revealed that the amplification approach with only the primer set specific for the mutant allele (574-Leu) was the most promising. The validation and estimation of the AS-LAMP performance evaluated by comparing the results with those of the molecular marker (cleaved amplified polymorphic sequences) indicated that, although the sensitivity and specificity were relatively high in all species (overall 100 and > 65%, respectively), precision was high for A. hybridus L. and A. retroflexus L. (75 and 79%, respectively), but quite low for A. tuberculatus (Moq.) J. D. Sauer (59%). The LAMP assay was also effective on crude genomic DNA extraction, allowing the quick detection of mutant plants in field situation (on site resistance detection). CONCLUSION The proposed AS-LAMP method has proven to be a promising technique for rapid detection of resistance as a result of Trp-574-Leu on the two monoecious weedy Amaranthus species but resulted less effective in the genetically variable dioecious species A. tuberculatus. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Andrea Milani
- Institute for Sustainable Plant Protection (IPSP-CNR), Legnaro, Italy
| | - Silvia Panozzo
- Institute for Sustainable Plant Protection (IPSP-CNR), Legnaro, Italy
| | | | - Laura Scarabel
- Institute for Sustainable Plant Protection (IPSP-CNR), Legnaro, Italy
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Sanmoung W, Sawangjaroen N, Jitueakul S, Buncherd H, Tun AW, Thanapongpichat S, Imwong M. Application of loop-mediated isothermal amplification combined with lateral flow assay visualization of Plasmodium falciparum kelch 13 C580Y mutation for artemisinin resistance detection in clinical samples. Acta Trop 2023; 246:106998. [PMID: 37544396 PMCID: PMC10465885 DOI: 10.1016/j.actatropica.2023.106998] [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: 05/01/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Resistance to the antimalarial drug artemisinin (ART) has emerged in Greater Mekong Subregion. The molecular marker predominantly used to identify ART resistance is the C580Y mutation in Pfkelch13 of Plasmodium falciparum. Rapid and accurate detection of ART resistance in the field is necessary to guide malaria containment and elimination interventions. Our study evaluates the PfC580Y by using the loop-mediated isothermal amplification and single nucleotide polymorphism analysis visualization using a lateral flow assay (LAMP-SNP-LFA) method for detecting ART resistance in clinical samples collected from Thailand between 2014 and 2019. The optimized incubation condition for the reaction was determined as 45 min at 56 °C, followed by visual detection of positive amplicons using LFA. The assay demonstrated high analytical sensitivity and specificity, with a limit of detection of 16.8 copies of C580Y plasmid/µL of and 100% accuracy for C580Y mutation detection. The PfC580Y LAMP-SNP-LFA method is faster and simpler than conventional polymerase chain reaction/DNA sequencing and has the potential to support antimalarial management policies, malaria control, and global elimination efforts.
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Affiliation(s)
- Wannida Sanmoung
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Nongyao Sawangjaroen
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Suwannee Jitueakul
- Haematology Unit, Department of Medical Technology and Pathology, Suratthani Hospital, Surat Thani Province, 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
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 10400, Thailand; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Wang M, Tang Z, Liao M, Cao H, Zhao N. Loop-mediated isothermal amplification for detecting the Ile-2041-Asn mutation in fenoxaprop-P-ethyl-resistant Alopecurus aequalis. PEST MANAGEMENT SCIENCE 2023; 79:711-718. [PMID: 36258292 DOI: 10.1002/ps.7239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/26/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Shortawn foxtail (Alopecurus aequalis Sobol.), a competitive grass weed severely infesting overwintering crops worldwide, has evolved resistance to the highly efficient acetyl-CoA carboxylase (ACCase)-inhibiting herbicide fenoxaprop-P-ethyl. The Ile-to-Asn substitution at codon position 2041 of ACCase is a dominant resistance mutation that has been associated with fenoxaprop-P-ethyl resistance in A. aequalis. However, its detection based on conventional methods such as polymerase chain reaction (PCR) and gene sequencing is rather labor- and time-consuming. RESULTS In order to facilitate its detection in field populations of A. aequalis, a simple and efficient method with high sensitivity to the Ile-2041-Asn mutation was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed to target a 244-bp fragment of ACCase comprising codon position 2041. Using the special primers and genomic DNA of A. aequalis, the concentrations of reaction components, temperature and time each were optimized. The LAMP reaction for the detection of the Ile-2041-Asn mutation was processed at 65 °C for 45 min followed by 80 °C for 10 min to stop the reaction. The LAMP method developed was 1000-fold more sensitive than the conventional PCR method, and the detection was also practicable when using crude DNA of A. aequalis as a template. CONCLUSION The low cost, simplicity and high sensitivity of the developed LAMP assay make the detection of the Ile-2041-Asn mutation easier and quicker, which may contribute to the monitoring and management of resistance development to fenoxaprop-P-ethyl in A. aequalis. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Mali Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Zhi Tang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Ning Zhao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
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4
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Wang J, Davidson JL, Kaur S, Dextre AA, Ranjbaran M, Kamel MS, Athalye SM, Verma MS. Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens. BIOSENSORS 2022; 12:bios12121094. [PMID: 36551061 PMCID: PMC9776365 DOI: 10.3390/bios12121094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 05/17/2023]
Abstract
Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andres A. Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohamed S. Kamel
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Shreya Milind Athalye
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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Hyman LB, Christopher CR, Romero PA. Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection. CELL REPORTS METHODS 2022; 2:100242. [PMID: 35880021 PMCID: PMC9308130 DOI: 10.1016/j.crmeth.2022.100242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 02/28/2022] [Accepted: 06/02/2022] [Indexed: 12/01/2022]
Abstract
In this work, we developed a simple and robust assay to rapidly detect SNPs in nucleic acid samples. Our approach combines loop-mediated isothermal amplification (LAMP)-based target amplification with fluorescent probes to detect SNPs with high specificity. A competitive "sink" strand preferentially binds to non-SNP amplicons and shifts the free energy landscape to favor specific activation by SNP products. We demonstrated the broad utility and reliability of our SNP-LAMP method by detecting three distinct SNPs across the human genome. We also designed an assay to rapidly detect highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from crude biological samples. This work demonstrates that competitive SNP-LAMP is a powerful and universal method that could be applied in point-of-care settings to detect any target SNP with high specificity and sensitivity. We additionally developed a publicly available web application for researchers to design SNP-LAMP probes for any target sequence of interest.
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Affiliation(s)
- Leland B. Hyman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Philip A. Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- The University of Wisconsin Carbone Cancer Center, Madison, WI, USA
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Zhang T, Zhao W, Zhao W, Si Y, Chen N, Chen X, Zhang X, Fan L, Sui G. Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Anal Chem 2021; 93:16184-16193. [PMID: 34818890 PMCID: PMC8672426 DOI: 10.1021/acs.analchem.1c04065] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022]
Abstract
Nowadays, rapid and accurate diagnosis of respiratory tract viruses is an urgent need to prevent another epidemic outbreak. To overcome this problem, we have developed a clustered, regularly interspaced short palindromic repeats (CRISPR) loop mediated amplification (LAMP) technology to detect influenza A virus, influenza B virus, respiratory syncytial A virus, respiratory syncytial B virus, and severe acute respiratory syndrome coronavirus 2, including variants of concern (B.1.1.7), which utilized CRISPR-associated protein 12a (Cas12a) to advance LAMP technology with the sensitivity increased 10 times. To reduce aerosol contamination in CRISPR-LAMP technology, an uracil-DNA-glycosylase-reverse transcription-LAMP system was also developed which can effectively remove dUTP-incorporated LAMP amplicons. In vitro Cas12a cleavage reaction with 28 crRNAs showed that there were no position constraints for Cas12a/CRISPR RNA (crRNA) recognition and cleavage in LAMP amplicons, and even the looped position of LAMP amplicons could be effectively recognized and cleaved. Wild-type or spike N501Y can be detected with a limit of detection of 10 copies/μL (wild-type) even at a 1% ratio level on the background (spike N501Y). Combining UDG-RT-LAMP technology, CRISPR-LAMP design, and mutation detection design, we developed a CRISPR-LAMP detection platform that can precisely diagnose pathogens with better stability and significantly improved point mutation detection efficiency.
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Affiliation(s)
- Tong Zhang
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Wei Zhao
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Wang Zhao
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Yuying Si
- Department
of Clinical Laboratory, Shanghai East Hospital, School of Medicine, Tong Ji University, 150 Ji Mo Road, Shanghai 200120, P. R. China
| | - Nianzhen Chen
- Department
of Clinical Laboratory, Shanghai East Hospital, School of Medicine, Tong Ji University, 150 Ji Mo Road, Shanghai 200120, P. R. China
| | - Xi Chen
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Xinlian Zhang
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Lieying Fan
- Department
of Clinical Laboratory, Shanghai East Hospital, School of Medicine, Tong Ji University, 150 Ji Mo Road, Shanghai 200120, P. R. China
| | - Guodong Sui
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
- Department
of Medical Microbiology and Parasitology, School of Basic Medical
Sciences, Fudan University, Shanghai 200032, P. R. China
- Jiangsu
Collaborative Innovation Center of Atmospheric Environment and Equipment
Technology (CICAEET), Nanjing University
of Information Science & Technology, Nanjing 210044, PR China
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7
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Development of a LAMP-Based Molecular Species Diagnosis Method for Four Major Agricultural Pests in the Genus Spodoptera (Lepidoptera: Noctuidae). INSECTS 2021; 12:insects12100883. [PMID: 34680652 PMCID: PMC8541213 DOI: 10.3390/insects12100883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Four major Spodoptera pests, S. exigua, S. frugiperda, S. litura, and S. littoralis, are widely distributed polyphagous pests affecting various crops. Despite different distribution areas, these four species cause serious damage to agriculture worldwide. As these species are morphologically similar at the larval stage, diagnostic methods have been developed and utilized for their identification. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for rapid and effective species diagnosis, along with PCR, to identify Korean field-collected or overseas samples. The optimal conditions for the LAMP assay were 61 °C for 60 min with four LAMP primers. Additional loop primers increased the amplification efficiency in S. exigua, whereas increased non-specific amplification was found in other species. A broad range of DNA concentrations was observed in the LAMP assay, and the minimum detectable DNA concentration was 1 pg. The DNA release method for LAMP involved incubation of larval or adult tissue samples for 5 min at 95 °C, without a DNA extraction step. Considering the gradual diversification invasive pest incidence, this simple and accurate LAMP assay can be used for intensive field monitoring of invasive pests and integrated management of these species. Abstract Molecular-based species identification tools are helpful to identify tiny insect and lepidopteran pests that show morphological similarities in the larval stage and are essential for quarantine as well as agricultural research. Here, we focused on four major Spodoptera pests: S. exigua, S. frugiperda, S. litura, and S. littoralis. S. exigua and S. litura mitochondrial genome sequences were newly identified and species-specific sequence regions were identified in the cytochrome c oxidase subunit II and III regions. Species primers were designed and applied in loop-mediated isothermal amplification (LAMP) and PCR to identify Korean field-collected or overseas samples. The optimal incubation conditions for LAMP were 61 °C for 60 min with four LAMP primers. Additional loop primers increased the amplification efficiency for S. exigua, and the nonspecific amplification for other species. The LAMP assay could detect a wide range of DNA concentrations, with the range 1 ng–1 pg in dependence of four LAMP primers. The DNA-releasing technique, without DNA extraction, in the LAMP assay involved larval or adult tissue sample incubation at 95 °C for 5 min. The entire process takes approximately 70 min. This new molecular diagnostic method is simple and accurate, with application in the field and laboratory and for monitoring and ecological studies.
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Medjigbodo AA, Djogbenou LS, Koumba AA, Djossou L, Badolo A, Adoha CJ, Ketoh GK, Mavoungou JF. Phenotypic Insecticide Resistance in Anopheles gambiae (Diptera: Culicidae): Specific Characterization of Underlying Resistance Mechanisms Still Matters. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:730-738. [PMID: 33043968 PMCID: PMC7954100 DOI: 10.1093/jme/tjaa195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Indexed: 06/11/2023]
Abstract
An effective control of malaria vectors requires an extensive knowledge of mechanisms underlying the resistance-phenotypes developed by these vectors against insecticides. We investigated Anopheles gambiae mosquitoes from Benin and Togo for their intensity of insecticide resistance and we discussed the involvement of genotyped mechanisms in the resistance-phenotypes observed. Three- to five-day-old adult mosquitoes emerged from field and laboratory An. gambiae larvae were assayed using WHO tube intensity tests against various doses of deltamethrin: 1× (0.05%); 2× (0.1%); 5× (0.25%); 7.5× (0.375%) and those of pirimiphos-methyl: 0.5× (0.125%); 1× (0.25%). Members of An. gambiae complex were screened in field populations using polymerase chain reaction (PCR) assays. The presence of kdrR(1014F/1014S) and ace-1R(119S) mutations was also investigated using TaqMan and PCR-RFLP techniques, respectively. Anopheles gambiae from field were very resistant to deltamethrin, whereas KisKdr and AcerKdrKis strains displayed 100% mortality rates at 2× the diagnostic dose. In contrast, the field mosquitoes displayed a low resistance-intensity against 1× the diagnostic dose of pirimiphos-methyl, whereas AcerKis and AcerKdrKis strains showed susceptibility at 0.5× the diagnostic dose. Anopheles gambiae s.s., Anopheles coluzzii, and Anopheles arabiensis were identified. Allelic frequencies of kdrR (1014F) and ace-1R (119S) mutations in the field populations varied from 0.65 to 1 and 0 to 0.84, respectively. The field An. gambiae displayed high-resistance levels against deltamethrin and pirimiphos-methyl when compared with those of the laboratory An. gambiae-resistant strains. These results exhibit the complexity of underlying insecticide resistance mechanisms in these field malaria vectors.
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Affiliation(s)
- Adandé A Medjigbodo
- Laboratory of Infectious Vector-Borne Diseases, Regional Institute of Public Health/University of Abomey-Calavi, Cotonou, Benin
- Laboratory of Fundamental and Applied Entomology, University Joseph KI-ZERBO, BP, Burkina Faso, West Africa
| | - Luc S Djogbenou
- Laboratory of Infectious Vector-Borne Diseases, Regional Institute of Public Health/University of Abomey-Calavi, Cotonou, Benin
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Aubin A Koumba
- Laboratory of Infectious Vector-Borne Diseases, Regional Institute of Public Health/University of Abomey-Calavi, Cotonou, Benin
- University of Science and Technology of Masuku (USTM), BP, Franceville, Gabon
| | - Laurette Djossou
- Laboratory of Infectious Vector-Borne Diseases, Regional Institute of Public Health/University of Abomey-Calavi, Cotonou, Benin
| | - Athanase Badolo
- Laboratory of Fundamental and Applied Entomology, University Joseph KI-ZERBO, BP, Burkina Faso, West Africa
| | - Constantin J Adoha
- Laboratory of Infectious Vector-Borne Diseases, Regional Institute of Public Health/University of Abomey-Calavi, Cotonou, Benin
| | | | - Jacques F Mavoungou
- University of Science and Technology of Masuku (USTM), BP, Franceville, Gabon
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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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Yongkiettrakul S, Kolié FR, Kongkasuriyachai D, Sattabongkot J, Nguitragool W, Nawattanapaibool N, Suansomjit C, Warit S, Kangwanrangsan N, Buates S. Validation of PfSNP-LAMP-Lateral Flow Dipstick for Detection of Single Nucleotide Polymorphism Associated with Pyrimethamine Resistance in Plasmodium falciparum. Diagnostics (Basel) 2020; 10:E948. [PMID: 33202937 PMCID: PMC7698237 DOI: 10.3390/diagnostics10110948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/03/2022] Open
Abstract
The loop-mediated isothermal amplification coupled with lateral flow dipstick (PfSNP-LAMP-LFD) was recently developed to detect single nucleotide polymorphism (AAT → ATT), corresponding to substitution of asparagine to isoleucine at amino acid position 51 in the P. falciparumdhfr-ts gene associated with antifolate resistance. In this present study, the PfSNP-LAMP-LFD was validated on 128 clinical malaria samples of broad ranged parasite densities (10 to 87,634 parasites per microliter of blood). The results showed 100% accuracy for the detection of single nucleotide polymorphism for N51I mutation. Indeed, the high prevalence of N51I in the Pfdhfr-ts gene detected in the clinical samples is in line with reports of widespread antifolate resistant P. falciparum in Thailand. The relationship between enzyme choice and reaction time was observed to have an effect on PfSNP-LAMP-LFD specificity; however, the method yielded consistent results once the conditions have been optimized. The results demonstrate that PfSNP-LAMP-LFD is a simple method with sufficient sensitivity and specificity to be deployed in routine surveillance of antifolate resistance molecular marker and inform antimalarial management policy.
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Affiliation(s)
- Suganya Yongkiettrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (S.Y.); (D.K.); (S.W.)
| | - Fassou René Kolié
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (F.R.K.); (N.N.)
| | - Darin Kongkasuriyachai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (S.Y.); (D.K.); (S.W.)
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.S.); (C.S.)
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Namfon Nawattanapaibool
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (F.R.K.); (N.N.)
| | - Chayanut Suansomjit
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.S.); (C.S.)
| | - Saradee Warit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (S.Y.); (D.K.); (S.W.)
| | - Niwat Kangwanrangsan
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Sureemas Buates
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (F.R.K.); (N.N.)
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Rapid detection of rifampicin-resistant Mycobacterium tuberculosis, based on isothermal DNA amplification and DNA chromatography. J Microbiol Methods 2020; 177:106062. [PMID: 32950563 DOI: 10.1016/j.mimet.2020.106062] [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: 08/20/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022]
Abstract
Rapid and easy detection of nucleotide point mutations in bacterial pathogens associated with drug resistance is essential for the proper use of antimicrobials. Here, we developed a rapid and simple method for the detection of mutations using Loop-mediated isothermal amplification (LAMP) combined with the single-tag hybridization (STH) chromatographic printed array strips (PAS) method. This procedure is able to detect four mutations (C1349 T, A1295C, G1303 T, A1304 T) in Rifampicin Resistance Determining Region (RRDR) of rifampicin-resistant Mycobacterium tuberculosis (RR-TB), simultaneously. LAMP reactions contained a LAMP primer and eight allele-specific primers for each mutation. The allele-specific primers products were detected by nucleic acid chromatography using PAS. Four detection lines were detected there, one of which was detected at different positions depend on the wild type and the mutant type. We carried out the four mutations detection using 31 genomic DNA (2 A1295T, 1 G1303 T, 6 A1304 T, 22 C1349 T) from clinical isolate. The mutations have been confirmed by sequence analysis. The detection results were completely consistent with the sequence analysis. In the present study, four mutations could be detected, but only 60% of RR-TB could be detected with these four. It is expected that the detection rate will increase by adding more mutant primers. The combined LAMP and STH chromatographic PAS method is a simple and rapid method for detecting point mutations in clinical isolates as a point-of-care testing (POCT) technique. In addition, it does not require special equipment and can meet the demand in areas where drug-resistant bacteria are endemic, such as developing countries.
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12
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Ji J, Chen Q, Sui C, Hu W, Yu Z, Zhang Z, Mu X, Xu X, Yao L, Kan Y, Xie Q. Rapid and visual detection of novel astroviruses causing fatal gout in goslings using one-step reverse transcription loop-mediated isothermal amplification. Poult Sci 2020; 99:4259-4264. [PMID: 32867970 PMCID: PMC7305742 DOI: 10.1016/j.psj.2020.05.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/02/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023] Open
Abstract
To visually and rapidly detect a novel goose astrovirus (N-GoAstV) causing fatal gout in goslings, an isothermal detection method based on one-step reverse transcription loop-mediated isothermal amplification (one-step RT-LAMP) was established. The one-step RT-LAMP assay for N-GoAstV detection, using Bst 3.0 DNA polymerase with strong reverse transcription activity and primer sets targeting the opening reading frame 1b (ORF1b) of N-GoAstV, could be completed in 30 min using a water bath at 61°C; the detection results could be visually observed by adding a pH-sensitive dye containing phenol red and cresol red. The detection limit of the one-step RT-LAMP assay was 57.8 copies, which was similar to that of reverse transcription–quantitative polymerase chain reaction. The assay specifically detected N-GoAstV without any cross-reaction with other reference viruses, and this was further confirmed using enzyme digestion. These results indicated that the newly established RT-LAMP assay could accomplish reverse transcription, amplification, and visual result determination in one step, and the results obtained via this rapid and cost-effective method could be used to support disease control on farms in terms of N-GoAstV infection.
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Affiliation(s)
- Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
| | - Qinxi Chen
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Chaoge Sui
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Wen Hu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Zhengli Yu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Zhibin Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Xinhao Mu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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Arjuna S, Chakraborty G, Venkataram R, Dechamma PN, Chakraborty A. Detection of epidermal growth factor receptor T790M mutation by allele-specific loop mediated isothermal amplification. J Carcinog 2020; 19:3. [PMID: 32684851 PMCID: PMC7363156 DOI: 10.4103/jcar.jcar_6_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Targeted therapy using specific inhibitors against tyrosine kinases (TKs) is a paradigm in non-small-cell lung cancer management. However, the success of TK inhibitor (TKI) therapy depends on certain activating or acquired mutations, which render sensitivity or resistance to TKIs in the patients. The acquisition of epidermal growth factor receptor (EGFR) T790M point mutation is the most common mechanism of resistance to TKI in non-small cell lung cancer. A number of molecular strategies are now available for molecular testing of non-small cell lung cancers. However, almost all of them are cost-intensive and laborious and require high-end advanced equipment. Thus, assays that are rapid, simple, and cost-effective, yet sensitive, are most ideal in clinical settings for screening such therapeutically relevant mutations. MATERIALS AND METHODS Allele-specific loop-mediated isothermal amplification assay (AS-LAMP), which is a variant of the original LAMP assay, is a promising diagnostic technique for screening single-nucleotide polymorphisms. Using commercially available plasmid constructs as template DNA, AS-LAMP assay for EGFR T790M mutation was optimized with six different sets of reaction mixture containing varying concentrations of buffer and primers. The results of AS-LAMP assay were further validated by ultrasensitive droplet digital polymerase chain reaction. RESULTS Only one of the six sets of reaction mixture could accurately distinguish between wild type and mutated DNA, indicating that the primers and buffer are the two most critical components that determine the accuracy of AS-LAMP. The optimized AS-LAMP assay was further used to screen germ line and somatic T790M mutations in non-small cell lung cancer using blood and tissue samples collected from patients. CONCLUSION Development of an accurate and rapid diagnostic assay that can detect resistant mutations without the need for sequencing is highly useful for clinicians in deciding on the eligibility of patients for TKI therapy. Considering its several inherent advantages, AS-LAMP assay could become an effective molecular tool for screening baseline or acquired EGFR T790M mutations in non-small cell lung cancer patients.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, Karnataka, India
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14
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Shimuta K, Nakayama SI, Takahashi H, Ohnishi M. A Loop-Mediated Isothermal Amplification Assay Targeting Neisseria gonorrhoeae penA-60.001. Antimicrob Agents Chemother 2019; 64:e01663-19. [PMID: 31658968 PMCID: PMC7187580 DOI: 10.1128/aac.01663-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/19/2019] [Indexed: 11/20/2022] Open
Abstract
Ceftriaxone (CRO) is widely used as the first-line treatment for gonococcal infections. However, CRO-resistant Neisseria gonorrhoeae strains carrying mosaic penA-60.001 have emerged recently and disseminated worldwide. To meet the urgent need to detect these strains, we report here a loop-mediated isothermal amplification (LAMP) assay system that targets N. gonorrhoeaepenA-60.001. This assay system can differentiate N. gonorrhoeae strains carrying mosaic penA-60.001 from strains carrying other penA alleles.
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Affiliation(s)
- Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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15
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Vontas J, Mavridis K. Vector population monitoring tools for insecticide resistance management: Myth or fact? PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 161:54-60. [PMID: 31685197 DOI: 10.1016/j.pestbp.2019.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/10/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Insecticide resistance is a large and growing problem for the control of mosquito disease vectors. The World Health Organization (WHO) established the Global Plan for Insecticide Resistance Management (GPIRM) in 2012. In that context, both classical and molecular tools, as well as entomological databases and decision support platforms have been developed and used for IRM. Despite major advances in the molecular elucidation of resistance mechanisms and the development of diagnostic tools, their impact on disease control programs has been limited. In most cases diagnostic tools provide a retrospective examination of changes imposed by insecticides rather than a prospective analysis to guide vector control strategies. The uncertainty of the predictive value of markers, the assay robustness and the common misconceptions in resistance diagnosis terminology are continuing challenges in monitoring vector resistance. Furthermore, an often logistics, as opposed to systematic scientific evidence, based approach to decision for the use of the very few alternative chemicals in vector control, has reduced the value of resistance monitoring in practice. The current deployment of new insecticidal active ingredients should necessitate the application of companion diagnostics (CDx) and the development of modern ways for interpretation and management of the data by trained programme managers. This will establish their real value for use in decision-making, in line with evidence based choice of chemicals in agriculture and medical applications.
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Affiliation(s)
- John Vontas
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece; Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Greece.
| | - Konstantinos Mavridis
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, GR-700 13 Heraklion, Crete, Greece
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16
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Ding S, Chen R, Chen G, Li M, Wang J, Zou J, Du F, Dong J, Cui X, Huang X, Deng Y, Tang Z. One-step colorimetric genotyping of single nucleotide polymorphism using probe-enhanced loop-mediated isothermal amplification (PE-LAMP). Am J Cancer Res 2019; 9:3723-3731. [PMID: 31281509 PMCID: PMC6587344 DOI: 10.7150/thno.33980] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphism (SNP) is the most abundant molecular marker associated with many physiologic and pathologic phenotypes. An isothermal, accurate and cost-effective SNP detection could make a great difference in point-of-care testing (POCT) or on-site diagnosis. However, there are two challenges, the expensive instrument and labor-intensive process, faced by the development of on-site SNP detection. We reported a novel SNP typing method based on the probe-enhanced loop-mediated isothermal amplification (PE-LAMP), which combines the oligonucleotide probe with a conventional LAMP to realize the SNP discrimination by analyzing the great discrepancy in amplification efficiency. Methods: We firstly constructed the genotyping method by combining the hybridization of the specific probe with the powerful amplification of LAMP. Then we validated the method by genotyping the SNP rs3741219 and we sought to realize one-step visualized typing. Finally, we applied the method to pharmacogenomic testing by genotyping CYP2C19*2 and MDR1 C3435T. Results: The PE-LAMP was successfully constructed to detect SNP and the sensitivity of our method is as low as 1000 copies of target DNA, which is sufficient to routine diagnosis. The high specificity in detecting mutant in the presence of excess wild-type allele could be achieved. It has shown good performance in helping predict the individual response of antiplatelet drug Clopidogrel through typing simply treated saliva samples. Conclusions: The proposed method is one-step, colorimetric, specific and sensitive enough to detect crudely treated samples, showing great potential in the pharmacogenomic study and POCT use.
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17
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Ren Y, Li Y, Duan X, Wang H, Wang H, Li Z. One-Step Quantitative Single Nucleotide Polymorphism (SNP) Diagnosis By Modified Loop-Mediated Isothermal Amplification (mLAMP). ChemistrySelect 2019. [DOI: 10.1002/slct.201802693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yiqian Ren
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Yanru Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Honghong Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Hui Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
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18
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Malpartida-Cardenas K, Rodriguez-Manzano J, Yu LS, Delves MJ, Nguon C, Chotivanich K, Baum J, Georgiou P. Allele-Specific Isothermal Amplification Method Using Unmodified Self-Stabilizing Competitive Primers. Anal Chem 2018; 90:11972-11980. [PMID: 30226760 PMCID: PMC6195307 DOI: 10.1021/acs.analchem.8b02416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022]
Abstract
Rapid and specific detection of single nucleotide polymorphisms (SNPs) related to drug resistance in infectious diseases is crucial for accurate prognostics, therapeutics and disease management at point-of-care. Here, we present a novel amplification method and provide universal guidelines for the detection of SNPs at isothermal conditions. This method, called USS-sbLAMP, consists of SNP-based loop-mediated isothermal amplification (sbLAMP) primers and unmodified self-stabilizing (USS) competitive primers that robustly delay or prevent unspecific amplification. Both sets of primers are incorporated into the same reaction mixture, but always targeting different alleles; one set specific to the wild type allele and the other to the mutant allele. The mechanism of action relies on thermodynamically favored hybridization of totally complementary primers, enabling allele-specific amplification. We successfully validate our method by detecting SNPs, C580Y and Y493H, in the Plasmodium falciparum kelch 13 gene that are responsible for resistance to artemisinin-based combination therapies currently used globally in the treatment of malaria. USS-sbLAMP primers can efficiently discriminate between SNPs with high sensitivity (limit of detection of 5 × 101 copies per reaction), efficiency, specificity and rapidness (<35 min) with the capability of quantitative measurements for point-of-care diagnosis, treatment guidance, and epidemiological reporting of drug-resistance.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jesus Rodriguez-Manzano
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Ling-Shan Yu
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Michael J. Delves
- Department
of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Chea Nguon
- National
Centre for Parasitology, Entomology and
Malaria Control, Phnom Penh 12302, Cambodia
| | - Kesinee Chotivanich
- Department
of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Jake Baum
- Department
of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Pantelis Georgiou
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
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19
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Best N, Rodoni B, Rawlin G, Beddoe T. The development and deployment of a field-based loop mediated isothermal amplification assay for virulent Dichelobacter nodosus detection on Australian sheep. PLoS One 2018; 13:e0204310. [PMID: 30260992 PMCID: PMC6160043 DOI: 10.1371/journal.pone.0204310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/05/2018] [Indexed: 11/19/2022] Open
Abstract
Dichelobacter nododus is the causative agent of footrot, a major disease of sheep that creates welfare concerns and large economic loss. The virulence of D. nododus depends on the presence of extracellular proteases, AprV2 and AprB2, which differ by one amino acid. Strains possessing AprV2 can cause clinically virulent disease, while AprB2 may cause clinically benign disease. Current methods for detecting D. nodosus are difficult, laborious and time consuming. New techniques capable of rapidly detecting and typing D. nodosus are needed to aid control programs. Molecular methods, like real-time polymerase chain reaction (rtPCR) can detect aprV2 and aprB2, however, this assay is not field-deployable and cannot support local decision-making during an outbreak. Here we present a field-based molecular assay for detecting aprV2, using loop mediated isothermal amplification (LAMP). The aprV2 LAMP (VDN LAMP) assay was optimised to reliably detect aprV2 from laboratory purified genomic (gDNA) of virulent D. nodosus down to 5x10(-3) ng μL-1, with time to positive (Tp) ≤ 16 minutes, while aprB2 was unreliably detected at 5 ng μL-1 from 16-20 minutes. The use of field collected samples that were rtPCR positive for aprB2 resulted in no amplification, while aprV2 positive field samples by VDN LAMP assay are defined as having Tps' of < 20 minutes and melting temperature between 88.0-88.9°C. When compared to rtPCR, the VDN LAMP was shown to have a diagnostic specificity of 100% and sensitivity of 83.33%. As proof of concept, the VDN LAMP was taken on farm, with all processing occurring in-field. The on farm VDN LAMP successfully detected 91.67% aprV2 positive samples, no aprB2 positive samples (n = 9) or D. nodosus negative (n = 23) samples, with a kappa agreement of 'almost perfect' to rtPCR. This highlights the potential of the assay to inform local treatment decisions for management.
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Affiliation(s)
- Nickala Best
- Department of Animal, Plant and Soil Science and Centre for AgriBioscience (AgriBio), La Trobe University, Bundoora, Melbourne, Victoria, Australia
| | - Brendan Rodoni
- Department of Economic Development, Jobs, Transport and Resources Centre for AgriBioscience (AgriBio), Victorian Government, Bundoora, Melbourne, Victoria, Australia
| | - Grant Rawlin
- Department of Economic Development, Jobs, Transport and Resources Centre for AgriBioscience (AgriBio), Victorian Government, Bundoora, Melbourne, Victoria, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science and Centre for AgriBioscience (AgriBio), La Trobe University, Bundoora, Melbourne, Victoria, Australia
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20
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Carlos FF, Veigas B, Matias AS, Doria G, Flores O, Baptista PV. Allele specific LAMP- gold nanoparticle for characterization of single nucleotide polymorphisms. ACTA ACUST UNITED AC 2017; 16:21-25. [PMID: 29124021 PMCID: PMC5671399 DOI: 10.1016/j.btre.2017.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/27/2022]
Abstract
Allele-specific isothermal amplification method (AS-LAMP) for SNP characterization. Use of ssDNA-functionalized gold nanoparticles (AuNPs) for SNP full discrimination. A simple and low-cost strategy to provide fast results in medium throughput settings. AS-LAMP amplification products can be easily interpreted in less than 15 min.
Due to their relevance as disease biomarkers and for diagnostics, screening of single nucleotide polymorphism (SNPs) requires simple and straightforward strategies capable to provide results in medium throughput settings. Suitable approaches relying on isothermal amplification techniques have been evolving to substitute the cumbersome and highly specialized PCR amplification detection schemes. Nonetheless, identification of an individual’s genotype still requires sophisticated equipment and laborious methods. Here, we present a low-cost and reliable approach based on the allele specific loop-mediated isothermal amplification (AS-LAMP) coupled to ssDNA functionalized gold nanoparticle (Au-nanoprobe) colorimetric sequence discrimination. The Au-nanoprobe integration allows for the colorimetric detection of AS-LAMP amplification product that can be easily interpreted in less than 15 min. We targeted a clinical relevant SNP responsible for lactose intolerance (-13910C/T dbSNP rs#: 4988235) to demonstrate its proof of concept and full potential of this novel approach.
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Affiliation(s)
- Fábio Ferreira Carlos
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- i3N/CENIMAT, Departamento de Ciências de Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Ana S. Matias
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Gonçalo Doria
- STABVIDA, Investigação e Serviços em Ciências Biológicas, Lda. Madan Parque, 2825-182 Caparica, Portugal
| | - Orfeu Flores
- STABVIDA, Investigação e Serviços em Ciências Biológicas, Lda. Madan Parque, 2825-182 Caparica, Portugal
| | - Pedro V. Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- Corresponding author.
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Imai K, Tarumoto N, Misawa K, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Murakami T, Maesaki S, Suzuki Y, Yamagishi J, Maeda T. A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer. BMC Infect Dis 2017; 17:621. [PMID: 28903726 PMCID: PMC5598014 DOI: 10.1186/s12879-017-2718-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A simple and accurate molecular diagnostic method for malaria is urgently needed due to the limitations of conventional microscopic examination. In this study, we demonstrate a new diagnostic procedure for human malaria using loop mediated isothermal amplification (LAMP) and the MinION™ nanopore sequencer. METHODS We generated specific LAMP primers targeting the 18S-rRNA gene of all five human Plasmodium species including two P. ovale subspecies (P. falciparum, P. vivax, P. ovale wallikeri, P. ovale curtisi, P. knowlesi and P. malariae) and examined human blood samples collected from 63 malaria patients in Indonesia. Additionally, we performed amplicon sequencing of our LAMP products using MinION™ nanopore sequencer to identify each Plasmodium species. RESULTS Our LAMP method allowed amplification of all targeted 18S-rRNA genes of the reference plasmids with detection limits of 10-100 copies per reaction. Among the 63 clinical samples, 54 and 55 samples were positive by nested PCR and our LAMP method, respectively. Identification of the Plasmodium species by LAMP amplicon sequencing analysis using the MinION™ was consistent with the reference plasmid sequences and the results of nested PCR. CONCLUSIONS Our diagnostic method combined with LAMP and MinION™ could become a simple and accurate tool for the identification of human Plasmodium species, even in resource-limited situations.
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Affiliation(s)
- Kazuo Imai
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Kazuhisa Misawa
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 359-8513, Japan
| | - Lucky Ronald Runtuwene
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Kyoko Hayashida
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Yuki Eshita
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Faculty of Medicine, Oita University, 1-1 Hasama-machi, Yufu, Oita, 879-5593, Japan.,Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Thung Phaya, Ratchathewi, Bangkok, 10400, Thailand.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryuichiro Maeda
- Division of Biomedical Sciences, Department of Basic Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Josef Tuda
- Department of Parasitology, Faculty of Medicine, Sam Ratulangi University, Kampus Unsrat, Manado, Bahu, 95115, Indonesia
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Junya Yamagishi
- Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan. .,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.
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22
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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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23
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Tamura S, Maeda T, Misawa K, Osa M, Hamamoto T, Yuki A, Imai K, Mikita K, Morichika K, Kawana A, Matsumoto H, Nonoyama S. Development of a highly resolved loop-mediated isothermal amplification method to detect the N526K ftsI mutation of β-lactamase-negative ampicillin-resistant Haemophilus influenzae. J Microbiol Methods 2017; 141:108-114. [PMID: 28807759 DOI: 10.1016/j.mimet.2017.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/24/2023]
Abstract
Rapid and easy detection of sequence polymorphisms, including nucleotide point mutations of bacterial pathogens responsible for amino acid substitutions linked to drug resistance, is essential for the proper use of antimicrobial agents. Here, a detection method using loop-mediated amplification (LAMP) combined with amplification refractory mutation system (ARMS) to accurately distinguish a different single nucleotide in the target sequence was established, named ARMS-SNP LAMP. This procedure is capable of species-specific detection of a nucleotide (1578T) in the ftsI gene on Haemophilus influenzae without amplifying the sequence carrying the point mutations (T1578G/A) in β-lactamase-negative ampicillin resistant (BLNAR) strains. Reactions were performed at 61°C for 45min. Successful target gene amplifications were detected by measuring real-time turbidity using a turbidimeter and visual detection. The assay had a detection limit of 10.0pg of genomic DNA per reaction and showed specificity against 52 types of pathogens, whereas amplifications were completely blocked in even 100.0ng/μL of genomic DNA with point mutations at T1578G and T1578A. The expected ARMS-SNP LAMP products were confirmed through identical melting curves in real-time LAMP procedures. This novel procedure was also used to analyze 57 clinical isolates of H. influenzae. All 25 clinical isolates with the naïve sequence of 1578T gave positive results. In addition, concordant negative results were obtained for 31 of the BLNAR strains with the T1578G mutation and one strain with the T1578A mutation. The ARMS-SNP LAMP method is a simple and rapid method for SNP-genotyping of a clinical isolate as point-of-care testing (POCT) technology. It is suitable for use in both resource-limited situations and well-equipped clinical settings because of its simplicity and convenience.
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Affiliation(s)
- Shinsuke Tamura
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Takuya Maeda
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan; Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan; Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan.
| | - Kazuhisa Misawa
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Morichika Osa
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Takaaki Hamamoto
- Department of Laboratory Medicine, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Atsushi Yuki
- Department of Laboratory Medicine, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuo Imai
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kei Mikita
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kyoko Morichika
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Akihiko Kawana
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
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24
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Ayukawa Y, Hanyuda S, Fujita N, Komatsu K, Arie T. Novel loop-mediated isothermal amplification (LAMP) assay with a universal QProbe can detect SNPs determining races in plant pathogenic fungi. Sci Rep 2017; 7:4253. [PMID: 28652587 PMCID: PMC5484703 DOI: 10.1038/s41598-017-04084-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is grouped into three races based on their pathogenicity to different host cultivars. Rapid detection and discrimination of Fol races in field soils is important to prevent tomato wilt disease. Although five types of point mutations in secreted in xylem 3 (SIX3) gene, which are characteristic of race 3, have been reported as a molecular marker for the race, detection of these point mutations is laborious. The aim of this study is to develop a rapid and accurate method for the detection of point mutations in SIX3 of Fol. Loop-mediated isothermal amplification (LAMP) of SIX3 gene with the universal QProbe as well as two joint DNAs followed by annealing curve analysis allowed us to specifically detect Fol and discriminate race 3 among other races in about one hour. Our developed method is applicable for detection of races of other plant pathogenic fungi as well as their pesticide-resistant mutants that arise through point mutations in a particular gene.
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Affiliation(s)
- Yu Ayukawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Saeri Hanyuda
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Naoko Fujita
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Ken Komatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
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25
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Stiedl CP, Weber K. Fast and simple detection methods for the 4-base pair deletion of canine MDR1/ ABCB1 gene by PCR and isothermal amplification. J Vet Diagn Invest 2017; 29:176-180. [PMID: 28061549 DOI: 10.1177/1040638716683213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Dogs with a 4-bp deletion in the MDR1 (or ABCB1) gene show intolerance to certain drugs routinely used in veterinary medicine, such as ivermectin, vincristine, and doxorubicin. The mutation leads to a dysfunctional P-glycoprotein drug transporter, which results in drug accumulation in the brain and severe neurotoxicity. A rapid and accurate in-house test to determine the genotype of patients in cases of acute neurotoxic signs or in tumor patients is desirable. We describe a cost-effective detection method with simple technical equipment for veterinary practice. Two allele-specific methods are presented, which allow discrimination of all genotypes, require little hands-on time, and show the results within ~1 h after DNA sampling. DNA from buccal swabs of 115 dogs with known genotype (no mutation, n = 54; heterozygous for the mutation, n = 37; homozygous for the mutation, n = 24) was extracted either by using a column-based extraction kit or by heating swabs in a simple NaOH-Tris buffer. Amplification was performed either by allele-specific fast polymerase chain reaction or by allele-specific loop-mediated isothermal amplification (LAMP). Analysis was done either on agarose gels, by simple endpoint visualization using ultraviolet light, or by measuring the increase of fluorescence and time to threshold crossing. Commercial master mixes reduced the preparation time and minimized sources of error in both methods. Both methods allowed the discrimination of all 3 genotypes, and the results of the new methods matched the results of the previous genotyping. The presented methods could be used for fast individual MDR1/ ABCB1 genotyping with less equipment than existing methods.
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Affiliation(s)
- Cathrin P Stiedl
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Karin Weber
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, Ludwig-Maximilians-Universität, Munich, Germany
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26
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Simple detection of single nucleotide polymorphism in Plasmodium falciparum by SNP-LAMP assay combined with lateral flow dipstick. Parasitol Int 2016; 66:964-971. [PMID: 27816495 DOI: 10.1016/j.parint.2016.10.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 11/20/2022]
Abstract
The significant strides made in reducing global malaria burden over the past decades are being threatened by the emergence of multi-drug resistant malaria. Mechanisms of resistance to several classes of antimalarial drugs have been linked to key mutations in the Plasmodium falciparum genes. Pyrimethamine targets the dihydrofolate reductase of the bifunctional dihydrofolate reductase thymidylate synthase (DHFR-TS), and specific point mutations in the dhfr-ts gene have been assigned to resistant phenotypes. Several molecular methods are available to detect the mutant genotypes including DNA sequencing and PCR-based methods. In this study, we report the development of PfSNP-LAMP to detect nucleotide polymorphism in the dhfr gene associated with N51I mutation and antifolate resistance. The PfSNP-LAMP method was validated with genomic DNA samples and parasite lysates prepared from sensitive and pyrimethamine resistant strains of P. falciparum.
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27
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Itonaga M, Matsuzaki I, Warigaya K, Tamura T, Shimizu Y, Fujimoto M, Kojima F, Ichinose M, Murata SI. Novel Methodology for Rapid Detection of KRAS Mutation Using PNA-LNA Mediated Loop-Mediated Isothermal Amplification. PLoS One 2016; 11:e0151654. [PMID: 26999437 PMCID: PMC4801409 DOI: 10.1371/journal.pone.0151654] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
Detecting point mutation of human cancer cells quickly and accurately is gaining in importance for pathological diagnosis and choice of therapeutic approach. In the present study, we present novel methodology, peptide nucleic acid—locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA mediated LAMP), for rapid detection of KRAS mutation using advantages of both artificial DNA and LAMP. PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. PNA-LNA mediated LAMP was applied for cDNA from 4 kinds of pancreatic carcinoma cell lines with or without KRAS point mutation. The amplified DNA products were verified by naked-eye as well as a real-time PCR equipment. By PNA-LNA mediated LAMP, amplification of wild type KRAS DNA was blocked by clamping PNA probe, whereas, mutant type KRAS DNA was significantly amplified within 50 min. Mutant alleles could be detected in samples which diluted until 0.1% of mutant-to-wild type ratio. On the other hand, mutant alleles could be reproducibly with a mutant-to-wild type ratio of 30% by direct sequencing and of 1% by PNA-clamping PCR. The limit of detection (LOD) of PNA-LNA mediated LAMP was much lower than the other conventional methods. Competition of LNA clamping primers complementary to two different subtypes (G12D and G12V) of mutant KRAS gene indicated different amplification time depend on subtypes of mutant cDNA. PNA-LNA mediated LAMP is a simple, rapid, specific and sensitive methodology for the detection of KRAS mutation.
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Affiliation(s)
- Masahiro Itonaga
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Ibu Matsuzaki
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Kenji Warigaya
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Takaaki Tamura
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Yuki Shimizu
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masakazu Fujimoto
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Fumiyoshi Kojima
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
| | - Masao Ichinose
- Second Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Shin-ichi Murata
- Department of Human Pathology, Wakayama Medical University, Wakayama, Japan
- * E-mail:
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28
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The detection of Atlantic cod (Gadus morhua) using loop mediated isothermal amplification in conjunction with a simplified DNA extraction process. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.05.038] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Development of Au-Nanoprobes Combined with Loop-Mediated Isothermal Amplification for Detection of Isoniazid Resistance in Mycobacterium tuberculosis. J CHEM-NY 2016. [DOI: 10.1155/2016/3474396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multidrug resistant tuberculosis (MDR-TB) is Mycobacterium tuberculosis that does not respond to isoniazid and rifampicin, so the condition worsens continuously and creates difficulties for treatment by public health control programmes, especially in developing countries. The real time polymerase chain reaction (PCR) combined with agarose gel electrophoresis or strip tests is useful molecular tools for diagnosis of MDR-TB. Novel loop-mediated isothermal amplification (LAMP) can also detect drug resistance, which is a one-point mutation, by designing inner primers of 5′ end specific with the mutant. Au-nanoprobes on hybridisation with LAMP products containing target-specific sequences remain red, whereas test samples without specific sequences in the probe turn purple due to salt-induced aggregation of the Au-nanoprobes. In this study, a strategy was designed based on the LAMP of a DNA sample coupled to specific Au-nanoprobes, which showed the potential to provide a rapid and sensitive method for detecting isoniazid resistance at katG gene position 315 (G→C). 46 clinical samples were tested and showed 100% specificity and sensitivity compared with Genotype® MDR-TB Plus. This method was advantageous because it is rapid, cheap, specific, and sensitive. Further, it does not require thermal cycles for MDR-TB detection.
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30
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Liu Y, Zhao Y, Qin Y, Du X, Wang Q, Lyu J. A novel microfluidic device that integrates nucleic acid extraction, amplification, and detection to identify an EGFR mutation in lung cancer tissues. RSC Adv 2016. [DOI: 10.1039/c5ra26225a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel microfluidic to detect a EGFR mutation in 40 min in an easy way for personalized medicine.
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Affiliation(s)
- Yuanbin Liu
- Key Laboratory of Laboratory Medicine
- Ministry of Education
- Zhejiang Provincial Key Laboratory of Medical Genetics
- Wenzhou Medical University
- Wenzhou
| | - Yang Zhao
- Department of Respiratory Medicine
- The Second Hospital
- Dalian Medical University
- Dalian 116023
- China
| | - Yongxin Qin
- Emergency Department
- The First Hospital
- Dalian Medical University
- Dalian 116011
- China
| | - Xiaohui Du
- Scientific Research Center
- The Second Hospital
- Dalian Medical University
- Dalian 116023
- China
| | - Qi Wang
- Department of Respiratory Medicine
- The Second Hospital
- Dalian Medical University
- Dalian 116023
- China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine
- Ministry of Education
- Zhejiang Provincial Key Laboratory of Medical Genetics
- Wenzhou Medical University
- Wenzhou
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31
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Badolo A, Bando H, Traoré A, Ko-Ketsu M, Guelbeogo WM, Kanuka H, Ranson H, Sagnon N, Fukumoto S. Detection of G119S ace-1 (R) mutation in field-collected Anopheles gambiae mosquitoes using allele-specific loop-mediated isothermal amplification (AS-LAMP) method. Malar J 2015; 14:477. [PMID: 26620269 PMCID: PMC4665897 DOI: 10.1186/s12936-015-0968-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/27/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Malaria vectors have developed resistance to the four families of insecticides available for public health purposes. For example, the kdr mutation is associated with organochlorines and pyrethroids resistance. It is of particular concern that organophosphate and carbamate resistance associated with the G119S ace-1 (R) mutation has recently increased in West Africa in extent and frequency, and is now spreading through the Anopheles gambiae malaria vector population. There is an urgent need to improve resistance management using existing insecticides and new tools to quickly assess resistance level for rapid decision-making. METHODS DNA extracted from field-collected mosquitoes was used to develop the method. Specific primers were designed manually to match the mutation region and an additional mismatched nucleotide in the penultimate position to increase specificity. Other primers used are common to both wild and mutant types. The allele specific (AS)-LAMP method was compared to the PCR restriction fragment length polymorphism (PCR-RFLP) and real-time PCR (RT-PCR) methods using the genomic DNA of 104 field-collected mosquitoes. RESULTS The primers designed for LAMP were able to distinguish between the wild type (ace-1 (S) ) and mutated type allele (ace-1 (R) ). Detection time was 50 min for the wild type homozygous and 64 min for the heterozygous. No amplification of the resistant allele took place within the 75-min test period when using the wild type primers. For the ace-1 (R) resistant type, detection time was 51 min for the resistant homozygous and 55 min for the heterozygous. No amplification of the wild type allele took place within the 75-min test period when using the resistant type primers. Gel electrophoresis of LAMP products confirmed that amplification was primer-DNA specific, i.e., primers could only amplify their target specific DNA. AS-LAMP, PCR-RFLP, and RT-PCR showed no significant difference in the sensitivity and specificity of their ace-1 (R) detection ability. CONCLUSIONS The AS-LAMP method could detect the ace-1 (R) mutation within 60 min, which is faster than conventional PCR-RFLP. This method may be used to quickly detect the ace-1 (R) mutation for rapid decision-making, even in less well-equipped laboratories.
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Affiliation(s)
- Athanase Badolo
- National Research Centre for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan. .,Centre National de Recherche et de Formation sur le Paludisme (CNRFP), BP 2208, Ouagadougou 01, Burkina Faso. .,Laboratoire d'Entomologie Fondamentale et Appliquée, Université de Ouagadougou, BP 7021, Ouagadougou 03, Burkina Faso.
| | - Hironori Bando
- National Research Centre for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan.
| | - Alphonse Traoré
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), BP 2208, Ouagadougou 01, Burkina Faso.
| | - Mami Ko-Ketsu
- National Research Centre for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan.
| | - Wamdaogo Moussa Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), BP 2208, Ouagadougou 01, Burkina Faso.
| | - Hirotaka Kanuka
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, 105-8461, Japan.
| | - Hilary Ranson
- Vector Group, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - N'Falé Sagnon
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), BP 2208, Ouagadougou 01, Burkina Faso.
| | - Shinya Fukumoto
- National Research Centre for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan.
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Silva APB, Santos JMM, Martins AJ. Mutations in the voltage-gated sodium channel gene of anophelines and their association with resistance to pyrethroids - a review. Parasit Vectors 2014; 7:450. [PMID: 25292318 PMCID: PMC4283120 DOI: 10.1186/1756-3305-7-450] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/01/2014] [Indexed: 12/14/2022] Open
Abstract
Constant and extensive use of chemical insecticides has created a selection pressure and favored resistance development in many insect species worldwide. One of the most important pyrethroid resistance mechanisms is classified as target site insensitivity, due to conformational changes in the target site that impair a proper binding of the insecticide molecule. The voltage-gated sodium channel (NaV) is the target of pyrethroids and DDT insecticides, used to control insects of medical, agricultural and veterinary importance, such as anophelines. It has been reported that the presence of a few non-silent point mutations in the NaV gene are associated with pyrethroid resistance, termed as 'kdr' (knockdown resistance) for preventing the knockdown effect of these insecticides. The presence of these mutations, as well as their effects, has been thoroughly studied in Anopheles mosquitoes. So far, kdr mutations have already been detected in at least 13 species (Anopheles gambiae, Anopheles arabiensis, Anopheles sinensis, Anopheles stephensi, Anopheles subpictus, Anopheles sacharovi, Anopheles culicifacies, Anopheles sundaicus, Anopheles aconitus, Anopheles vagus, Anopheles paraliae, Anopheles peditaeniatus and Anopheles albimanus) from populations of African, Asian and, more recently, American continents. Seven mutational variants (L1014F, L1014S, L1014C, L1014W, N1013S, N1575Y and V1010L) were described, with the highest prevalence of L1014F, which occurs at the 1014 site in NaV IIS6 domain. The increase of frequency and distribution of kdr mutations clearly shows the importance of this mechanism in the process of pyrethroid resistance. In this sense, several species-specific and highly sensitive methods have been designed in order to genotype individual mosquitoes for kdr in large scale, which may serve as important tolls for monitoring the dynamics of pyrethroid resistance in natural populations. We also briefly discuss investigations concerning the course of Plasmodium infection in kdr individuals. Considering the limitation of insecticides available for employment in public health campaigns and the absence of a vaccine able to brake the life cycle of the malaria parasites, the use of pyrethroids is likely to remain as the main strategy against mosquitoes by either indoor residual spraying (IR) and insecticide treated nets (ITN). Therefore, monitoring insecticide resistance programs is a crucial need in malaria endemic countries.
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Affiliation(s)
- Ana Paula B Silva
- />Laboratório de Malária e Dengue, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Petrópolis, CEP 69067-375 Manaus, Amazonas Brazil
| | - Joselita Maria M Santos
- />Laboratório de Malária e Dengue, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Petrópolis, CEP 69067-375 Manaus, Amazonas Brazil
| | - Ademir J Martins
- />Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- />Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, Brazil
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Bai L, Zhu GD, Zhou HY, Tang JX, Li JL, Xu S, Zhang MH, Yao LN, Huang GQ, Wang YB, Zhang HW, Wang SB, Cao J, Gao Q. Development and application of an AllGlo probe-based qPCR assay for detecting knockdown resistance (kdr) mutations in Anopheles sinensis. Malar J 2014; 13:379. [PMID: 25245258 PMCID: PMC4182860 DOI: 10.1186/1475-2875-13-379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/20/2014] [Indexed: 01/12/2023] Open
Abstract
Background Anopheles sinensis is one of the most important malaria vectors in China and other Southeast Asian countries. High levels of resistance have been reported in this species due to the long-term use of insecticides, especially pyrethroids, for public health and agricultural purposes. Knockdown resistance (kdr) caused by a single base pair mutation in the gene encoding the sodium channel is strongly associated with pyrethroid insecticide resistance in many Anopheles mosquitoes. There are few methods currently available for detecting kdr mutations in An. sinensis. Methods A novel AllGlo probe-based qPCR (AllGlo-qPCR) method was developed to screen for the predominant kdr mutations in An. sinensis mosquitoes from the Jiangsu Province. The results from AllGlo-qPCR, allele-specific PCR (AS-PCR), and TaqMan-MGB probe-based qPCR (TaqMan-qPCR) were compared. A comparative analysis of the equipment required, ease of use and cost of the available methods was also performed. Finally, the AllGlo-qPCR method was used to detect the frequencies of kdr mutations from the other four provinces in central China. Results Six kdr genotypes were detected in An. sinensis from the Jiangsu Province by DNA sequencing. The AllGlo-qPCR method detected all of the kdr genotypes with a high level of accuracy (97% sensitivity and 98% specificity). AllGlo-qPCR correctly determined the kdr genotypes of 98.73% of 158 An. sinensis samples, whereas TaqMan-qPCR and AS-PCR correctly identified 96.84% and 88.61% of mutations, respectively. Furthermore, the AllGlo-qPCR method is simpler to perform, requires less equipment, and exhibits a moderate expense cost comparing with the other tested methods of kdr mutation detection. Samples collected from four of the other provinces in central China showed a high frequency of kdr mutation in An. sinensis, as detected by the established AllGlo-qPCR method. Conclusion The novel AllGlo-qPCR method developed for kdr mutation detection in An. sinensis exhibits greater specificity and sensitivity than currently available methods and is more cost-effective; therefore, it represents a useful tool for entomological surveillance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jun Cao
- Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), and Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, People's Republic of China.
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Aonuma H, Badolo A, Okado K, Kanuka H. Detection of mutation by allele-specific loop-mediated isothermal amplification (AS-LAMP). Methods Mol Biol 2014; 1039:121-7. [PMID: 24026691 DOI: 10.1007/978-1-62703-535-4_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For effective control of pathogen-transmitting mosquitoes, precise surveillance data of mosquito distribution are essential. Recently, an increase of insecticide resistance due to the kdr mutation in Anopheles gambiae, a mosquito that transmits the malaria parasite, has been reported. With the aim of developing a simple and effective method for surveying resistant mosquitoes, LAMP was applied to the allele-specific detection of the kdr gene in An. gambiae. Allele-specific LAMP (AS-LAMP) method successfully distinguished the kdr homozygote from the heterozygote and the wild type. The robustness of AS-LAMP suggests its usefulness for routine identification of insects, not only mosquitoes but also other vectors and agricultural pests. Here we describe the method of AS-LAMP to detect mutation in Anopheles mosquitoes.
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Affiliation(s)
- Hiroka Aonuma
- Department of Tropical Medicine, The Jikei University School of Medicine, Tokyo, Japan
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