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Feddema JJ, Fernald KDS, Keijser BJF, Kieboom J, van de Burgwal LHM. Commercial Opportunity or Addressing Unmet Needs-Loop-Mediated Isothermal Amplification (LAMP) as the Future of Rapid Diagnostic Testing? Diagnostics (Basel) 2024; 14:1845. [PMID: 39272630 PMCID: PMC11394392 DOI: 10.3390/diagnostics14171845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 09/15/2024] Open
Abstract
Loop-Mediated Isothermal Amplification (LAMP) technology is emerging as a rapid pathogen testing method, potentially challenging the RT-PCR "gold standard". Despite recent advancements, LAMP's widespread adoption remains limited. This study provides a comprehensive market overview and assesses future growth prospects to aid stakeholders in strategic decision-making and policy formulation. Using a dataset of 1134 LAMP patent documents, we analyzed lifecycle and geographic distribution, applicant profiles, CPC code classifications, and patent claims. Additionally, we examined clinical developments from 21 curated clinical trials, focusing on trends, geographic engagement, sponsor types, and the conditions and pathogens investigated. Our analysis highlights LAMP's potential as a promising rapid pathogen testing alternative, especially in resource-limited areas. It also reveals a gap between clinical research, which targets bacterial and parasitic diseases like malaria, leishmaniasis, and tuberculosis, and basic research and commercial efforts that prioritize viral diseases such as SARS-CoV-2 and influenza. European stakeholders emphasize the societal impact of addressing unmet needs in resource-limited areas, while American and Asian organizations focus more on research, innovation, and commercialization.
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Affiliation(s)
- Jelle J Feddema
- Athena Institute, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Kenneth D S Fernald
- Athena Institute, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Bart J F Keijser
- TNO Healthy Living and Work, Microbiology and Systems Biology, Sylviusweg 71, 2333 BE Leiden, The Netherlands
| | - Jasper Kieboom
- TNO Healthy Living and Work, Microbiology and Systems Biology, Sylviusweg 71, 2333 BE Leiden, The Netherlands
| | - Linda H M van de Burgwal
- Athena Institute, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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2
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Zhuang L, Gong J, Zhang P, Zhang D, Zhao Y, Yang J, Liu G, Zhang Y, Shen Q. Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications. DISCOVER NANO 2024; 19:124. [PMID: 39105889 PMCID: PMC11303641 DOI: 10.1186/s11671-024-04075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, People's Republic of China
| | - Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Guofang Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing, 211102, People's Republic of China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212400, People's Republic of China.
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Fu S, Jiang Y, Qin X, Yang T, Chen S, Yang X, Zhang W, Qu Y, Man C. Electricity-free amplification and visual detection of Cronobacter species in powdered infant formula. J Dairy Sci 2020; 103:6882-6893. [PMID: 32505404 DOI: 10.3168/jds.2019-17661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/09/2020] [Indexed: 01/24/2023]
Abstract
Due to the lack of electricity and thermostatic instruments in certain settings for convenient detection of Cronobacter species in powdered infant formula (PIF), a novel investigation was conducted to establish an electricity-free visual detection system for rapid detection of Cronobacter species in PIF. This system included a portable electricity-free heater that could use the exothermic reaction of calcium oxide and water and 3 kinds of phase change materials to supply 3 constant temperatures for immunomagnetic separation, DNA extraction, and loop-mediated isothermal amplification assay. Meanwhile, the amplified reaction combined with hydroxynaphthol blue could achieve rapid visual detection. Primers designed based on the 16S-23S ribosomal RNA internal transcribed spacer were used in loop-mediated isothermal amplification to specifically monitor Cronobacter species, and the detection limit can reach 4.2 × 102 cfu/g in PIF by an electricity-free heater in 2 h 30 min. Moreover, 2 h of pre-enrichment was necessary when the level of the PIF samples with Cronobacter spp. was 100 cfu/g. The stability of the system was evaluated in ambient temperature at 4°C, 25°C, and 37°C. The results suggested that the electricity-free heater can maintain 3 constant temperatures to support different processes. Therefore, this amplification and visual system is applicable for use in many fields for rapid and specific detection of Cronobacter species in PIF.
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Affiliation(s)
- Shiqian Fu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Tao Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Sihan Chen
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Wei Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanyan Qu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China.
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4
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Grabicoski EMG, Jaccoud-Filho DDS, Lee D, Henneberg L, Pileggi M. Real-Time Quantitative and Ion-Metal Indicator LAMP-Based Assays for Rapid Detection of Sclerotinia sclerotiorum. PLANT DISEASE 2020; 104:1514-1526. [PMID: 32105572 DOI: 10.1094/pdis-07-19-1455-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum is one of the most devastating and cosmopolitan plant pathogens. Rapid detection of S. sclerotiorum can provide growers an advantage in knowing what control measures should be taken to minimize crop damage and financial losses caused by it. Loop-mediated isothermal amplification (LAMP) is a fast, sensitive, and specific nucleic acid amplification method that does not require a thermal cycler. This study aimed to develop a LAMP-based assay for the specific detection of S. sclerotiorum (Ss-LAMP). A real-time quantitative LAMP reaction (Ss-qLAMP) and a calcein ion indicator-based LAMP reaction (Ss-cLAMP) were designed, optimized, and tested on fungi, plant, and soil samples. The Ss-LAMP reactions were very specific and sensitive. Applying the artificially inoculated soil samples with DNA purified by five protocols in the Ss-qLAMP reaction, it was possible to detect and quantify the pathogen DNA, regardless of the extraction protocol. Naturally infected soybean tissues had the pathogen detected by Ss-cLAMP directly in the reaction tube with no DNA extraction requirement. The assays should be applicable for many types of samples, such as soil, spore traps, and plant tissues from several crops, with no requirement for DNA extraction. The Ss-LAMP reactions took less than 1 h to complete, and they can be made directly in the field with real-time quantitative results (Ss-qLAMP) or qualitative naked-eye visual results (Ss-cLAMP). Results were obtained with 10 pg of DNA or 10 ng of crude mycelium, suggesting a detection limit close to a single DNA copy. Ss-LAMP reactions will allow rapid and accurate diagnosis of S. sclerotiorum and assist in pathogen management and control.
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Affiliation(s)
- Edilaine Mauricia Gelinski Grabicoski
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
- State University of Maringá, Department of Agronomy, Jardim Universitário, 87020-900, Maringá, PR, Brazil
| | - David de Souza Jaccoud-Filho
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| | - David Lee
- National Institute of Agricultural Botany, Cambridge CB3 0LE, United Kingdom
| | - Luciane Henneberg
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| | - Marcos Pileggi
- State University of Ponta Grossa, Department of Structural, Molecular and Genetic Biology, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
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5
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Reduced False Positives and Improved Reporting of Loop-Mediated Isothermal Amplification using Quenched Fluorescent Primers. Sci Rep 2019; 9:7400. [PMID: 31089184 PMCID: PMC6517417 DOI: 10.1038/s41598-019-43817-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 11/08/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as an alternative to PCR based methods. There are numerous reported techniques to detect the LAMP amplification including turbidity, bioluminescence and intercalating fluorescent dyes. In this report we show that quenched fluorescent labels on various LAMP primers can be used to quantify and detect target DNA molecules down to single copy numbers. By selecting different fluorophores, this method can be simply multiplexed. Moreover this highly specific LAMP detection technique can reduce the incidence of false positives originating from mispriming events. Attribution of these events to particular primers will help inform and improve LAMP primer design.
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6
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Goertz JP, Colvin KM, Lippe AB, Daristotle JL, Kofinas P, White IM. Multistage Chemical Heating for Instrument-Free Biosensing. ACS APPLIED MATERIALS & INTERFACES 2018; 10:33043-33048. [PMID: 30207445 DOI: 10.1021/acsami.8b11611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Improving the portability of diagnostic medicine is crucial for alleviating global access-to-care deficiencies. This requires not only designing devices that are small and lightweight, but also autonomous and independent of electricity. Here, we present a strategy for conducting automated multistep diagnostic assays using chemically generated, passively regulated heat. Ligation and polymerization reagents for rolling circle amplification of nucleic acids are separated by meltable phase-change partitions, thus replacing precise manual reagent additions with automated partition melting. To actuate these barriers and individually initiate the various steps of the reaction, field ration heaters exothermically generate heat in a thermos, whereas fatty acids embedded in a carbonaceous matrix passively buffer the temperature around their melting points. Achieving multistage temperature profiles extend the capability of instrument-free diagnostic devices and improve the portability of reaction automation systems built around phase-change partitions.
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7
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The application of loop-mediated isothermal amplification (LAMP) assays for the rapid diagnosis of food-borne mycotoxigenic fungi. Curr Opin Food Sci 2018. [DOI: 10.1016/j.cofs.2018.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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8
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Yang Q, Domesle KJ, Ge B. Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions. Foodborne Pathog Dis 2018; 15:309-331. [PMID: 29902082 PMCID: PMC6004089 DOI: 10.1089/fpd.2018.2445] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed.
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Affiliation(s)
- Qianru Yang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
| | - Kelly J Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
| | - Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
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9
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Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens. Int J Mol Sci 2018; 19:ijms19020524. [PMID: 29425124 PMCID: PMC5855746 DOI: 10.3390/ijms19020524] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.
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10
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An integrated versatile lab-on-a-chip platform for the isolation and nucleic acid-based detection of pathogens. Future Sci OA 2017; 3:FSO177. [PMID: 28670469 PMCID: PMC5481810 DOI: 10.4155/fsoa-2016-0088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/18/2017] [Indexed: 11/29/2022] Open
Abstract
Aim: Processing of the samples in molecular diagnostics is complex and labor-intensive. An integrated and automated platform for sample preparation and nucleic acid-based detection can significantly relieve this burden for the users. Results: We present a prototype of a versatile and integrated platform for the detection of pathogens in various liquid media. We describe a proof-of-concept for the integrated isolation of bacteria, cell lysis with optional DNA extraction, DNA amplification and detection in two different reactions, loop-mediated isothermal amplification and PCR, on a single microfluidic platform. Conclusion: The platform enables the transition from large sample volume to microfluidic format. The design and open interface enable its versatile application for various nucleic acid-based assays, from simple to complex setups. DNA-based detection of the pathogens in liquid samples demands many complex steps, various pieces of equipment, and experienced personnel. We developed and demonstrated a platform that can perform these steps automatically on a single instrument. This can enable molecular diagnostics in the places and situations where it was not possible before.
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11
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Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C. Miniaturized devices for point of care molecular detection of HIV. LAB ON A CHIP 2017; 17:382-394. [PMID: 28092381 PMCID: PMC5285266 DOI: 10.1039/c6lc01239f] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The HIV pandemic affects 36.7 million people worldwide, predominantly in resource-poor settings. Nucleic acid-based molecular detection of HIV plays a significant role in antiretroviral treatment monitoring for HIV patients, as well as diagnosis of HIV infection in infants. Currently available molecular diagnostic methods are complex, time-consuming and relatively expensive, thus limiting their use in resource-poor settings. Recent advances in microfluidics technology have made possible low-cost integrated miniaturized devices for molecular detection and quantification of HIV at the point of care. We review recent technical advances in molecular testing of HIV using microfluidic technology, with a focus on assays based on isothermal nucleic acid amplification. Microfluidic components for sample preparation, isothermal amplification and result detection are discussed and compared. We also discuss the challenges and future directions for developing an integrated "sample-to-result" microfluidic platform for HIV molecular detection.
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Affiliation(s)
- Michael Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Robert Gross
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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12
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Liao SC, Peng J, Mauk MG, Awasthi S, Song J, Friedman H, Bau HH, Liu C. Smart Cup: A Minimally-Instrumented, Smartphone-Based Point-of-Care Molecular Diagnostic Device. SENSORS AND ACTUATORS. B, CHEMICAL 2016; 229:232-238. [PMID: 26900258 PMCID: PMC4756427 DOI: 10.1016/j.snb.2016.01.073] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleic acid amplification-based diagnostics offer rapid, sensitive, and specific means for detecting and monitoring the progression of infectious diseases. However, this method typically requires extensive sample preparation, expensive instruments, and trained personnel. All of which hinder its use in resource-limited settings, where many infectious diseases are endemic. Here, we report on a simple, inexpensive, minimally-instrumented, smart cup platform for rapid, quantitative molecular diagnostics of pathogens at the point of care. Our smart cup takes advantage of water-triggered, exothermic chemical reaction to supply heat for the nucleic acid-based, isothermal amplification. The amplification temperature is regulated with a phase-change material (PCM). The PCM maintains the amplification reactor at a constant temperature, typically, 60-65°C, when ambient temperatures range from 12 to 35°C. To eliminate the need for an optical detector and minimize cost, we use the smartphone's flashlight to excite the fluorescent dye and the phone camera to record real-time fluorescence emission during the amplification process. The smartphone can concurrently monitor multiple amplification reactors and analyze the recorded data. Our smart cup's utility was demonstrated by amplifying and quantifying herpes simplex virus type 2 (HSV-2) with LAMP assay in our custom-made microfluidic diagnostic chip. We have consistently detected as few as 100 copies of HSV-2 viral DNA per sample. Our system does not require any lab facilities and is suitable for use at home, in the field, and in the clinic, as well as in resource-poor settings, where access to sophisticated laboratories is impractical, unaffordable, or nonexistent.
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Affiliation(s)
- Shih-Chuan Liao
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan, ROC
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sita Awasthi
- Infectious Diseases Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Harvey Friedman
- Infectious Diseases Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Corresponding author: Dr. Changchun Liu, Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, 216 Towne Building, 220 South 33 St., Philadelphia, Pennsylvania 19104-6315, USA, Phone: (215)898-1380,
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13
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Schwenkbier L, Pollok S, Rudloff A, Sailer S, Cialla-May D, Weber K, Popp J. Non-instrumented DNA isolation, amplification and microarray-based hybridization for a rapid on-site detection of devastating Phytophthora kernoviae. Analyst 2015; 140:6610-8. [PMID: 26331157 DOI: 10.1039/c5an00855g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A rapid and simple instrument-free detection system was developed for the identification of the plant pathogen Phytophthora kernoviae (P. kernoviae). The on-site operable analysis steps include magnetic particle based DNA isolation, helicase-dependent amplification (HDA) and chip-based DNA hybridization. The isothermal approach enabled the convenient amplification of the yeast GTP-binding protein (Ypt1) target gene in a miniaturized HDA-zeolite-heater (HZH) by an exothermic reaction. The amplicon detection on the chip was performed under room temperature conditions – either by successive hybridization and enzyme binding or by a combined step. A positive signal is displayed by enzymatically generated silver nanoparticle deposits, which serve as robust endpoint signals allowing an immediate visual readout. The hybridization assay enabled the reliable detection of 10 pg μL(-1) target DNA. This is the first report of an entirely electricity-free, field applicable detection approach for devastating Phytophthora species, exemplarily shown for P. kernoviae.
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Affiliation(s)
- Lydia Schwenkbier
- Leibniz Institute of Photonic Technology (IPHT Jena), Jenaer BioChip Initiative, Albert-Einstein-Straße 9, 07745 Jena, Germany
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14
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Kubota R, Jenkins DM. Real-time duplex applications of loop-mediated AMPlification (LAMP) by assimilating probes. Int J Mol Sci 2015; 16:4786-99. [PMID: 25741765 PMCID: PMC4394449 DOI: 10.3390/ijms16034786] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 12/15/2022] Open
Abstract
Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.
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Affiliation(s)
- Ryo Kubota
- Diagenetix, Inc., Honolulu, HI 96822, USA.
- Department of Molecular Biosciences and Bioengineering, University of Hawai'.i, Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA.
| | - Daniel M Jenkins
- Department of Molecular Biosciences and Bioengineering, University of Hawai'.i, Mānoa, 1955 East-West Road, Honolulu, HI 96822, USA.
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Abstract
We describe design parameters for the synthesis and analytical application of a label-free RNA molecular beacon, termed Spinach.ST. The RNA aptamer Spinach fluoresces upon binding the small-molecule fluorophore DFHBI ((Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1H-imidazol-5(4H)-one). Spinach has been reengineered by extending its 5'- and 3'-ends to create Spinach.ST, which is predicted to fold into an inactive conformation that fails to bind DHFBI. Hybridization of a trigger oligonucleotide to a designed toehold on Spinach.ST initiates toehold-mediated strand displacement and restores the DFHBI-binding, fluorescence-enhancing conformation of Spinach. The versatile Spinach.ST sensor can detect DNA or RNA trigger sequences and can readily distinguish single-nucleotide mismatches in the trigger toehold. Primer design techniques are described that augment amplicons produced by enzymatic amplification with Spinach.ST triggers. Interaction between these triggers and Spinach.ST molecular beacons leads to the real-time, sequence-specific quantitation of these amplicons. The use of Spinach.ST with isothermal amplification reactions such as nucleic acid sequence-based amplification (NASBA) may enable point-of-care applications. The same design principles could also be used to adapt Spinach reporters to the assay of nonnucleic acid analytes in trans.
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