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Shoorashetty MR, Pooja P, Shakuntala PN, Madhu K. A novel fluoro colorimetric Loop mediated isothermal amplification (LAMP) assay for detection of Trichomonas vaginalis. Indian J Med Microbiol 2024:100610. [PMID: 38735643 DOI: 10.1016/j.ijmmb.2024.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND & objective: Trichomoniasis is a curable, non-viral, sexually transmitted infection. Early diagnosis and treatment of cases can prevent complications and further spread of infection. Rapid diagnostics tests, which can be performed on-site, will help in early diagnosis. The study aims to develop a rapid diagnostic test based on the principle of fluoro-colorimetric LAMP for detecting Trichomonas vaginalis (TV). MATERIALS AND METHODS T. vaginalis was grown in a modified CPLM medium, and DNA was extracted. Three pairs of LAMP primers targeting the actin gene were designed using the primerexplorer V.5 online tool. The LAMP assay was standardized for temperature and time. To determine the LAMP assay's detection limit, diluted TV DNA and spiked urine samples were used. Conventional PCR was done using previously published primers and compared with LAMP results. The sensitivity and specificity to detect TV from clinical specimens were assessed. RESULTS The optimum performance of the LAMP assay was determined to be 63°C for 60 minutes and terminated at 80°C for 5 minutes. The LAMP assay could detect 60 fg/μl of diluted TV DNA and up to 1 parasite/ml of spiked samples. The assay was 1000 times more sensitive than PCR. The LAMP assay was 100% sensitive and specific with crude extract, and reactions were visually discernible. INTERPRETATION & CONCLUSIONS The LAMP assay developed in the study is easy to perform and interpret, affordable, rapid, and highly sensitive to detect T. vaginalis. It is ideally suited for the point-of-care test, as it fulfills WHO's recommended ASSURED characteristics.
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Affiliation(s)
| | - Pareyam Pooja
- Department of Microbiology, ESIC MC PGIMSR & MH, Rajajinagar, Bengaluru -560010, Karnataka, India.
| | | | - Kanta Madhu
- Biotechnology Scholar, C-709, KG Signature City, Adayalampattu, Chennai-600095.
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Kaur M, Ayarnah K, Duanis-Assaf D, Alkan N, Eltzov E. Rapid and simple colorimetric detection of quiescent Colletotrichum in harvested fruit using reverse transcriptional loop-mediated isothermal amplification (RT-LAMP) technology. Talanta 2023; 255:124251. [PMID: 36630787 DOI: 10.1016/j.talanta.2023.124251] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/27/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023]
Abstract
Anthracnose, caused by the fungus Colletotrichum gloeosporioides, is one of the major causes of postharvest decay of fruits and vegetables. Detection of the pathogen at an early stage of infection is crucial to developing a disease management strategy. In this work, a loop-mediated isothermal amplification (LAMP) assay was developed for the rapid detection of C. gloeosporioides targeting the transcript enoyl-CoA hydratase (ECH) that significantly upregulates only during C. gloeosporioides quiescent stage. The assay enabled a naked-eye detection of C. gloeosporioides RNA within 23 min based on a color change of LAMP products from pink to yellow. The detection limit of the LAMP assay was 1 pg of total RNA extracted from fruit peel in a 25 μL reaction. Positive results were obtained only in samples carrying the ECH gene, whereas no cross-reaction was observed for a different quiescent marker (histone deacetylase (HDAC)) or an appressorium marker (scytalone dehydratase, (SD)), indicating the high specificity of the method. Hence, the results indicate that the developed LAMP assay is a rapid, highly sensitive, and specific tool for the early detection of quiescent C. gloeosporioides and could be employed to manage postharvest diseases.
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Ren WC, Wang SJ, Wang ZQ, Zhu MQ, Zhang YH, Lian S, Li BH, Dong XL, Liu N. Detection of Cytb Point Mutation (G143A) that Confers High-Level Resistance to Pyraclostrobin in Glomerella cingulata Using LAMP Method. Plant Dis 2023; 107:1166-1171. [PMID: 36205690 DOI: 10.1094/pdis-08-22-1992-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glomerella leaf spot (GLS) caused by Glomerella cingulata is a newly emerging disease that results in severe defoliation and fruit spots in apples. In China, the compound of pyraclostrobin and tebuconazole was registered to control GLS in 2018 and has achieved excellent control efficiency. In this study, we showed that the high-level resistant isolates of G. cingulata to pyraclostrobin, caused by the point mutation at codon 143 (GGT→GCT, G143A) in the cytochrome b gene, has appeared in apple orchards in Shandong Province in 2020, and the resistance frequency was 4.8%. Based on the genotype of the resistant isolates, we developed a loop-mediated isothermal amplification (LAMP) assay for detection of the pyraclostrobin resistance. The LAMP assay was demonstrated to have good specificity, sensitivity, and repeatability, and it exhibited high accuracy in detecting pyraclostrobin resistance in the field. This study reported the resistance status of GLS to pyraclostrobin in Shandong Province and developed a molecular tool for the detection of pyraclostrobin resistance, which is of practical significance for the scientific control of GLS.
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Affiliation(s)
- Wei-Chao Ren
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Si-Jia Wang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Zhong-Qiang Wang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Mei-Qi Zhu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yi-Han Zhang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Sen Lian
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Bao-Hua Li
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Xiang-Li Dong
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Na Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
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Nayak S, Do Carmo Lobo N, Anupama KP, Nayak A, Akshay SD, Maiti B. Evaluation of loop-mediated isothermal amplification assay for visual detection of Acinetobacter baumannii directly from soil and water sample from Mangalore. Lett Appl Microbiol 2023; 76:7043462. [PMID: 36796791 DOI: 10.1093/lambio/ovad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Acinetobacter baumannii is a well-known nosocomial pathogen that commonly inhabits soil and water and has been implicated in numerous hospital-acquired infections. The existing methods for detecting A. baumannii have several drawbacks, such as being time-consuming, expensive, labor-intensive, and unable to distinguish between closely related Acinetobacter species. Thus, it is important to have a simple, rapid, sensitive, and specific method for its detection. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay using hydroxynaphthol blue dye to visualize A. baumannii by targeting its pgaD gene. The LAMP assay was performed using a simple dry bath and was shown to be specific and highly sensitive, as it could detect up to 10 pg/μl of A. baumannii DNA. Further, the optimized assay was used to detect A. baumannii in soil and water samples by culture-medium enrichment. Out of 27 samples tested, 14 (51.85%) samples were positive for A. baumannii through LAMP assay, while only 5 (18.51%) samples were found to be positive through conventional methods. Thus, the LAMP assay has been found to be a simple, rapid, sensitive, and specific method that can be used as a point-of-care diagnostic tool for detecting A. baumannii.
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Affiliation(s)
- Srajana Nayak
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangalore 575018, India
| | - Nia Do Carmo Lobo
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangalore 575018, India
| | - Karanth Padyana Anupama
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangalore 575018, India
| | - Ashwath Nayak
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangalore 575018, India
| | - Sadanand Dangari Akshay
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangalore 575018, India
| | - Biswajit Maiti
- Division of Infectious Diseases, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Deralakatte, Mangalore 575018, India
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Blin M, Senghor B, Boissier J, Mulero S, Rey O, Portela J. Development of environmental loop-mediated isothermal amplification (eLAMP) diagnostic tool for Bulinus truncatus field detection. Parasit Vectors 2023; 16:78. [PMID: 36855192 PMCID: PMC9972309 DOI: 10.1186/s13071-023-05705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Global changes are reshaping the distribution of vector-borne diseases by spreading vectors to previously non-endemic areas. Since 2013, urogenital schistosomiasis has emerged in Corsica and threatens European countries. Gastropod vectors release schistosome larvae that can infect humans who come into contact with freshwater bodies. Monitoring schistosomiasis host vectors is a prerequisite to understand and subsequently to control this pathogen transmission. Because malacological surveys are time consuming and require special expertise, the use of a simple molecular method is desirable. METHODS The aim of this study is to develop a ready-to-use protocol using the LAMP (loop-mediated isothermal amplification) method to detect environmental DNA of Bulinus truncatus, vector of Schistosoma haematobium. Interestingly, LAMP method possesses all the characteristics required for adaptability to field conditions particularly in low-income countries: speed, simplicity, lyophilized reagents, low cost and robustness against DNA amplification inhibitors. We have tested this new method on Corsican water samples previously analysed by qPCR and ddPCR. RESULTS We demonstrate that our diagnostic tool B. truncatus eLAMP (Bt-eLAMP) can detect the eDNA of Bulinus truncatus as effectively as the two other methods. Bt-eLAMP can even detect 1/4 of positive samples not detectable by qPCR. Moreover, the complete Bt-eLAMP protocol (sampling, sample pre-process, amplification and revelation) does not require sophisticated equipment and can be done in 1 ½ h. CONCLUSIONS LAMP detection of environmental DNA provides large-scale sensitive surveillance of urogenital schistosomiasis possible by identifying potentially threatened areas. More generally, eLAMP method has great potential in vector-borne diseases and ecology.
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Affiliation(s)
- Manon Blin
- Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860, Perpignan, France. .,SAS ParaDev®, 66860, Perpignan, France.
| | - Bruno Senghor
- VITROME, IRD-UCAD International Campus, 1386 Dakar, Senegal
| | - Jérôme Boissier
- grid.11136.340000 0001 2192 5916Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860 Perpignan, France
| | - Stephen Mulero
- grid.11136.340000 0001 2192 5916Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860 Perpignan, France ,Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS-LECA, 38000 Grenoble, France
| | - Olivier Rey
- grid.11136.340000 0001 2192 5916Hosts Pathogens Environment Interactions, UMR 5244, CNRS, IFREMER, UM, University of Perpignan, Via Domitia, 66860 Perpignan, France
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Tittel-Elmer M, de Tejada BM, Renzi G, Schrenzel J. Performance of the HiberGene Group B Streptococcus kit, a loop-mediated isothermal amplification-based assay for GBS screening during pregnancy. Eur J Clin Microbiol Infect Dis 2023; 42:217-219. [PMID: 36449147 PMCID: PMC9836968 DOI: 10.1007/s10096-022-04534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Timely and accurate detection of Group B Streptococcus (GBS) carriage in pregnant women allows for targeted peripartum prophylaxis. Replacing culture-based screening by molecular biology assays enables faster results obtention, better targeted antibiotic prophylaxis, and reduces the laboratory workload. Here, we present a comparative analysis between a Loop Mediated Isothermal Amplification assay (HiberGene GBS kit) and culture (gold-standard). The HiberGene GBS kit showed a sensitivity of 97.9% and a specificity of 96.8% compared with culture. The limit of detection was estimated at 103 cfu/ml and results were obtained within 30 min. HiberGene GBS assay can be used for peripartum GBS screening and targeted antibiotic prophylaxis provided sample processing can be swiftly performed around the clock.
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Affiliation(s)
- Mireille Tittel-Elmer
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Begoña Martinez de Tejada
- Obstetrics Division, Departement of Pediatrics, Gynecology and Obstetrics, Geneva University Hospitals, Geneva, Switzerland ,Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland ,Faculty of Medicine, University of Geneva, Geneva, Switzerland ,Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals, Geneva, Switzerland
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Hong-min Z, Jian Y, Ying L, Yuan Y, Cui-ping W, Yu-cheng D, Jia-jia C. Rapid detection of Heterobasidion annosum using a loop-mediated isothermal amplification assay. Front Cell Infect Microbiol 2023; 13:1134921. [PMID: 37187469 PMCID: PMC10175688 DOI: 10.3389/fcimb.2023.1134921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Heterobasidion annosum is one of the most aggressive pathogens of Pinus forests in Europe, causing considerable economic losses. To detect H. annosum for disease diagnosis and control, we developed a loop-mediated isothermal amplification (LAMP) reaction with a primer set designed from the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA sequences of H. annosum. In our study, this LAMP assay was found to be capable of efficiently amplifying the target gene within 60 min at 63°C. In specificity tests, H. annosum was positively detected, and other species were negative. The detection limit of this assay was found to be 100 pg·μL-1, and the assay was also successfully tested for use with basidiospore suspensions and wood samples. This study provides a rapid method for diagnosing root and butt rot caused by H. annosum, which will be of use in port surveillance of logs imported from Europe.
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Affiliation(s)
- Zhou Hong-min
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Yu Jian
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Liu Ying
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
| | - Yuan Yuan
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wu Cui-ping
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, China
| | - Dai Yu-cheng
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- *Correspondence: Dai Yu-cheng, ; Chen Jia-jia,
| | - Chen Jia-jia
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang, China
- *Correspondence: Dai Yu-cheng, ; Chen Jia-jia,
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Cao G, Lin K, Ai J, Cai J, Zhang H, Yu Y, Liu Q, Zhang X, Zhang Y, Fu Z, Song J, Wang H, Yuan G, Wang S, Guan M, Zhang W. A diagnostic accuracy study comparing RNA LAMP, direct LAMP, and rapid antigen testing from nasopharyngeal swabs. Front Microbiol 2022; 13:1063414. [PMID: 36620063 PMCID: PMC9813509 DOI: 10.3389/fmicb.2022.1063414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction During the coronavirus disease 2019 (COVID-19) pandemic, the early detection and isolation of individuals infected with severe acute respiratory syndrome coronavirus disease 2 (SARS-CoV-2) through mass testing can effectively prevent disease transmission. SARS-CoV-2 nucleic acid rapid detection based on loop-mediated isothermal amplification (LAMP) may be appropriate to include in testing procedures. Methods We used 860 nasopharyngeal specimens from healthcare workers of Huashan Hospital and COVID-19 patients collected from April 7th to 21st, 2022, to assess the clinical diagnostic performance of the LAMP assay marketed by Shanghai GeneSc Biotech and compared it to the result of a rapid antigen test (RAT) head-to-head. Results Overall, the diagnostic performance of LAMP assay and RAT were as follows. The LAMP assay represented higher sensitivity and specificity than RAT, especially in the extracted RNA samples. The sensitivity was 70.92% and 92.91% for direct LAMP and RNA-LAMP assay, respectively, while the specificity was 99.86% and 98.33%. The LAMP assay had overall better diagnostic performance on the specimens with relatively lower C t values or collected in the early phase (≤7 days) of COVID-19. The combination of LAMP assay and RAT improved diagnostic efficiency, providing new strategies for rapidly detecting SARS-CoV-2. Conclusion The LAMP assay are suitable for mass screenings of SARS-CoV-2 infections in the general population.
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Affiliation(s)
- Guojun Cao
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianpeng Cai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiqi Yu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Qihui Liu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinyun Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jieyu Song
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Sen Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,*Correspondence: Sen Wang,
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,Ming Guan,
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China,Wenhong Zhang,
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Mu J, Li Q, Yan X, Mao X, Shi Y, Qin Y, Liu C, Wang W. Detection of Brucella S2 vaccine strain by a loop-mediated isothermal amplification (LAMP) method. Front Cell Infect Microbiol 2022; 12:1023243. [PMID: 36530431 PMCID: PMC9755167 DOI: 10.3389/fcimb.2022.1023243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Brucellosis is a highly prevalent zoonotic disease caused by Brucella spp. Brucella suis S2 vaccination is an effective strategy to prevent animal brucellosis. However, S2 induces antibodies against the smooth lipopolysaccharide,making it challenging to distinguish field infected from vaccinated livestock. Early and accurate diagnosis is essential for infection control and prevention. In this study, we aimed to develop a quick and accurate assay to distinguish the BrucellaS2 vaccine strain from closely related B. abortus and B. melitensis. Methods Whole-genome sequencing of B. suis S2 was performed, and the sequence was compared with that of the genomes of B. abortus and B. melitensis. One specific gene, GL_0002189, was selected as a marker to differentiate the BrucellaS2vaccine strain from B. abortus and B. melitensis. A loop-mediated isothermal amplification (LAMP) assay was developed, based on the GL_0002189 gene, and then assessed for target specificity, lower limit of detection, and repeatability. Results Our results revealed that there was no cross-reaction with other strains, and the LAMP assay displayed high sensitivity for detecting S2 with a minimum detection limit of 18.9×103 copies/µL DNA input, it is nearly 100 times higher than conventional PCR technology. Concordance between the LAMP assay and a conventional polymerase chain reaction method was assessed using 54 blood samples collected from sheep with suspected brucellosis. Total concordance between the two assays was 92.6%, without a significant difference (p > 0.05) in the test results. Conclusion This is the first report of a LAMP assay for the detection of the B. suis S2vaccine strain. Our approach can be helpful for the control and eradication of brucellosis, and its simplicity in requiring no specialized equipment or personnel makes it useful for implementation in resource-limited settings as well as for field use.
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Affiliation(s)
- Jiaming Mu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China
| | - Qi Li
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China
| | - Xu Yan
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China
| | - Xiaowei Mao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China
| | - Yaqin Shi
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China
| | - Yun Qin
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China
| | - Chunxia Liu
- College of Life Science, Inner Mongolia Agricultural University, Huhehot, China,*Correspondence: Wenlong Wang, ; Chunxia Liu,
| | - Wenlong Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhehot, China,*Correspondence: Wenlong Wang, ; Chunxia Liu,
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Doria G, Clemente C, Coelho E, Colaço J, Crespo R, Semikhodskii A, Mansinho H, Dinis M, Carvalho MF, Casmarrinha M, Samina C, Vidal AC, Delarue F, Graúdo S, Santos AC, Peças D, Carreira O, Marques R, Gaspar C, Flores O. An isothermal lab-on-phone test for easy molecular diagnosis of SARS-CoV-2 near patients and in less than 1 hour. Int J Infect Dis 2022; 123:1-8. [PMID: 35878801 PMCID: PMC9307284 DOI: 10.1016/j.ijid.2022.07.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 06/29/2022] [Accepted: 07/15/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES The performance of a new point-of-care CE-IVD-marked isothermal lab-on-phone COVID-19 assay was assessed in comparison to a gold standard real-time reverse transcriptase-PCR method. METHODS The study was conducted following a nonprobability sampling of ≥16-year-old volunteers from three different laboratories, using direct mouthwash (N = 24) or nasopharyngeal (N = 191) clinical samples. RESULTS The assay demonstrated 95.19% sensitivity and 100% specificity for detection of SARS-CoV-2 in direct nasopharyngeal crude samples and 78.95% sensitivity and 100% specificity in direct mouthwash crude samples. It also successfully detected currently predominant SARS-CoV-2 variants of concern (Beta B.1.351, Delta B.1.617.2, and Omicron B.1.1.529) and demonstrated to be inert against potential cross-reactions of other common respiratory pathogens that cause infections that present similar symptoms to COVID-19. CONCLUSION This lab-on-phone pocket-sized assay relies on an isothermal amplification of SARS-CoV-2's N and E genes, taking just 50 minutes from sample to result, with only 2 minutes of hands-on time. It presents good performance when using direct nasopharyngeal crude samples, enabling a low-cost, real-time, rapid, and accurate identification of SARS-CoV-2 infections at the point of care, which is important for both clinical management and population screening, as a tool to break the chain of transmission of COVID-19 pandemic, especially in low-resources environments.
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Affiliation(s)
- Gonçalo Doria
- STAB VIDA Lda, Rua dos Inventores, Caparica, Portugal,Correspondence to: Att. Gonçalo Doria, STAB VIDA Lda, Madan Parque - Rua dos Inventores, Sala 2.18, 2825-182 Caparica, Portugal
| | | | | | - João Colaço
- STAB VIDA Lda, Rua dos Inventores, Caparica, Portugal
| | - Rui Crespo
- STAB VIDA Lda, Rua dos Inventores, Caparica, Portugal
| | - Andrei Semikhodskii
- Medical Genomics Ltd, London, United Kingdom,King Saud Bin Abdulaziz's University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | | | - Magno Dinis
- Oncology Service, Garcia de Orta Hospital, Almada, Portugal
| | | | | | - Cátia Samina
- Oncology Service, Garcia de Orta Hospital, Almada, Portugal
| | - Ana Cristina Vidal
- Garcia de Orta Center, Garcia de Orta Hospital, Almada, Portugal,Escola Superior de Saúde Egas Moniz, Caparica, Portugal
| | - Francisca Delarue
- Internal Medicine Service - Garcia de Orta Center, Garcia de Orta Hospital, Almada, Portugal
| | - Susana Graúdo
- Internal Medicine Service - Garcia de Orta Center, Garcia de Orta Hospital, Almada, Portugal
| | - Ana Catarina Santos
- Internal Medicine Service - Garcia de Orta Center, Garcia de Orta Hospital, Almada, Portugal
| | - David Peças
- Internal Medicine Service - Garcia de Orta Center, Garcia de Orta Hospital, Almada, Portugal
| | - Olga Carreira
- Clinical Pathology Service, Garcia de Orta Hospital, Almada, Portugal
| | - Raquel Marques
- Clinical Pathology Service, Garcia de Orta Hospital, Almada, Portugal
| | - Carina Gaspar
- Clinical Pathology Service, Garcia de Orta Hospital, Almada, Portugal
| | - Orfeu Flores
- STAB VIDA Lda, Rua dos Inventores, Caparica, Portugal
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11
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Abstract
OBJECTIVE To evaluate the accuracy of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in community or primary-care settings. METHOD We systematically searched the Web of Science, Embase, PubMed, and Cochrane Library databases. We conducted quality evaluation using ReviewManager software (version 5.0). We then used MetaDisc software (version 1.4) and Stata software (version 12.0) to build forest plots, along with a Deeks funnel plot and a bivariate boxplot for analysis. RESULT Overall, the sensitivity, specificity, and diagnostic odds ratio were 0.79, 0.97, and 328.18, respectively. The sensitivity for the subgroup with RNA extraction appeared to be higher, at 0.88 (0.86-0.90), compared to the subgroup without RNA extraction, at 0.50 (0.45-0.55), with no significant difference in specificity. CONCLUSION RT-LAMP assay exhibited high specificity regarding current SARS-CoV-2 infection. However, its overall sensitivity was relatively moderate. Extracting RNA was found to be beneficial in improving sensitivity.
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Affiliation(s)
| | | | - Xin Luo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Wan-Jun Liu
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Shi-Ming Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Clinical Medicine, The First Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Min Lin
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Chinese and Western Medicine in Clinical Medicine, The Clinical School of Chinese and Western Medicine of Guangzhou Medical University, Guangzhou, China
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12
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Ali H, Alkhaursi K, Holton T. Development of a colorimetric RT- LAMP assay for the detection of SARS-COV-2 isolated from Oman. J Infect Dev Ctries 2022; 16:952-958. [PMID: 35797288 DOI: 10.3855/jidc.15377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/09/2022] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION A rapid and sensitive COVID-19 diagnostic test is required to aid in the prevention and control of the current COVID-19 pandemic spread. We developed a colorimetric, rapid, and sensitive RT-LAMP assay for the diagnosis of COVID-19 viral infection. METHODOLOGY Complete genome sequences of 41 SARS-CoV-2 isolates from Oman were used in this study. Three primer sets (CoV_S1, CoV_S2, CoV_M1) were developed from all Omani SARS-CoV-2 genome sequences available at the time, targeting the spike protein gene and the M gene. The primer set (CoV_S1) was found to be the most sensitive and specific among the three designed sets. The sensitivity and specificity of the assay were compared to that of qRT-PCR. Direct testing of SARS-CoV-2 spiked saliva with the developed assay was evaluated. Lyophilized colorimetric assays were stored at room temperature and 4 °C and their ability to detect positive samples were tested for a period of 8 weeks. RESULTS The RT-LAMP assay was validated by testing 145 COVID-19 clinical samples with a sensitivity of 96.9% and specificity of 94.7% when compared to the validated qRT-PCR assay. The assay specificity was tested against SARS-CoV Frankfurt 1 RNA virus and avian coronaviruses as they tested negative with the developed assay. The assay was lyophilized and managed to detect the positive samples colorimetrically when stored at 4 °C for up to 8 weeks. CONCLUSIONS The assay can be utilized in its current form as a screening assay with the advantages of being simpler, quicker, and cheaper than the qRT-PCR.
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Affiliation(s)
- Haytham Ali
- Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman.
| | - Khaddia Alkhaursi
- Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Timothy Holton
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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13
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Ng WWY, Ho YII, Wong AH, Leung ECM, Lee ALH, Chow VCY. Comparison of PneumID real-time PCR assay with Amplex eazyplex LAMP assay for laboratory diagnosis of Pneumocystis jirovecii Pneumonia. Med Mycol 2022; 60:myac043. [PMID: 35700147 DOI: 10.1093/mmy/myac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We compared PneumID PCR with Amplex eazyplex LAMP assay for the diagnosis of Pneumocystis jirovecii pneumonia (PJP). Both assays enable accurate diagnosis of definite PJP. Cut-off cycle threshold of the PneumID assay was < 26.68 while the cut-off time-to-positivity of the eazyplex assay was 16:02 (minutes:seconds). The positive and negative percentage agreement of eazyplex assay with PneumID assay was 75.0% and 100.0% respectively, while the overall agreement was substantial with kappa = 0.80. For both assays, establishment of cut-off values to differentiate probable PJP from colonization was not feasible as results overlapped.
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Affiliation(s)
- Willy W Y Ng
- Department of Microbiology, Alice Ho Miu Ling Nethersole Hospital, Hong Kong, China
| | - Yolanda I I Ho
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, China
| | - Ann H Wong
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, China
| | - Eddie C M Leung
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, China
| | - Alfred L H Lee
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, China
| | - Viola C Y Chow
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, China
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14
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Moosavian M, Keshavarzi R, Abbasi Montazeri E, Hajiani E. Loop mediated isothermal amplification of Clostridioides difficile isolates in gastrointestinal patients. AMB Express 2022; 12:42. [PMID: 35412160 PMCID: PMC9005576 DOI: 10.1186/s13568-022-01382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
This study investigated the prevalence of Clostridioides difficile by culture, multiplex polymerase chain reaction (M-PCR), and loop mediated isothermal amplification (LAMP) in patients with suspected C. difficile infections (CDIs). Also, the results of three methods were compared. All stool specimens collected from CDI suspected patients were cultured on selective C. difficile cycloserine-cefoxitin fructose agar and incubated in an anaerobic jar up to 7 days. The bacterial isolates were identified using standard tests. Multiplex-PCR (M-PCR) was performed for detection of tcdA, tcdB, and tpi genes. The LAMP assay was performed to detect the tcdB gene of C. difficile. C. difficile was isolated from 20.0% (n = 10/50) of samples by culture. M-PCR showed that 34.0% (n = 17/50) of the specimens were positive for C. difficile based on the presence of tpi gene. Out of the 17 C. difficile, 13 strains (76.0%) were positive for tcdB gene using M-PCR. However, the LAMP assay showed that 30.0% (15/50) of specimens were positive for the presence of tcdB gene. M-PCR and LAMP methods showed 100.0% sensitivity compared to the culture method. However, the specificity of the LAMP (87.5%) was relatively higher than the M-PCR (82.5%) compared to the culture. Based on the results of this study, the prevalence of toxigenic C. difficile strains was high in suspected CDI patients. So, the differentiation between toxigenic and non-toxigenic strains is necessary. Our data showed that the LAMP assay is a good method for direct detection of toxigenic C. difficile strains from stool specimens.
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15
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Krishnan N, Kumari S, Kumar R, Pandey KK, Singh J. Loop-mediated isothermal amplification assay for quicker detection of tomato leaf curl Joydebpur virus infection in chilli. J Virol Methods 2022; 302:114474. [PMID: 35077721 DOI: 10.1016/j.jviromet.2022.114474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 12/21/2021] [Accepted: 01/20/2022] [Indexed: 11/26/2022]
Abstract
Chilli leaf curl disease caused by whitefly transmitted begomoviruses is an important constraint to chilli (Capsicum anuum L.) cultivation in India. Tomato leaf curl Joydebpur virus (ToLCJoV) was characterized and identified as incitant of leaf curl disease through rolling circle amplification (RCA) and PCR assay from the symptomatic samples collected from Uttar Pradesh, India. Although PCR assay provides the gold standard in diagnostics, this method consumes more time and requires convenient portable instruments. Therefore, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of ToLCJoV by targeting the AC1 and AC2 region. Detection has been achieved through a laddered pattern of amplification in agarose gel electrophoresis. The assay has detected ToLCJoV in a total DNA concentration of 1 × 10-1 ng indicating 200-fold higher sensitivity than that of the PCR. Further, the replacement of total DNA with leaf extracts using the grinding buffer and GES buffer coupled with LAMP assay also detected the presence of ToLCJoV in the infected chilli samples. With this assay, ToLCJoV can be detected in less than 2 h without DNA extraction. Besides, this assay will be highly useful in discriminating the leaf curl disease etiology by ToLCJoV from other begomoviruses and insects (thrips and mites). To the best of our knowledge, this is the first report of a LAMP assay for the detection of ToLCJoV.
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Affiliation(s)
- Nagendran Krishnan
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India.
| | - Shweta Kumari
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | - Rajesh Kumar
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
| | | | - Jagdish Singh
- ICAR-Indian Institute of Vegetable Research, Varanasi, 221305, Uttar Pradesh, India
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16
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Belizario VY, Delos Trinos JPCR, Sison OT, Destura RV, Medina JR, Gigataras AJE, Petronio-Santos JAG, Abarientos AB. Evaluation of loop-mediated isothermal amplification assay and enzyme-linked immunosorbent assay in detecting Schistosoma japonicum in Siargao Island, Surigao del Norte, the Philippines. Acta Trop 2022; 228:106306. [PMID: 35038427 DOI: 10.1016/j.actatropica.2022.106306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/11/2021] [Accepted: 01/06/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study aimed to describe the prevalence and seroprevalence of schistosomiasis in Siargao Island, Surigao del Norte and to compare the performance of enzyme-linked immunosorbent assay antibody test (ELISA Ab) and loop-mediated isothermal amplification assay (LAMP) for diagnosis of schistosomiasis. METHODS The study was conducted in selected barangays (villages) in five municipalities in Siargao Island, Surigao del Norte and included school-age children (SAC) who submitted stool and blood samples. Stool samples were examined using the Kato-Katz technique. Blood samples were collected through venipuncture. The stool samples and the blood samples collected were tested using LAMP assay and polymerase chain reaction (PCR). The blood samples were examined using ELISA Ab. Diagnostic performance of LAMP assay using stool specimen was evaluated using Kato-Katz technique and PCR assay as the composite reference standard, while PCR assay was used as the reference standard to evaluate LAMP assay and ELISA Ab using blood specimens. RESULTS A total of 417 stool samples from SAC were examined. The prevalence of schistosomiasis and moderate-heavy intensity (MHI) schistosomiasis were 3.8% and 1.4%, respectively. Schistosomiasis and soil-transmitted helminthiases (STH) coinfection prevalence were 2.6%. A total of 425 blood samples were examined using ELISA Ab. Seroprevalence was 61.6%. The municipality of San Isidro had the highest seroprevalence at 84.8%, while Burgos had the lowest seroprevalence at 48.5%.LAMP assay had higher sensitivity and positive predictive value but lower specificity when using stool than when using blood samples. Its negative predictive value was similar regardless of the specimen used. ELISA Ab has higher sensitivity and negative predictive value than LAMP assay although it has lower specificity and positive predictive value. This may be due to ELISA Ab measuring Schistosoma exposure and is thus unable to distinguish past from active infection. CONCLUSIONS Schistosomiasis remains a public health concern in Siargao Island, Surigao del Norte. The locally developed LAMP assay offers a simpler diagnostic test for schistosomiasis compared with PCR, while minimizing the risk of misdiagnosis compared with Kato-Katz technique. It could serve as a point of care diagnostics for schistosomiasis. ELISA Ab is more useful in surveillance particularly in low-endemicity areas where determination of exposure is more important than differentiating past from active infection. ELISA Ab may be helpful in the clinical setting when coupled with the expertise of a physician who is familiar with schistosomiasis.
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Affiliation(s)
- Vicente Y Belizario
- College of Public Health, University of the Philippines (UP) Manila, Manila, Philippines; Neglected Tropical Diseases Study Group, National Institutes of Health (NIH), UP Manila, Manila, Philippines
| | - John Paul Caesar R Delos Trinos
- Neglected Tropical Diseases Study Group, National Institutes of Health (NIH), UP Manila, Manila, Philippines; Kirby Institute, University of New South Wales-Sydney, Australia
| | - Olivia T Sison
- Institute of Clinical Epidemiology, NIH, UP Manila, Manila, Philippines
| | - Raul V Destura
- Institute of Molecular Biology and Biotechnology, NIH, UP Manila, Manila, Philippines; Research and Biotechnology Division, Manila HealthTek, Marikina, Philippines
| | - John Robert Medina
- College of Public Health, University of the Philippines (UP) Manila, Manila, Philippines
| | - April Joy E Gigataras
- Neglected Tropical Diseases Study Group, National Institutes of Health (NIH), UP Manila, Manila, Philippines
| | | | - Adrian B Abarientos
- Institute of Molecular Biology and Biotechnology, NIH, UP Manila, Manila, Philippines
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Khangembam R, Tóth M, Vass N, Várady M, Czeglédi L, Farkas R, Antonopoulos A. Point of care colourimetric and lateral flow LAMP assay for the detection of Haemonchus contortus in ruminant faecal samples. Parasite 2021; 28:82. [PMID: 34907897 PMCID: PMC8672678 DOI: 10.1051/parasite/2021078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 11/23/2021] [Indexed: 11/25/2022] Open
Abstract
In this study, we present an optimised colourimetric and a lateral flow LAMP assay for the detection of Haemonchus contortus in small ruminant faecal samples. Using a previously published LAMP primer set, we made use of commercially available colourimetric LAMP and lateral flow kits and combined this into an optimised diagnostic assay which was then tested on field faecal samples from Eastern and South-Eastern Hungary as well as a pure H. contortus egg faecal sample from Košice, Slovakia. Both assays showed no conflicts in visual detection of the results. Additionally, we modified and tested several centrifuge-free DNA extraction methods and one bead-beating egg lysis DNA extraction method to develop a true point of care protocol, as the source of the starting DNA is the main rate-limiting step in farm-level molecular diagnosis. Out of the various methods trialed, promising results were obtained with the magnetic bead extraction method. Sample solutions from the Fill-FLOTAC® technique were also utilised, which demonstrated that it could be efficiently adapted for field-level egg concentration to extract DNA. This proof of concept study showed that isothermal amplification technologies with a colourimetric detection or when combined with a lateral flow assay could be an important step for a true point of care molecular diagnostic assay for H. contortus.
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Affiliation(s)
- Rojesh Khangembam
- Department of Animal Science, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi ut. 138, University of Debrecen, Debrecen 4032, Hungary - Doctoral School of Animal Science, University of Debrecen, Debrecen 4032, Hungary
| | - Mariann Tóth
- Department of Animal Science, Institute for Agricultural Research and Educational Farm, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi ut. 138, University of Debrecen, Debrecen 4032, Hungary - Doctoral School of Animal Science, University of Debrecen, Debrecen 4032, Hungary
| | - Nóra Vass
- Department of Animal Science, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi ut. 138, University of Debrecen, Debrecen 4032, Hungary
| | - Marián Várady
- Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
| | - Levente Czeglédi
- Department of Animal Science, Institute of Animal Science, Biotechnology and Nature Conservation, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi ut. 138, University of Debrecen, Debrecen 4032, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, István u. 2, Budapest 1078, Hungary
| | - Alistair Antonopoulos
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, Garscube Campus Bearsden Road, University of Glasgow, Glasgow G61 1QH, Scotland
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Wanjala BW, Ateka EM, Miano DW, Fuentes S, Perez A, Low JW, Kreuze JF. Loop-Mediated Isothermal Amplification assays for on-site detection of the main sweetpotato infecting viruses. J Virol Methods 2021; 298:114301. [PMID: 34560111 PMCID: PMC8543070 DOI: 10.1016/j.jviromet.2021.114301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022]
Abstract
Globally, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) occur frequently and in combination cause sweetpotato virus disease (SPVD). Many viral diseases are economically important and negatively impact the production and movement of germplasm across regions. Rapid detection of viruses is critical for effective control. Detection and quantification of viruses directly from sweetpotato remains a challenge. Current diagnostic tests are not sensitive enough to reliably detect viruses directly from the plant or require expensive laboratory equipment and expertise to perform. We developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay for the detection of SPFMV, SPCSV and begomoviruses related to sweet potato leaf curl virus (SPLCV). Laboratory validation recorded 100 % diagnostic sensitivity for all the three viruses. The LAMP assays were customized for field testing using a lyophilized thermostable isothermal master mix in a ready-to-use form that required no cold chain. The average time to positivity (TTP) was: SPFMV 5-30 min, SPCSV 15-43 min s and begomoviruses 28-45 mins. LAMP on-site testing results were comparable to PCR and RT-PCR confirmatory laboratory tests. The LAMP assay is a powerful tool for rapid sweetpotato virus detection at a reasonable cost and thus could serve as quality control systems for planting materials.
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Affiliation(s)
- Bramwel W Wanjala
- International Potato Center, SSA Regional Office, PO Box 25171, 00603, Nairobi, Kenya; Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya.
| | - Elijah M Ateka
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, 00200, Nairobi, Kenya.
| | - Douglas W Miano
- University of Nairobi, P.O. Box: 30197, 00100, Nairobi, Kenya.
| | - Segundo Fuentes
- International Potato Center, Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru.
| | - Ana Perez
- International Potato Center, Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru.
| | - Jan W Low
- International Potato Center, SSA Regional Office, PO Box 25171, 00603, Nairobi, Kenya.
| | - Jan F Kreuze
- International Potato Center, Avenida La Molina 1895, La Molina, Apartado Postal 1558, Lima, Peru.
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Ullah I, Daymond AJ, Hadley P, End MJ, Umaharan P, Dunwell JM. Identification of Cacao Mild Mosaic Virus (CaMMV) and Cacao Yellow Vein-Banding Virus (CYVBV) in Cocoa ( Theobroma cacao) Germplasm. Viruses 2021; 13:2152. [PMID: 34834959 DOI: 10.3390/v13112152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 11/16/2022] Open
Abstract
Cocoa, Theobroma cacao, is an important tropical perennial crop grown widely in the humid tropics. The exchange of cocoa germplasm between germplasm collections and breeding centres is vital for varietal development. Intermediate quarantine facilities, such as the International Cocoa Quarantine Centre, Reading UK (ICQC-R) play a vital role in ensuring the transfer of germplasm whilst minimising the risk of spreading pests and diseases. Current screening procedures combine visual inspection and molecular techniques, which are effective in detecting Cocoa swollen shoot virus (CSSV), a badnavirus, which causes severe losses but are restricted to West Africa. However, the detection of latent or mild virus infections that produce no visual symptoms has been a challenge. Recently two badnavirus species of cocoa producing mild symptoms, cacao mild mosaic virus (CaMMV) and cacao yellow vein-banding virus (CYVBV), have been sequenced. Here, we report new assays for the detection of these two species, for the first time in non-symptomatic accessions. Evolutionary and bioinformatic analyses of the viruses suggest their most recent source was from Trinidad, though there is historic evidence that these viruses may have their origin in South America and then become widespread globally over the last century. We also report a novel colorimetric Loop-mediated isothermal amplification (LAMP) assay for the detection of CYVBV. This simple and accurate method could be employed in field virus testing.
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Feng H, Ye W, Liu Z, Wang Y, Chen J, Wang Y, Zheng X. Development of LAMP Assays Using a Novel Target Gene for Specific Detection of Pythium terrestris, Pythium spinosum, and ' Candidatus Pythium huanghuaiense'. Plant Dis 2021; 105:2888-2897. [PMID: 33823611 DOI: 10.1094/pdis-01-21-0068-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pythium terrestris, Pythium spinosum, and 'Candidatus Pythium huanghuaiense' are closely related species and important pathogens of soybean that cause root rot. However, the sequences of commonly used molecular markers, such as rDNA internal transcribed spacer 2 and cytochrome oxidase 1 gene, are similar among these species, making it difficult to design species-specific primers for loop-mediated isothermal amplification (LAMP) assays. The genome sequences of these species are also currently unavailable. Based on a comparative genomic analysis and de novo RNA-sequencing transcript assemblies, we identified and cloned the sequences of the M90 gene, a conserved but highly polymorphic single-copy gene encoding a Puf family RNA-binding protein among oomycetes. After primer design and screening, three LAMP assays were developed that specifically amplified the targeted DNA sequences in P. terrestris and P. spinosum at 62°C for 70 min and in 'Ca. Pythium huanghuaiense' at 62°C for 60 min. After adding SYBR Green I, a positive yellow-green color (under natural light) or intense green fluorescence (under ultraviolet light) was observed by the naked eye only in the presence of the target species. The minimum concentration of target DNA detected in all three LAMP assays was 100 pg·μl-1. The assays also successfully detected the target Pythium spp. with high accuracy and sensitivity from inoculated soybean seedlings and soils collected from soybean fields. This study provides a method for identification and cloning of candidate detection targets without a reference genome sequence and identified M90 as a novel specific target for molecular detection of three Pythium species causing soybean root rot.
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Affiliation(s)
- Hui Feng
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Zhuoyuan Liu
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Yang Wang
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Jiajia Chen
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China
| | - Yuanchao Wang
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
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Azam M, Upmanyu K, Gupta R, Sruthy KS, Matlani M, Savargaonkar D, Singh R. Development of Two-Tube Loop-Mediated Isothermal Amplification Assay for Differential Diagnosis of Plasmodium falciparum and Plasmodium vivax and Its Comparison with Loopamp™ Malaria. Diagnostics (Basel) 2021; 11:diagnostics11091689. [PMID: 34574030 PMCID: PMC8467429 DOI: 10.3390/diagnostics11091689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/04/2022] Open
Abstract
To strengthen malaria surveillance, field-appropriate diagnostics requiring limited technical resources are of critical significance. Loop-mediated isothermal amplification (LAMP) based malaria diagnostic assays are potential point-of-care tests with high sensitivity and specificity and have been used in low-resource settings. Plasmodium vivax–specific consensus repeat sequence (CRS)-based and Plasmodium falciparum–specific 18S rRNA primers were designed, and a two-tube LAMP assay was developed. The diagnostic performance of a closed-tube LAMP assay and Loopamp™ Malaria Detection (Pan/Pf, Pv) kit was investigated using nested PCR confirmed mono- and co-infections of P. vivax and P. falciparum positive (n = 149) and negative (n = 67) samples. The closed-tube Pv LAMP assay showed positive amplification in 40 min (limit of detection, LOD 0.7 parasites/µL) and Pf LAMP assay in 30 min (LOD 2 parasites/µL). Pv LAMP and Pf LAMP demonstrated a sensitivity and specificity of 100% (95% CI, 95.96–100% and 89.85–100%, respectively). The LoopampTM Pan/Pf Malaria Detection kit demonstrated a sensitivity and specificity of 100%, whereas LoopampTM Pv showed a sensitivity of 98.36% (95% CI, 91.28–99.71%) and specificity of 100% (95% CI, 87.54–100%). The developed two-tube LAMP assay is highly sensitive (LOD ≤ 2 parasite/µL), demonstrating comparable results with the commercial Loopamp™ Malaria Detection (Pf/pan) kit, and was superior in detecting the P. vivax co-infection that remained undetected by the Loopamp™ Pv kit. The developed indigenous two-tube Pf/Pv malaria detection can reliably be used for mass screening in resource-limited areas endemic for both P. falciparum and P. vivax malaria.
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Affiliation(s)
- Mudsser Azam
- Molecular Biology Laboratory, ICMR- National Institute of Pathology, New Delhi 110029, India; (M.A.); (K.U.); (K.S.S.)
| | - Kirti Upmanyu
- Molecular Biology Laboratory, ICMR- National Institute of Pathology, New Delhi 110029, India; (M.A.); (K.U.); (K.S.S.)
| | - Ratan Gupta
- Department of Paediatrics, VMMC and Safdarjung Hospital, New Delhi 110029, India;
| | - Karugatharayil Sasi Sruthy
- Molecular Biology Laboratory, ICMR- National Institute of Pathology, New Delhi 110029, India; (M.A.); (K.U.); (K.S.S.)
| | - Monika Matlani
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi 110029, India;
| | | | - Ruchi Singh
- Molecular Biology Laboratory, ICMR- National Institute of Pathology, New Delhi 110029, India; (M.A.); (K.U.); (K.S.S.)
- Correspondence: or ; Tel.:+91-11-2616-61-24; Fax: 91-11-26198401
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Yang B, Shi Z, Ma Y, Wang L, Cao L, Luo J, Wan Y, Song R, Yan Y, Yuan K, Tian H, Zheng H. LAMP assay coupled with CRISPR/Cas12a system for portable detection of African swine fever virus. Transbound Emerg Dis 2021; 69:e216-e223. [PMID: 34370390 DOI: 10.1111/tbed.14285] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 02/05/2021] [Accepted: 08/07/2021] [Indexed: 12/26/2022]
Abstract
African swine fever (ASF) is one of the most severe infectious diseases of pigs. In this study, a loop-mediated isothermal amplification (LAMP) assay coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system was established in one tube for the detection of the African swine fever virus (ASFV) p72 gene. The single-stranded DNA-fluorophore quencher reporter and CRISPR-derived RNA were screened and selected for the CRISPR detection system. In combination with LAMP amplification assay, the detection limit for the LAMP-CRISPR assay can reach 7 copies/μl of p72 gene per reaction. Furthermore, this method displays no cross-reactivity with other porcine DNA or RNA viruses. The performance of the LAMP-CRISPR assay was compared with real-time qPCR tests for clinical samples; a good consistency between the LAMP-CRISPR assay and real-time qPCR was observed. The method shed a light on the convenient, portable, low cost, highly sensitive and specific detection of ASFV, demonstrating a great application potential for monitoring on-site ASFV in the field.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Research and Development Department, Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, China
| | - Zhengwang Shi
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yuan Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lijuan Wang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Liyan Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Juncong Luo
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ying Wan
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rui Song
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yiyong Yan
- Research and Development Department, Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, China
| | - Kehu Yuan
- Research and Development Department, Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, China
| | - Hong Tian
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Abstract
Background Loop-mediated isothermal amplification (LAMP) is one of the most promising tools for rapidly detecting Leptospira spp. However, LAMP is hampered by cold storage to maintain the enzymatic activity of Bst DNA polymerase. Objective To overcome the drawback of cold storage requirement for LAMP reagents we modified the reagents by adding sucrose as stabilizer. We then sought to determine the stability at room temperature of the premixed LAMP reagents containing sucrose. Method Premixed LAMP reagents with sucrose and without sucrose were prepared. The prepared mixtures were stored at room temperature for up to 60 days, and were subjected to LAMP reactions at various intervals using rat kidney samples to detect leptospiral DNA. Results The premixed LAMP reagents with sucrose remained stable for 45 days while sucrose-free premixed LAMP reagents showed no amplification from day 1 of storage at room temperature up to day 14. Conclusion The LAMP reagent system can be refined by using sucrose as stabilizer, thus allowing their storage at room temperature without the need for cold storage. The modified method enables greater feasibility of LAMP for field surveillance and epidemiology in resource-limited settings.
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Affiliation(s)
- Pui-Yuei Lee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
| | - Yien-Ping Wong
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
| | - Shuhaidah Othman
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
| | - Hui-Yee Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400Serdang, Selangor, Malaysia
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Duś-Ilnicka I, Szymczak A, Małodobra-Mazur M, Tokarski M. Role of Laboratory Medicine in SARS-CoV-2 Diagnostics. Lessons Learned from a Pandemic. Healthcare (Basel) 2021; 9:915. [PMID: 34356292 DOI: 10.3390/healthcare9070915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/21/2022] Open
Abstract
Since the 2019 novel coronavirus outbreak began in Wuhan, China, diagnostic methods in the field of molecular biology have been developing faster than ever under the vigilant eye of world's research community. Unfortunately, the medical community was not prepared for testing such large volumes or ranges of biological materials, whether blood samples for antibody immunological testing, or salivary/swab samples for real-time PCR. For this reason, many medical diagnostic laboratories have made the switch to working in the field of molecular biology, and research undertaken to speed up the flow of samples through laboratory. The aim of this narrative review is to evaluate the current literature on laboratory techniques for the diagnosis of SARS-CoV-2 infection available on pubmed.gov, Google Scholar, and according to the writers' knowledge and experience of the laboratory medicine. It assesses the available information in the field of molecular biology by comparing real-time PCR, LAMP technique, RNA sequencing, and immunological diagnostics, and examines the newest techniques along with their limitations for use in SARS-CoV-2 diagnostics.
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Kreitlow A, Becker A, Ahmed MFE, Kittler S, Schotte U, Plötz M, Abdulmawjood A. Combined Loop-Mediated Isothermal Amplification Assays for Rapid Detection and One-Step Differentiation of Campylobacter jejuni and Campylobacter coli in Meat Products. Front Microbiol 2021; 12:668824. [PMID: 34177847 PMCID: PMC8219907 DOI: 10.3389/fmicb.2021.668824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/29/2021] [Indexed: 11/25/2022] Open
Abstract
A loop-mediated isothermal amplification (LAMP) assay system was established, allowing rplD gene-based simultaneous detection of Campylobacter jejuni and Campylobacter coli in enriched meat products. Additionally, one-step differentiation of target species on agar plates was enabled by cdtC gene- and gyrA gene-based duplex LAMP. Both the rplD and cdtC–gyrA LAMP assays amplified the target sequences in all 62 C. jejuni and 27 C. coli strains used for determining inclusivity and revealed 100% exclusivity toward 85 tested non-target species. Throughout the entire experiments, C. jejuni and C. coli strains were 100% distinguishable by melting curves of cdtC and gyrA LAMP products. After 24-h enrichment, the rplD LAMP assay reliably detected initial inoculation levels of 10–100 CFU/g in artificially contaminated minced meat. Investigation of naturally contaminated meat samples revealed a diagnostic accuracy of 95% toward real-time PCR and 94.1% toward the standard culture method applying the 24-h incubation period. Diagnostic sensitivity and specificity, and positive and negative predictive values were 89.8, 100, 100, and 91.2%, respectively, when measured against real-time PCR, and 89.6, 98.1, 97.7, and 91.2%, respectively, when measured against the standard culture method. After 48-h enrichment, the detection limit of the rplD LAMP assay improved to initial inoculation levels of 1–10 CFU/g in artificially contaminated minced meat. Applying the 48-h incubation period on naturally contaminated meat samples resulted in 100% concordant results between rplD LAMP, real-time PCR, and the standard culture method. The established LAMP assay system was proved to be suitable for rapid meat sample screening. Furthermore, it constitutes a promising tool for investigating other Campylobacter sources and could therefore make a valuable contribution to protect consumers from foodborne illness.
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Affiliation(s)
- Antonia Kreitlow
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - André Becker
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Marwa F E Ahmed
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behavior, University of Veterinary Medicine Hannover, Hanover, Germany.,Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Sophie Kittler
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Ulrich Schotte
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kronshagen, Germany
| | - Madeleine Plötz
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Amir Abdulmawjood
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hanover, Germany
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Banger S, Pal V, Tripathi NK, Goel AK. Development of a set of three real-time loop-mediated isothermal amplification (LAMP) assays for detection of Bacillus anthracis, the causative agent of anthrax. Folia Microbiol (Praha) 2021; 66:587-96. [PMID: 33834427 DOI: 10.1007/s12223-021-00869-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/03/2021] [Indexed: 10/21/2022]
Abstract
Bacillus anthracis, the causative agent of anthrax is a Gram-positive, non-motile, spore forming bacterium. Its spores can persist in soil and water for years and can also be aerosolized. A rapid, sensitive and specific method to detect B. anthracis is important for clinical management and preventing spread of anthrax. Loop-mediated isothermal amplification (LAMP) assay is a rapid technique that amplifies target DNA in isothermal conditions with high sensitivity and specificity. In this study, a LAMP assay set targeting a chromosomal and two plasmid markers was developed. The individual assays of the LAMP set targeting pXO1 plasmid (lef), pXO2 plasmid (capB), and chromosome (BA5345) sequences could detect 10, 250, and 100 fg of genomic DNA and 10, 100, and 50 copies of the DNA targets harboured in recombinant plasmids, respectively. The lef and capB LAMP assays could detect ≥ 1 × 103 CFU per mL of bacteria in spiked human blood samples, while BA5345 LAMP assay could detect ≥ 1 × 104 CFU of bacteria per mL of spiked blood. The amplification was monitored in real-time by turbidimeter, and visual detection was also accomplished under normal and UV light after adding SYBR Green 1 dye on completion of the reaction. The assay set was found to be highly sensitive and did not cross-react with the closely related Bacillus spp. and other bacterial strains used in the study.
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Kumar B, Maharana BR, Brahmbhatt NN, Thakre BJ, Parmar VL. Development of a loop-mediated isothermal amplification assay based on RoTat1.2 gene for detection of Trypanosoma evansi in domesticated animals. Parasitol Res 2021; 120:1873-82. [PMID: 33712930 DOI: 10.1007/s00436-021-07118-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 03/04/2021] [Indexed: 01/02/2023]
Abstract
The early containment of trypanosomosis depends on early, sensitive, and accurate diagnosis in endemic areas with low-intensity infections. The study was planned to develop a simple read out loop-mediated isothermal amplification (LAMP) assay targeting a partial RoTat1.2 VSG gene of Trypanosoma evansi with naked eye visualization of LAMP products by adding SYBR® Green I dye. The visual results were further confirmed with those of agarose gel electrophoresis, restriction enzyme digestion of LAMP products with AluI, and sequencing of the PCR products using LAMP outer primers. The LAMP primers did not show cross reactivity and non-specific reactions with regional common hemoparasitic DNA revealing high specificity of the assay. The threshold sensitivity level of the LAMP assay was determined to be 0.003 fg compared to 0.03 fg RoTat1.2 amplified DNA fragments of T. evansi by PCR assay. Moreover, assessment of 500 blood samples collected from unhealthy domestic animals in field suspected for various hemoparasitic infections was carried out for the presence of T. evansi by microscopy, RoTat1.2 VSG PCR, and LAMP assay. LAMP could detect T. evansi in 36 samples, while PCR and microscopy could detect 33 and 12 samples, respectively. All the samples positive by microscopy and PCR were also confirmed positive by the LAMP assay. The current LAMP assay has appealing point of care characteristics to visually monitor the results, lessen the need of post DNA amplification procedure, and enable this method to be applied as a rapid and sensitive molecular diagnostic tool in under resourced laboratories and field setup.
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Diallo K, Feteh VF, Ibe L, Antonio M, Caugant DA, du Plessis M, Deghmane AE, Feavers IM, Fernandez K, Fox LM, Rodrigues CMC, Ronveaux O, Taha MK, Wang X, Brueggemann AB, Maiden MCJ, Harrison OB. Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review. EBioMedicine 2021; 65:103274. [PMID: 33721818 PMCID: PMC7957090 DOI: 10.1016/j.ebiom.2021.103274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.
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Affiliation(s)
- Kanny Diallo
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Cote d'Ivoire
| | - Vitalis F Feteh
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Lilian Ibe
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Atlantic Boulevard, Fajara, PO Box 273, Banjul, Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Dominique A Caugant
- WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo N-0213, Norway
| | - Mignon du Plessis
- A division of the National Health Laboratory Service (NHLS), National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | | | - Ian M Feavers
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | | | - LeAnne M Fox
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Charlene M C Rodrigues
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom; Department of Paediatric Infectious Diseases, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | | | | | - Xin Wang
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Division of Bacterial Diseases, Meningitis and Vaccine Preventable Diseases Branch, United States
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom
| | - Odile B Harrison
- Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3SY, United Kingdom.
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Zhou Y, Fan F, Wang L, Chaisiri C, Yin LF, Yin WX, Luo CX. Development of a loop-mediated isothermal amplification method for the rapid detection of Venturia carpophila on peach. Pest Manag Sci 2021; 77:1383-1391. [PMID: 33098187 DOI: 10.1002/ps.6154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Peach scab, caused by Venturia carpophila, can significantly reduce both the yield and quality of peach fruit. It is difficult to distinguish peach scab from other peach diseases such as black spot and bacterial spot. An efficient assay is needed to identify V. carpophila in order to develop scientific management strategies. RESULTS A set of loop-mediated isothermal amplification (LAMP) primers was designed based on the internal transcribed spacer (rDNA-ITS) sequence to detect V. carpophila. Compared with the conventional polymerase chain reaction (PCR) method, the LAMP method not only exhibited higher sensitivity and specificity in the detection of V. carpophila, but also required simpler equipment and less operational time. The minimum detectable concentration of V. carpophila genomic DNA with the LAMP method was 56.6 fg μl-1 , which was 100 times lower than with the conventional PCR method. When eight fungal species including V. carpophila (23 isolates from 14 provinces) and one bacterial species were used with LAMP detection, only V. carpophila showed a color change, from brown to yellowish green, and ladder-like bands in electrophoresis, indicating successful amplification. Moreover, when crude DNAs of peach fruit samples were used in LAMP detection, amplification was observed only from diseased fruits, and not from healthy fruits and the negative control. CONCLUSION The LAMP assay shows simplicity, rapidity, high sensitivity and specificity, and will be useful in distinguishing scab caused by Venturia carpophila from other diseases with similar symptoms. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Yang Zhou
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Fan
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Wang
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liang-Fen Yin
- Experimental Teaching Center of Crop Science, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei-Xiao Yin
- Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao-Xi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Anupama KP, Nayak A, Karunasagar I, Karunasagar I, Maiti B. Evaluation of loop-mediated isothermal amplification assay along with conventional and real-time PCR assay for sensitive detection of pathogenic Vibrio parahaemolyticus from seafood sample without enrichment. Mol Biol Rep 2021; 48:1009-1016. [PMID: 33423185 PMCID: PMC7796815 DOI: 10.1007/s11033-020-06116-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/20/2020] [Indexed: 12/04/2022]
Abstract
The primary reason for foodborne illness is improper seafood safety testing, and hence, an appropriate tool for testing is the key to control the outbreaks. The current study aimed to develop a loop-mediated isothermal amplification (LAMP) assay to detect pathogenic Vibrio parahaemolyticus, important foodborne pathogen, targeting tdh, and trh genes. The specificity of the LAMP assay was good without any false-positive and false-negative results. The assay was highly sensitive and could detect the pathogenic V. parahaemolyticus as low as 1 CFU/reaction in spiked seafood samples and 1 pg of extracted DNA. Out of 62 seafood samples from India’s southwest coastal region tested with LAMP assay, eight (12.9%) were positive for trh, and seven (11.29%) samples were positive tdh gene. LAMP-based on tdh and trh was found to be significantly more sensitive (p < 0.05) than conventional PCR and nearly equal sensitive as real-time PCR (RT-PCR) for the detection of pathogenic V. parahaemolyticus. Our study shows that LAMP assay can be a better approach as a point-of-care (POC) diagnostic tool and could detect pathogenic V. parahaemolyticus on seafood samples directly without enrichment and isolation. The high sensitivity and simplicity make LAMP assay a better alternative method than the conventional method and RT-PCR for the detection of pathogens. LAMP assay can be considered as a good alternative to PCR for the routine detection of pathogenic V. parahaemolyticus in seafood.
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Affiliation(s)
- Karanth Padyana Anupama
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Ashwath Nayak
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore, 575018, India.
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Michiwaki Y, Tanaka T, Wakamiya T, Tabei Y, Samura K, Suehiro E, Kawashima M. Emergent Carotid Artery Stenting Following Intravenous Alteplase Infusion After Rapid Negative Diagnosis for COVID-19 by Loop-Mediated Isothermal Amplification Assay. World Neurosurg 2020; 145:356-359. [PMID: 33045450 PMCID: PMC7546639 DOI: 10.1016/j.wneu.2020.09.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 10/30/2022]
Abstract
BACKGROUND During the coronavirus disease 2019 (COVID-19) pandemic, a rapid screening method for COVID-19 detection is needed to decide the appropriate strategy to treat stroke patients. In acute ischemic stroke treatment, the efficacy and safety of emergent carotid artery stenting (eCAS) for hyperacute ischemic stroke (hAIS) due to internal carotid artery stenosis (ICS) have not been sufficiently established. CASE DESCRIPTION A 71-year-old man with hAIS caused by severe ICS was treated via intravenous alteplase infusion. The patient underwent screening for COVID-19 by the loop-mediated isothermal amplification (LAMP) assay shortly after arrival at our institution. The LAMP result was obtained within 90 minutes, during intravenous alteplase infusion, and turned out to be negative. The symptom of hemiplegia worsened during alteplase infusion, and he, therefore, underwent eCAS after administration of aspirin (200 mg). Recanalization was achieved successfully by eCAS, and dual antiplatelet therapy and argatroban were administrated following eCAS. Hemorrhagic complications or restenosis/occlusion of the carotid artery were not observed. He was discharged without neurologic deficits 15 days following eCAS. Because of the rapid negative diagnosis for COVID-19 using the LAMP method, eCAS could be performed following standard procedures, along with infectious defense, without delay. CONCLUSIONS This case report suggests that eCAS for hAIS due to ICS following intravenous alteplase can be an effective treatment, along with appropriate antiplatelet medication and management in select patients. During the COVID-19 pandemic, the LAMP assay for COVID-19 detection might be a suitable diagnostic strategy preceding stroke treatment because of the rapid turnaround time.
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Affiliation(s)
- Yuhei Michiwaki
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan.
| | - Tatsuya Tanaka
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan
| | - Tomihiro Wakamiya
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan
| | - Yusuke Tabei
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan
| | - Kazuhiro Samura
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan
| | - Eiichi Suehiro
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan
| | - Masatou Kawashima
- Department of Neurosurgery, International University of Health and Welfare, School of Medicine, Narita Hospital, Narita City, Chiba, Japan
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Babu US, Harrison LM, Mammel MK, Bigley EC 3rd, Hiett KL, Balan KV. A loop-mediated isothermal amplification (LAMP) assay for the consensus detection of human pathogenic Campylobacter species. J Microbiol Methods 2020; 176:106009. [PMID: 32707152 DOI: 10.1016/j.mimet.2020.106009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/07/2020] [Accepted: 07/17/2020] [Indexed: 02/02/2023]
Abstract
Most rapid identification methods for Campylobacter are designed to detect thermotolerant Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli). A growing number of thermosensitive Campylobacter species are now gaining recognition as emerging human pathogens. Methods are lacking for the rapid screening of these emerging species. Loop-mediated Isothermal Amplification (LAMP) is a nucleic acid amplification method that allows for the rapid and cost-effective detection of bacteria. Degenerate primers against the 16S rRNA sequences for C. jejuni, C. coli, C. lari, C. upsaliensis, C. ureolyticus, C. fetus, C. gracilis, C. rectus, and C. concisus were designed. Isothermal amplification was conducted using ATCC reference strains at 68 °C for 30 min using WarmStart® Colorimetric LAMP reagents. Positive reactions were indicated by a color change from pink to yellow; specificity to Campylobacter was confirmed using a restriction enzyme digest (RsaI). The developed LAMP reaction was specific for the reference strains, which was confirmed against an exclusivity panel that consisted of other enteric pathogens, including E. coli, Salmonella, Shigella, Helicobacter, and Arcobacter. This method was also evaluated for the detection of C. jejuni, C. coli, and C. lari in primary enrichment media from artificially contaminated fresh spinach samples. The LAMP method provides an option to rapidly screen for the presence of pathogenic Campylobacter spp. in field surveillance and trace-back analysis.
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Fan SJ, Tan HK, Xu YC, Chen YZ, Xie TA, Pan ZY, Ouyang S, Li Q, Li XY, Li ZX, Guo XG. A pooled analysis of the LAMP assay for the detection of Neisseria meningitidis. BMC Infect Dis 2020; 20:525. [PMID: 32689953 PMCID: PMC7372874 DOI: 10.1186/s12879-020-05250-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 07/14/2020] [Indexed: 12/13/2022] Open
Abstract
Background Neisseria meningitidis is a major cause of bacterial meningitis, and these infections are associated with a high mortality rate. Rapid and reliable diagnosis of bacterial meningitis is critical in clinical practice. However, this disease often occurs in economically depressed areas, so an inexpensive, easy to use, and accurate technology is needed. We performed a pooled-analysis to assess the potential of the recently developed loop-mediated isothermal amplification (LAMP) assay for detection of meningococcus. Methods Pubmed, Embase, and Web of Science were searched to identify original studies that used the LAMP assay to detect meningococcus. After pooling of data, the sensitivity and specificity were calculated, a summary receiver operating characteristic (SROC) curve was determined, and the area under the SROC curve was computed to determine diagnostic accuracy. Publication bias was assessed using Deek’s funnel plot. Results We examined 14 studies within 6 publications. The LAMP assay had high sensitivity (94%) and specificity (100%) in the detection of meningococcus in all studies. The area under the SROC curve (0.980) indicated high overall accuracy of the LAMP assay. There was no evidence of publication bias. Discussion The LAMP assay has accuracy comparable to bacterial culture and PCR for detection of meningococcus, but is less expensive and easier to use. We suggest the adoption of the LAMP assay to detect meningococcus, especially in economically depressed areas.
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Affiliation(s)
- Shu-Jin Fan
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Hong-Kun Tan
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Yu-Cheng Xu
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Yuan-Zhi Chen
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhi-Yong Pan
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Shi Ouyang
- Department of infectious disease, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qin Li
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, USA
| | - Xiao-Yan Li
- Department of Laboratory Medicine, The Affiliated Shunde Hospital of Guangzhou Medical University, Foshan, China
| | - Zhen-Xing Li
- Department of respiratory, The third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China. .,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150, China.
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Buella Parivallal P, Prasanna Kumar MK, Vasanthakumar KC, Thavuroollah FF, Manoharan Y, Muthu S. LAMP Assay: Could it be a Boon for the Molecular Diagnosis of COVID-19? Indian J Clin Biochem 2020;:1-2. [PMID: 32837033 DOI: 10.1007/s12291-020-00915-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022]
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Anupama KP, Nayak A, Karunasagar I, Maiti B. Rapid visual detection of Vibrio parahaemolyticus in seafood samples by loop-mediated isothermal amplification with hydroxynaphthol blue dye. World J Microbiol Biotechnol 2020; 36:76. [PMID: 32390085 DOI: 10.1007/s11274-020-02851-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
The detection and monitoring of Vibrio parahaemolyticus pathogen in aquatic foods have become essential for preventing outbreaks. In this study, loop-mediated isothermal amplification (LAMP) assay with the azo dye, hydroxynaphthol blue (HNB) was developed targeting species-specific tlh gene. The assay was carried out on 62 seafood samples that included clam and shrimp and compared with conventional LAMP assay performed with the commonly used fluorescent dye, conventional PCR, and real-time PCR (RT-PCR). Of 62 samples studied for tlh gene, 32 (51.61%) gave positive by HNB-LAMP, which comprised 22 (70.96%) clam samples and 10 (32.25%) shrimp samples. The HNB-LAMP assay was found to be highly sensitive, specific, and superior to conventional PCR (p > 0.05). RT-PCR presented higher sensitivity than HNB-LAMP; however, it has the limitation of being cost-intensive and requiring technical expertise to perform. HNB-LAMP is affordable, rapid, simple, and easy to perform, allowing naked eye visualization.
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Ngari MG, Mwangi IN, Njoroge MP, Kinyua J, Osuna FA, Kimeu BM, Okanya PW, Agola EL. Development and evaluation of a loop-mediated isothermal amplification (LAMP) diagnostic test for detection of whipworm, Trichuris trichiura, in faecal samples. J Helminthol 2020; 94:e142. [PMID: 32238209 DOI: 10.1017/S0022149X2000022X] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Whipworm infection or trichuriasis caused by Trichuris trichiura is of major public health concern in sub-Saharan Africa, particularly among pre-school and school-going children. It is among the neglected tropical diseases targeted for elimination through mass drug administration (MDA). One of the outcomes of MDA is a rapid decline in levels of infection intensity, making it difficult to monitor effectiveness of control measures using the conventional Kato-Katz procedure, which relies on the microscopic detection of parasite ova in faecal samples. In the present study, a loop-mediated isothermal amplification (LAMP) test was developed for the detection of T. trichiura infection in faecal samples. LAMP technology offers greater sensitivity and specificity than the microscopy-based tests. A set of four specific primers targeting the internal transcribed spacer 2 region of the ribosomal DNA were designed using Primer Explorer software. DNA was extracted from faecal samples using the alkaline lysis method (HotSHOT) and the LAMP reaction performed at 63°C for 1 h. The amplicons were visualized by both gel electrophoresis and with the naked eye following staining with SYBR green dye. Sensitivity and specificity tests were determined using the standard Kato-Katz diagnostic procedure as a reference test. The developed LAMP assay reliably detected T. trichiura DNA in faecal samples, with a specificity and sensitivity of 88% and 77%, respectively. No cross-reactivity was observed with several common helminth parasites. The developed LAMP assay is an appropriate diagnostic method for the detection of T. trichiura DNA in human faecal samples due to its simplicity, low cost, high sensitivity and specificity.
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Singh MD, Singh H, Singh NK, Singh NK, Sood NK, Rath SS. Evaluation of a Loop-Mediated Isothermal Amplification Technique for the Rapid Visual Detection of Hepatozoon canis Infection. Acta Parasitol 2020; 65:151-5. [PMID: 31729613 DOI: 10.2478/s11686-019-00143-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/06/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Laboratory diagnosis of Hepatozoon canis infection is tedious, especially in chronic and/or latent infections. PURPOSE The study was planned to develop a simple read out loop mediated isothermal amplification (LAMP) assay targeting a partial 18S rRNA gene of H. canis with naked eye visualisation of LAMP products. METHODS A LAMP assay was employed to assess the DNA amplification by adding SYBR Green I dye for naked eye inspection of DNA accumulating in reaction tubes. Positive amplification was read through observation of change in colour of reaction mixture following addition of dye. The visual results were further verified with those of agarose gel electrophoresis. Genomic DNA of other haemoparasites of dog viz. Babesia vogeli, B. gibsoni, Ehrlichia canis and Trypanosoma evansi along with no-template control were used to determine the specificity of assay. RESULTS Among the 109 blood samples presented at Small Animal Clinics, Teaching Veterinary Clinical Complex, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab (India) tested, 39 revealed colour change from orange to green indicating positive reaction while 70 were negative as revealed by no colour change. The results of visual inspection were comparable to those obtained by agarose gel electrophoresis. The LAMP primers specifically amplified H. canis DNA, whereas no amplification was detected in DNA samples of other haemoparasites and no-template control revealing specificity of the assay. The diagnostic sensitivity and specificity (95% CI) of visual LAMP assay with respect to microscopy in detection of H. canis varied from 100% (15.81-100.00%) and 65.42% (55.61-74.35%), respectively. CONCLUSION The present investigation has developed a specific and rapid LAMP assay for the detection of H. canis, using SYBR Green I dye, which has practical applications for the screening of field samples.
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Ahmad S, Ali N, Kausar M, Misbah H, Wahid A. Road toward rapid-molecular point of care test to detect novel SARS-coronavirus 2019 (COVID-19): Review from updated literature. Allergol Immunopathol (Madr) 2020; 48:518-520. [PMID: 32636083 PMCID: PMC7328543 DOI: 10.1016/j.aller.2020.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/20/2020] [Indexed: 11/30/2022]
Abstract
Coronavirus disease 2019 (COVID-19) named by the WHO as a result of the global public health emergency. COVID-19 is caused by a new coronavirus named as novel coronavirus (2019-nCOV). From the first case reported in December 2019 it is now a pandemic situation and a major public health emergency. The COVID-19 transmission rate is very high, infecting two to three persons on average with contact to an already infected person. There is a need for the health system, specially in developing countries such as in Pakistan, to combat such a novel disease by rapid, accurate, and high quality diagnostic testing in order to screen suspected cases and also surveillance of the disease. A rapid, accurate and low-cost diagnostic point-of-care device is needed for timely diagnosis of COVID-19 and is essential to combat such outbreaks for compelling preventive measures against the disease spread. This review is to highlight the importance of point-of-care diagnostics device for robust and accurate diagnosis of COVID-19 in physician offices and other urgent healthcare-type settings and encourage academics and stake holders towards advancement in order to control outbreaks and develop the public health surveillance system.
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Affiliation(s)
- S. Ahmad
- College of Medical technology MTI- BKMC Mardan, Khyber Pakhtunkhwa, Pakistan,Corresponding author
| | - N. Ali
- College of Medical technology MTI- BKMC Mardan, Khyber Pakhtunkhwa, Pakistan
| | - M. Kausar
- Rehman College of Allied Health Sciences, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - H. Misbah
- North West General Hospital and Research Center, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - A. Wahid
- Rehman College of Allied Health Sciences, Peshawar, Khyber Pakhtunkhwa, Pakistan
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Askari N, Momtaz H, Tajbakhsh E. Prevalence and phenotypic pattern of antibiotic resistance of Acinetobacter baumannii isolated from different types of raw meat samples in Isfahan, Iran. Vet Med Sci 2019; 6:147-153. [PMID: 31576672 PMCID: PMC7036315 DOI: 10.1002/vms3.199] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 02/02/2023] Open
Abstract
Resistant Acinetobacter baumannii isolates are not only known as opportunistic nosocomial bacteria but may also be regarded as emerging bacterial contaminants in foods of animal origins. The present investigation was done to assess the prevalence and antibiotic resistance pattern of A. baumannii isolated from different types of raw meat samples. One hundred and ninety-four raw meat samples were collected and cultured for A. baumannii isolates. Culture-positive bacteria were also approved using the loop-mediated isothermal amplification (LAMP) technique. The disc diffusion method was used for antibiotic susceptibility testing. Out of 194 raw meat samples, 39 (20.10%) were positive for A. baumannii isolates. Ovine raw meat was the most commonly contaminated samples (32.14%). All of the culture-positive A. baumannii isolates were also approved using the LAMP assay. A. baumannii isolates harboured the highest prevalence of resistance against gentamicin (87.17%), tetracycline (79.48%), erythromycin (74.35%), azithromycin (66.66%), ciprofloxacin (58.97%), trimethoprim/sulphamethoxazole (56.41%) and rifampin (51.28%). The lowest prevalence of resistance was found against imipenem (17.94%) and chloramphenicol (28.20%). Raw bovine, ovine, caprine, camel and poultry meat samples were considered as the important sources of isolates resistant to some of the categories of antimicrobials used to treat infections caused by A. baumannii. Further studies are required to find the exact role of resistant A. baumannii isolates in the dissemination of antibiotic resistance to human population.
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Affiliation(s)
- Neda Askari
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hassan Momtaz
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Elahe Tajbakhsh
- Department of Microbiology, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Siddique MP, Jang WJ, Lee JM, Hasan MT, Kim CH, Kong IS. Detection of Vibrio anguillarum and Vibrio alginolyticus by Singleplex and Duplex Loop-Mediated Isothermal Amplification (LAMP) Assays Targeted to groEL and fklB Genes. Int Microbiol 2019; 22:501-509. [PMID: 31098824 DOI: 10.1007/s10123-019-00079-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/01/2019] [Accepted: 04/07/2019] [Indexed: 12/15/2022]
Abstract
Singleplex and duplex loop-mediated isothermal amplification (LAMP) assays were developed for detecting Vibrio anguillarum, a major bacterial pathogen of fish, and Vibrio alginolyticus, a pathogen of fish and humans, separately and simultaneously from contaminated seawater by targeting the groEL gene of V. anguillarum, which encodes a molecular chaperone protein, and the fklB gene of V. alginolyticus, which encodes a 22 kilodalton (kDa) peptidyl prolyl isomerase. The optimal reaction conditions to produce consistent results were 65 °C for 30 min, 63 °C for 30 min, and 63 °C for 40 min for the groEL (singleplex for V. anguillarum), fklB (singleplex for V. alginolyticus), and groEL + flkB (duplex) LAMP assays, respectively, analyzed via visual detection methods (use of calcein, and SYBR Green I) and agarose gel electrophoresis. The assays were found to be species-specific, as closely related Vibrio spp. were not detected. The limits of detection (LoDs) of the LAMP assays for DNA template from pure culture and artificially contaminated seawater were 10 and 14 fg (groEL assay; for V. anguillarum), 12.5 and 17 fg (fklB assay; for V. alginolyticus), and 50 and 70 fg (duplex assay) per reaction, respectively, which were much better than the LoDs of conventional polymerase chain reaction (PCR). Singleplex and duplex LAMP assays were found to be rapid, species-specific, and sensitive for the detection of V. anguillarum and V. alginolyticus and are applicable to laboratory and field diagnostics.
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Affiliation(s)
- Mahbubul Pratik Siddique
- Department of Biotechnology, Pukyong National University, Busan, 48513, Republic of Korea.,Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Won Je Jang
- Department of Biotechnology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jong Min Lee
- Industrial Bio-materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Md Tawheed Hasan
- Department of Biotechnology, Pukyong National University, Busan, 48513, Republic of Korea.,Department of Aquaculture, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Chang-Hoon Kim
- Department of Marine Bio-materials & Aquaculture, Pukyong National University, Busan, 48513, Republic of Korea
| | - In-Soo Kong
- Department of Biotechnology, Pukyong National University, Busan, 48513, Republic of Korea.
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Rajput R, Singh P, Sarin R, Sethi P, Sharma S. Diagnostic accuracy of loop-mediated isothermal amplification assay for extra-pulmonary tuberculosis in Indian population. J Microbiol Methods 2019; 158:59-65. [PMID: 30703448 DOI: 10.1016/j.mimet.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Confirmatory diagnosis of extra-pulmonary tuberculosis remains a true challenge owing to difficulty in procuring appropriate specimen, inefficient laboratory methods and paucibacillary nature of infection. These obstructions become all the very difficult in pediatric EPTB cases, due to non-specific clinical signs and symptoms, low sensitivity of smear microscopy and culture, lack of awareness among clinicians, etc. AIM OF THE STUDY: The present study aimed to evaluate the diagnostic accuracy of rapid and cost-effective loop-mediated isothermal amplification (LAMP) assay for EPTB diagnosis in children. METHODS A total of 154 cases were analyzed by EPTB-site smear microscopy, culture, PCRs for IS6110, MPB64 & Pab genes, nested PCR and LAMP assay. Single-gene PCRs were performed by custom-synthesized primers. Nested PCR was performed using the 3B BIOTUB Kit and the LAMP assay was done using the Nu-LAMP TB kit. RESULTS We observed that the molecular tests displayed 4-fold higher positivity rate (minimum 46%) in comparison to the microbiological tests (maximum 11.03%). In contrast to the composite reference standard, LAMP assay was found to be 79.6% sensitive and 78% specific for EPTB diagnosis in childhood cases. CONCLUSIONS Our results indicate that LAMP assay is a promising technique for efficient diagnosis of EPTB in children belonging to resource-limited regions.
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Affiliation(s)
- Roopali Rajput
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Paras Singh
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India.
| | - Rohit Sarin
- Department of TB and Respiratory Diseases and Director, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Prabhpreet Sethi
- Department of TB and Respiratory Diseases, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Sangeeta Sharma
- Department of Paediatrics, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
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Singh MD, Singh H, Singh NK, Singh NK, Kashyap N, Sood NK, Rath SS. Development of loop-mediated isothermal amplification (LAMP) assay for detection of Hepatozoon canis infection in dogs. Ticks Tick Borne Dis 2018; 10:371-376. [PMID: 30503892 DOI: 10.1016/j.ttbdis.2018.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022]
Abstract
The laboratory diagnosis of canine hepatozoonosis, caused by Hepatozoon canis is tedious, especially in chronic and latent infections. In the present investigation, a loop mediated isothermal amplification (LAMP) assay was developed and standardized targeting the partial 18S rRNA gene (GenBank accession no. KU096058). The LAMP primers specifically amplified H. canis DNA, whereas no amplification was detected in DNA samples from dogs infected with Babesia vogeli, B. gibsoni, Ehrlichia canis and Trypanosoma evansi, and no amplification was observed in DNA samples from H. canis-free dogs. The threshold sensitivity level of the assay was determined to be 15 fg of genomic DNA of H. canis. Furthermore, evaluation of blood samples collected from 250 dogs presented at Small Animal Clinics, Teaching Veterinary Clinical Complex, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab (India) was carried out for the presence of H. canis by microscopy, 18S PCR assay and LAMP assay. Of the total samples subjected to these tests, LAMP detected H. canis in 75 samples, while 18S PCR and microscopy detected H. canis in 28 and 9 samples, respectively. The present investigation has developed, for the first time, a highly sensitive, specific and rapid LAMP assay for the detection of H. canis, which has practical applications for the screening of field samples.
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Affiliation(s)
- Manraj Deep Singh
- Department of Veterinary Parasitology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Harkirat Singh
- Department of Veterinary Parasitology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India.
| | - Nirbhay Kumar Singh
- Department of Veterinary Parasitology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Niraj Kumar Singh
- Department of Animal Biotechnology, School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, India
| | - Neeraj Kashyap
- Department of Animal Genetics & Breeding, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Naresh Kumar Sood
- Department of Teaching Veterinary Clinical Complex, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Shitanshu Shekar Rath
- Department of Veterinary Parasitology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
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Akram A, Islam SMR, Munshi SU, Tabassum S. Detection of Hepatitis B Virus DNA among Chronic and potential Occult HBV patients in resource-limited settings by Loop-Mediated Isothermal Amplification assay. J Viral Hepat 2018; 25:1306-1311. [PMID: 29768691 DOI: 10.1111/jvh.12931] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/26/2018] [Indexed: 12/13/2022]
Abstract
Transmission of Hepatitis B Virus (HBV) usually occurs due to the transfusion of blood or blood products from chronic HBV (CHB) or occult HBV-infected (OBI) patients. Besides serological tests, e.g. HBsAg and anti- HBc (total), detection of HBVDNA is necessary for the diagnosis of OBI patients. Different nucleic acid tests (NATs) including real- time-Polymerase Chain Reaction (qPCR) are used to detect HBV- DNA. The NATs are expensive and require technical expertise which are barriers to introduce them in resource-limited settings. This study was undertaken to evaluate the use of Loop-Mediated Isothermal Amplification (LAMP) assay as an alternative to qPCR for the detection of HBV-DNA in CHB and potential OBI patients in resource-limited settings. Following the published protocols with some modifications, a LAMP assay was developed for detection of HBV-DNA by either using a heat block followed by detection in an agarose gel or using a qPCR thermocycler. The LAMP assay was applied to supernatant prepared from heat-treated serum collected from CHB and potential OBI patients. HBV viral load in serum was measured by qPCR using a single-step HBV-DNA quantification kit. Among 200 samples tested, qPCR was capable to detect HBV-DNA in 25.5% of cases, whereas LAMP assay detected HBV-DNA in 43.5% cases. The qPCR was able to detect 11 (9.16%) potential OBI cases, whereas LAMP assay identified HBV-DNA in 43 (35.83%) cases. In addition to tests for HBsAg and/or anti-HBc (total), detection of HBV-DNA by LAMP assay may aid in preventing post-transfusion HBV infection in resource-limited settings.
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Affiliation(s)
- A Akram
- Department of Virology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - S M R Islam
- Department of Virology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - S U Munshi
- Department of Virology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - S Tabassum
- Department of Virology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
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Shin DS, Heo GI, Son SH, Oh CS, Lee YK, Cha JS. Development of an Improved Loop-Mediated Isothermal Amplification Assay for On-Site Diagnosis of Fire Blight in Apple and Pear. Plant Pathol J 2018; 34:191-198. [PMID: 29887775 PMCID: PMC5985645 DOI: 10.5423/ppj.ft.03.2018.0055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 05/25/2023]
Abstract
Fast and accurate diagnosis is needed to eradicate and manage economically important and invasive diseases like fire blight. Loop-mediated isothermal amplification (LAMP) is known as the best on-site diagnostic, because it is fast, highly specific to a target, and less sensitive to inhibitors in samples. In this study, LAMP assay that gives more consistent results for on-site diagnosis of fire blight than the previous developed LAMP assays was developed. Primers for new LAMP assay (named as DS-LAMP) were designed from a histidine-tRNA ligase gene (EAMY_RS32025) of E. amylovora CFBP1430 genome. The DS-LAMP amplified DNA (positive detection) only from genomic DNA of E. amylovora strains, not from either E. pyrifoliae (causing black shoot blight) or from Pseudomonas syringae pv. syringae (causing shoot blight on apple trees). The detection limit of DS-LAMP was 10 cells per LAMP reaction, equivalent to 104 cells per ml of the sample extract. DS-LAMP successfully diagnosed the pathogens on four fire-blight infected apple and pear orchards. In addition, it could distinguish black shoot blight from fire blight. The Bühlmann-LAMP, developed previously for on-site diagnosis of fire blight, did not give consistent results for specificity to E. amylovora and on-site diagnosis; it gave positive reactions to three strains of E. pyrifoliae and two strains of P. syringae pv. syringae. It also, gave positive reactions to some healthy sample extracts. DS-LAMP, developed in this study, would give more accurate on-site diagnosis of fire blight, especially in the Republic of Korea, where fire blight and black shoot blight coexist.
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Affiliation(s)
- Doo-San Shin
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Gwang-Il Heo
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Soo-Hyeong Son
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, Kyung Hee University, Yongin 17104,
Korea
| | - Young-Kee Lee
- Department of Agro-food Safety and Crop Protection, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Jae-Soon Cha
- Major in Plant Medicine, School of Applied Plant Science & Biotechnology, Chungbuk National University, Cheongju 28644,
Korea
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Kakizaki E, Sonoda A, Sakai M, Yukawa N. Simple detection of bacterioplankton using a loop-mediated isothermal amplification (LAMP) assay: First practical approach to 72 cases of suspected drowning. Forensic Sci Int 2018; 289:289-303. [PMID: 29920446 DOI: 10.1016/j.forsciint.2018.05.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 05/22/2018] [Indexed: 11/22/2022]
Abstract
We developed a novel molecular tool for assisting the diagnosis of death by drowning and evaluated its validity in forensic practical cases. Two novel sets of loop-mediated isothermal amplification (LAMP) primers were designed to detect either representative freshwater (Aeromonas) or marine (Vibrio, Photobacterium, Listonella) bacterioplankton (aquatic bacteria) in one tube using the LAMP technique. The assay involves only mixing template DNA with seven reagents and incubating at 64°C for 80min and does not require special or expensive equipment because detection is based on visual observation under natural light. The assay's excellent specificity was also demonstrated using 17 standard (control) strains and 124 other bacterial strains cultured from drowning and non-drowning victims in our previous studies. We then assayed 299 specimens (135 lung, 164 blood) from 72 victims, including 45 who had drowned in rivers, ditches, seas, and around estuaries. LAMP assay results could provide effective information to assist the diagnosis of death by drowning in practical cases. The LAMP assay would be useful for suspected drowning cases, as it is a less-laborious and less-expensive minimal test when death by drowning is sufficiently confirmed or negated from only autopsy findings and environmental data or when diatom testing is not performed due to logistic, personnel, or budgetary limitations. Moreover, the assay could serve as a simple additional test when the density of diatoms in the lungs is very low due to low density in the water.
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De Koninck AS, Cnops L, Hofmans M, Jacobs J, Van den Bossche D, Philippé J. Diagnostic performance of the loop-mediated isothermal amplification (LAMP) based illumigene ® malaria assay in a non-endemic region. Malar J 2017; 16:418. [PMID: 29041927 PMCID: PMC5645927 DOI: 10.1186/s12936-017-2065-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 10/13/2017] [Indexed: 01/09/2023] Open
Abstract
Background Light microscopy and antigen-based rapid diagnostic tests are the primary diagnostic tools for detecting malaria, although being labour-intensive and frequently challenged by lack of personnel’s experience and low levels of parasite density. The latter being especially important in non-endemic settings. Novel molecular techniques aim to overcome this drawback. The objective of this study was to assess the diagnostic performance of the illumigene malaria assay® (Meridian Bioscience) compared to microscopy, RDT and real-time PCR. This loop-mediated isothermal amplification (LAMP) assay is a qualitative in vitro diagnostic test for the direct detection of Plasmodium spp. DNA in human venous whole blood samples. Methods The illumigene assay was assessed on a retrospective panel of stored blood samples (n = 103) from returned travellers and external quality control samples (n = 12). Additionally the assay was prospectively assessed on 30 fresh routine samples with a request for malaria diagnosis. The illumigene assay was compared to microscopy, RDT and Plasmodium species specific real-time PCR. Results In the retrospective evaluation, the illumigene assay showed 100% agreement with the real-time PCR, RDT and microscopy yielding a sensitivity and specificity of 100% (95% CI 95.1–100% and 89.7–100%, respectively). Seven samples from patients recently treated for Plasmodium falciparum infection that were RDT positive and microscopy negative yielded positive test results. The performance of the illumigene assay equals that of microscopy combined with RDT in the prospective panel with three false negative RDT results and one false negative microscopy result. Excellent concordance with PCR was observed. The limit of detection of the assay approached 0.5 parasites/µL for both P. falciparum and Plasmodium vivax. Conclusion In non-endemic regions where the diagnostic process for malaria infections is questioned by lack of experience and low levels of parasite densities, the illumigene assay can be of value. Due to its high sensitivity, the LAMP assay may be considered as primary diagnostic test. The results of this study indicate that negative screen results do not need further confirmation. However, before implementation, this approach needs to be confirmed in larger, prospective studies. A shortcoming of this assay is that no species identification nor determination of parasite density are possible.
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Affiliation(s)
- Anne-Sophie De Koninck
- Department of Laboratory Medicine, Ghent University Hospital (GUH), De Pintelaan 185, 9000, Ghent, Belgium
| | - Lieselotte Cnops
- Institute of Tropical Medicine (ITM) Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Mattias Hofmans
- Department of Laboratory Medicine, Ghent University Hospital (GUH), De Pintelaan 185, 9000, Ghent, Belgium
| | - Jan Jacobs
- Institute of Tropical Medicine (ITM) Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Dorien Van den Bossche
- Institute of Tropical Medicine (ITM) Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | - Jan Philippé
- Department of Laboratory Medicine, Ghent University Hospital (GUH), De Pintelaan 185, 9000, Ghent, Belgium.
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Pal V, Saxena A, Singh S, Goel AK, Kumar JS, Parida MM, Rai GP. Development of a real-time loop-mediated isothermal amplification assay for detection of Burkholderia mallei. Transbound Emerg Dis 2017. [PMID: 28649808 DOI: 10.1111/tbed.12665] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Burkholderia mallei is the aetiological agent of glanders, a highly contagious and re-emerging zoonotic disease. Early diagnosis of glanders is critically important to ensure timely treatment with appropriate antibiotics in humans, and to prevent spread of infection in animals. Molecular detection of B. mallei has always been troublesome because of its genetic similarity with Burkholderia pseudomallei, the causative agent of melioidosis. In present investigation, a set of six B. mallei-specific primers were designed and a simple, rapid, specific and sensitive real-time loop-mediated isothermal amplification (LAMP) assay was developed for detection of B. mallei. The LAMP assay could detect as low as 1 pg of B. mallei genomic DNA and 5.5 × 103 CFU/ml of B. mallei in spiked human blood. The assay was highly specific for B. mallei as it did not cross-react with other bacterial strains used in the study. The established LAMP assay is field adaptable and can be a better and viable alternative to PCR-based techniques for detection of B. mallei in glanders endemic areas with resource-limited settings.
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Affiliation(s)
- V Pal
- Microbiology Division, Defence Research and Development Establishment, Gwalior, India
| | - A Saxena
- Microbiology Division, Defence Research and Development Establishment, Gwalior, India
| | - S Singh
- Microbiology Division, Defence Research and Development Establishment, Gwalior, India
| | - A K Goel
- Biotechnology Division, Defence Research and Development Establishment, Gwalior, India
| | - J S Kumar
- Virology Division, Defence Research and Development Establishment, Gwalior, India
| | - M M Parida
- Virology Division, Defence Research and Development Establishment, Gwalior, India
| | - G P Rai
- Microbiology Division, Defence Research and Development Establishment, Gwalior, India
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Deb R, Sengar GS, Singh U, Kumar S, Alyethodi RR, Alex R, Raja TV, Das AK, Prakash B. Application of a Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cow Components Adulterated in Buffalo Milk/Meat. Mol Biotechnol 2017; 58:850-860. [PMID: 27761701 DOI: 10.1007/s12033-016-9984-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a diagnostic method for amplification of DNA with rapid and minimal equipment requirement. In the present study, we applied the LAMP assay for rapid detection of cow components adulteration in buffalo milk/meat samples. The test can be completed within around 1 h 40 min starting from DNA extraction and can be performed in water bath without requirement of thermocycler. The cow DNA in buffalo samples were identified in the developed LAMP assay by either visualizing with SYBR Green I/HNB dyes or observing the typical ladder pattern on gel electrophoresis. The test can detect up to 5 % level of cow milk/meat mixed in buffalo counterparts. Due to the simplicity and specificity, the developed LAMP test can be easily adapted in any laboratory for rapid detection of cow species identification in livestock by products.
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Affiliation(s)
- Rajib Deb
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India.
| | - Gyanendra Singh Sengar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - Umesh Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - Sushil Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - R R Alyethodi
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - Rani Alex
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - T V Raja
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - A K Das
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
| | - B Prakash
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut, Uttar Pradesh, 250 001, India
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Wang J, Zhang Y, Cui Y, Yan Y, Wang X, Wang R, Jian F, Zhang L, Ning C. A rapid, simple and sensitive loop-mediated isothermal amplification method to detect Anaplasma bovis in sheep and goats samples. Parasitol Int 2018; 67:70-3. [PMID: 28351721 DOI: 10.1016/j.parint.2017.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/17/2017] [Accepted: 03/24/2017] [Indexed: 11/22/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) technique has been widely used in detecting the nucleic acid of various pathogenic bacteria. In this study, a set of four LAMP primers was designed to specifically test Anaplasma bovis. The LAMP assay was performed at 62°C for 60min in a water bath. The specificity was confirmed by amplifying A. bovis isolate, while no cross reaction was observed with other five pathogens (Anaplasma bovis, Anaplasma phagocytophilum, Theileria luwenshuni, Babesia motasi and Schistosoma japonicum). The sensitivity of LAMP was 5×100copies/μL, 100 times more than that of conventional PCR (5×102copies/μL). Of 120 blood DNA extracted from sheep and goats field samples, 81 (67.5%), 22 (18.3%) and 43 (35.8%) were positively detected by LAMP, conventional PCR and nested PCR, respectively. The findings indicated that the developed LAMP assay is a new convenient tool for rapid and cost-effective detection of A. bovis.
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Almasi MA, Almasi G. Loop Mediated Isothermal Amplification (LAMP) for Embryo Sex Determination in Pregnant Women at Eight Weeks of Pregnancy. J Reprod Infertil 2017; 18:197-204. [PMID: 28377900 PMCID: PMC5359858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND In human, SRY (sex-determining region of the Y chromosome) is the major gene for the testis-determining factor which is found in normal XY males and in the rare XX males, and it is absent in normal XX females and many XY females. There are several methods which can indicate a male genotype by the presence of the amplified product of SRY gene. The aim of this study was to identify the SRY gene for embryo sex determination in human during pregnancy using loop mediated isothermal amplification (LAMP) method. METHODS A total of 15 blood samples from pregnant women at eight weeks of pregnancy were collected, and Plasma DNA was extracted. LAMP assay was performed using DNA obtained for detection of SRY gene. Furthermore, colorimetric LAMP assay for rapid and easy detection of SRY gene was developed. RESULTS LAMP results revealed that the positive reaction was highly specific only with samples containing XY chromosomes, while no amplification was found in samples containing XX chromosomes. A total of 15 blood samples from pregnant women were seven male embryos (46.6%) and eight female embryos (53.4%). All used visual components in the colorimetric assay could successfully make a clear distinction between positive and negative ones. CONCLUSION The LAMP assay developed in this study is a valuable tool capable of monitoring the purity and detection of SRY gene for sex determination.
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Affiliation(s)
- Mohammad Amin Almasi
- Corresponding Author: Mohammad Amin Almasi, Young Researchers and Elites Club, North Tehran Branch, Islamic Azad University, Tehran, Iran E-mail:
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