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Pioz MJ, Espinosa RL, Laguna MF, Santamaria B, Murillo AMM, Hueros ÁL, Quintero S, Tramarin L, Valle LG, Herreros P, Bellido A, Casquel R, Holgado M. A review of Optical Point-of-Care devices to Estimate the Technology Transfer of These Cutting-Edge Technologies. BIOSENSORS 2022; 12:bios12121091. [PMID: 36551058 PMCID: PMC9776401 DOI: 10.3390/bios12121091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/12/2022] [Accepted: 11/18/2022] [Indexed: 06/07/2023]
Abstract
Despite the remarkable development related to Point-of-Care devices based on optical technology, their difficulties when used outside of research laboratories are notable. In this sense, it would be interesting to ask ourselves what the degree of transferability of the research work to the market is, for example, by analysing the relation between the scientific work developed and the registered one, through patent. In this work, we provide an overview of the state-of-the-art in the sector of optical Point-of-Care devices, not only in the research area but also regarding their transfer to market. To this end, we explored a methodology for searching articles and patents to obtain an indicator that relates to both. This figure of merit to estimate this transfer is based on classifying the relevant research articles in the area and the patents that have been generated from these ones. To delimit the scope of this study, we researched the results of a large enough number of publications in the period from 2015 to 2020, by using keywords "biosensor", "optic", and "device" to obtain the most representative articles from Web of Science and Scopus. Then, we classified them according to a particular classification of the optical PoC devices. Once we had this sampling frame, we defined a patent search strategy to cross-link the article with a registered patent (by surfing Google Patents) and classified them accordingly to the categories described. Finally, we proposed a relative figure called Index of Technology Transference (IoTT), which estimates to what extent our findings in science materialized in published articles are protected by patent.
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Affiliation(s)
- María Jesús Pioz
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- University of Nebrija, C/del Hostal, Campus Berzosa, 28248 Madrid, Spain
| | - Rocío L. Espinosa
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - María Fe Laguna
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Beatriz Santamaria
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Metch, Chem & Industrial Design Engineering Department, Escuela Técnica Superior de Ingeniería y Diseño Industrial, Universidad Politécnica de Madrid, Ronda de Valencia 3, 28012 Madrid, Spain
| | - Ana María M. Murillo
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
| | - Álvaro Lavín Hueros
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Sergio Quintero
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
| | - Luca Tramarin
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
| | - Luis G Valle
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
| | - Pedro Herreros
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Alberto Bellido
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Multiplex Molecular Diagnostics S.L. C/ Munner 10, 08022 Barcelona, Spain
| | - Rafael Casquel
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Miguel Holgado
- Optics, Photonics and Biophotonics Group, Center for Biomedical Technology, Optics, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
- Group of Organ and Tissue on-a-Chip and In-Vitro Detection, Health Research Institute of the Hospital Clínico San Carlos IdISSC, C/Profesor Martín Lagos s/n, 4ª _Planta Sur, 28040 Madrid, Spain
- Department of Applied Physics and Materials Engineering, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid, C/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2. ELECTRONICS 2021. [DOI: 10.3390/electronics10172065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An artificial intelligence-assisted low-cost portable device for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is presented here. This standalone temperature-controlled device houses tubes designed for conducting reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays. Moreover, the device utilises tubes illuminated by LEDs, an in-built camera, and a small onboard computer with automated image acquisition and processing algorithms. This intelligent device significantly reduces the normal assay run time and removes the subjectivity associated with operator interpretation of colourimetric RT-LAMP results. To further improve this device’s usability, a mobile app has been integrated into the system to control the LAMP assay environment and to visually display the assay results by connecting the device to a smartphone via Bluetooth. This study was undertaken using ~5000 images produced from the ~200 LAMP amplification assays using the prototype device. Synthetic RNA and a small panel of positive and negative SARS-CoV-2 patient samples were assayed for this study. State-of-the-art image processing and artificial intelligence algorithms were applied to these images to analyse them and to select the most efficient algorithm. The template matching algorithm for image extraction and MobileNet CNN architecture for classification results provided 98.0% accuracy with an average run time of 20 min to confirm the endpoint result. Two working points were chosen based on the best compromise between sensitivity and specificity. The high sensitivity point has a sensitivity value of 99.12% and specificity value of 70.8%, while at the high specificity point, the sensitivity is 96.05% and specificity 93.59%. Furthermore, this device provides an efficient and cost-effective platform for non-health professionals to detect not only SARS-CoV-2 but also other pathogens in resource-limited laboratories, factories, airports, schools, universities, and homes.
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Development of a Low-Cost, Wireless Smart Thermostat for Isothermal DNA Amplification in Lab-On-A-Chip Devices. MICROMACHINES 2019; 10:mi10070437. [PMID: 31262090 PMCID: PMC6680506 DOI: 10.3390/mi10070437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 01/16/2023]
Abstract
Nucleic acid amplification tests (NAAT) are widely used for the detection of living organisms, recently applied in Lab-on-a-Chip (LoC) devices to make portable DNA analysis platforms. While portable LoC-NAAT can provide definitive test results on the spot, it requires specialized temperature control equipment. This work focuses on delivering a generalized low-cost, wireless smart thermostat for isothermal NAAT protocols in 2 cm × 3 cm LoC cartridges. We report on the design, prototyping, and evaluation results of our smart thermostat. The thermostat was evaluated by experimental and simulated thermal analysis using 3D printed LoC cartridges, in order to verify its applicability to various isothermal NAAT protocols. Furthermore, it was tested at the boundaries of its operating ambient temperature range as well as its battery life was evaluated. The prototype thermostat was proven functional in 20–30 °C ambient range, capable of maintaining the required reaction temperature of 12 isothermal NAAT protocols with 0.7 °C steady-state error in the worst case.
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Zopf D, Pittner A, Dathe A, Grosse N, Csáki A, Arstila K, Toppari JJ, Schott W, Dontsov D, Uhlrich G, Fritzsche W, Stranik O. Plasmonic Nanosensor Array for Multiplexed DNA-based Pathogen Detection. ACS Sens 2019; 4:335-343. [PMID: 30657315 DOI: 10.1021/acssensors.8b01073] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this research we introduce a plasmonic nanoparticle based optical biosensor for monitoring of molecular binding events. The sensor utilizes spotted gold nanoparticle arrays as sensing platform. The nanoparticle spots are functionalized with capture DNA sequences complementary to the analyte (target) DNA. Upon incubation with the target sequence, it will bind on the respectively complementary functionalized particle spot. This binding changes the local refractive index, which is detected spectroscopically as the resulting changes of the localized surface plasmon resonance (LSPR) peak wavelength. In order to increase the signal, a small gold nanoparticle label is introduced. The binding can be reversed using chemical means (10 mM HCl). It is demonstrated that multiplexed detection and identification of several fungal pathogen DNA sequences subsequently on one sensor array are possible by this approach.
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Affiliation(s)
- David Zopf
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Angelina Pittner
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - André Dathe
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena University Hospital, Friedrich-Schiller-University, Teichgraben 8, 07743 Jena, Germany
| | - Norman Grosse
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Andrea Csáki
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Kai Arstila
- University of Jyväskylä, Department of Physics and Nanoscience Center, P.O. Box 35, 40014 Jyväskylä, Finland
| | - J. Jussi Toppari
- University of Jyväskylä, Department of Physics and Nanoscience Center, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Walter Schott
- SIOS Meßtechnik GmbH, Am Vogelherd 46, 98693 Ilmenau, Germany
| | - Denis Dontsov
- SIOS Meßtechnik GmbH, Am Vogelherd 46, 98693 Ilmenau, Germany
| | - Günter Uhlrich
- ABS Gesellschaft für Automatisierung, Bildverarbeitung und Software mbH, Stockholmer Straße 3, 07747 Jena, Germany
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Ondrej Stranik
- Leibniz Institute of Photonic Technology (IPHT) Jena, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745 Jena, Germany
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LampPort: a handheld digital microfluidic device for loop-mediated isothermal amplification (LAMP). Biomed Microdevices 2019; 21:9. [DOI: 10.1007/s10544-018-0354-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Snodgrass R, Gardner A, Semeere A, Kopparthy VL, Duru J, Maurer T, Martin J, Cesarman E, Erickson D. A portable device for nucleic acid quantification powered by sunlight, a flame or electricity. Nat Biomed Eng 2018; 2:657-665. [PMID: 30906647 PMCID: PMC6425734 DOI: 10.1038/s41551-018-0286-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A decentralized approach to diagnostics can decrease the time to
treatment of infectious diseases in resource-limited settings. Yet most modern
diagnostic tools require stable electricity and are not portable. Here, we
describe a portable device for isothermal nucleic-acid quantification that can
operate with power from electricity, sunlight or a flame, and that can store
heat from intermittent energy sources, for operation when electrical power is
not available or reliable. We deployed the device in two Ugandan health clinics,
where it successfully operated through multiple power outages, with equivalent
performance when powered via sunlight or electricity. A direct comparison
between the portable device and commercial qPCR (quantitative polymerase chain
reaction) machines for samples from 71 Ugandan patients (29 of which were tested
in Uganda) for the presence of Kaposi’s sarcoma-associated herpesvirus
DNA showed 94% agreement, with the four discordant samples having the lowest
concentration of the herpesvirus DNA. The device’s flexibility in power
supply provides a needed solution for on-field diagnostics.
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Affiliation(s)
- Ryan Snodgrass
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Andrea Gardner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Jens Duru
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA
| | - Toby Maurer
- Department of Dermatology, University of California, San Francisco, CA, USA
| | - Jeffrey Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
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Vasileva Wand NI, Bonney LC, Watson RJ, Graham V, Hewson R. Point-of-care diagnostic assay for the detection of Zika virus using the recombinase polymerase amplification method. J Gen Virol 2018; 99:1012-1026. [PMID: 29897329 PMCID: PMC6171711 DOI: 10.1099/jgv.0.001083] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/05/2018] [Indexed: 01/25/2023] Open
Abstract
The sudden and explosive expansion of Zika virus (ZIKV) from the African continent through Oceania and culminating in the outbreak in South America has highlighted the importance of new rapid point-of-care diagnostic tools for the control and prevention of transmission. ZIKV infection has devastating consequences, such as neurological congenital malformations in infants born to infected mothers and Guillain-Barré syndrome in adults. Additionally, its potential for transmission through vector bites, as well as from person to person through blood transfusions and sexual contact, are important considerations for prompt diagnosis. Recombinase polymerase amplification (RPA), an isothermal method, was developed as an alternative field-applicable assay to PCR. Here we report the development of a novel ZIKV real-time reverse transcriptase RPA (RT-RPA) assay capable of detecting a range of different ZIKV strains from a variety of geographical locations. The ZIKV RT-RPA was shown to be highly sensitive, being capable of detecting as few as five copies of target nucleic acid per reaction, and suitable for use with a battery-operated portable device. The ZIKV RT-RPA demonstrated 100 % specificity and 83 % sensitivity in clinical samples. Furthermore, we determined that the ZIKV RT-RPA is a versatile assay that can be applied to crude samples, such as saliva and serum, and can be used as a vector surveillance tool on crude mosquito homogenates. Therefore, the developed ZIKV RT-RPA is a useful diagnostic tool that can be transferred to a resource-limited location, eliminating the need for a specialized and sophisticated laboratory environment and highly trained staff.
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Affiliation(s)
- Nadina I. Vasileva Wand
- Public Health England, National Infection Service, Microbiology Services Division, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Laura C. Bonney
- Public Health England, National Infection Service, Microbiology Services Division, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Robert J. Watson
- Public Health England, National Infection Service, Microbiology Services Division, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Victoria Graham
- Public Health England, National Infection Service, Microbiology Services Division, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Roger Hewson
- Public Health England, National Infection Service, Microbiology Services Division, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
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Ereku LT, Mackay RE, Craw P, Naveenathayalan A, Stead T, Branavan M, Balachandran W. RPA using a multiplexed cartridge for low cost point of care diagnostics in the field. Anal Biochem 2018; 547:84-88. [PMID: 29447855 PMCID: PMC5884738 DOI: 10.1016/j.ab.2018.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/12/2018] [Accepted: 02/09/2018] [Indexed: 10/26/2022]
Abstract
A point of care device utilising Lab-on-a-Chip technologies that is applicable for biological pathogens was designed, fabricated and tested showing sample in to answer out capabilities. The purpose of the design was to develop a cartridge with the capability to perform nucleic acid extraction and purification from a sample using a chitosan membrane at an acidic pH. Waste was stored within the cartridge with the use of sodium polyacrylate to solidify or gelate the sample in a single chamber. Nucleic acid elution was conducted using the RPA amplification reagents (alkaline pH). Passive valves were used to regulate the fluid flow and a multiplexer was designed to distribute the fluid into six microchambers for amplification reactions. Cartridges were produced using soft lithography of silicone from 3D printed moulds, bonded to glass substrates. The isothermal technique, RPA is employed for amplification. This paper shows the results from two separate experiments: the first using the RPA control nucleic acid, the second showing successful amplification from Chlamydia Trachomatis. Endpoint analysis conducted for the RPA analysis was gel electrophoresis that showed 143 base pair DNA was amplified successfully for positive samples whilst negative samples did not show amplification. End point analysis for Chlamydia Trachomatis samples was fluorescence detection that showed successful detection of 1 copy/μL and 10 copies/μL spiked in a MES buffer.
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Affiliation(s)
- Luck Tosan Ereku
- Centre for Electronic Systems Research, Electronic and Computer Engineering, CEDPS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
| | - Ruth E Mackay
- Mechanical, Aerospace and Civil Engineering, CEDPS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK.
| | - Pascal Craw
- Oceans and Atmosphere Flagship, Commonwealth Science and Industrial Research Organisation (CSIRO), Hobart, Tasmania 7001, Australia
| | - Angel Naveenathayalan
- Mechanical, Aerospace and Civil Engineering, CEDPS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
| | - Thomas Stead
- Centre for Electronic Systems Research, Electronic and Computer Engineering, CEDPS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
| | - Manorharanehru Branavan
- Centre for Electronic Systems Research, Electronic and Computer Engineering, CEDPS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
| | - Wamadeva Balachandran
- Centre for Electronic Systems Research, Electronic and Computer Engineering, CEDPS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK
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Barreda-García S, Miranda-Castro R, de-Los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Helicase-dependent isothermal amplification: a novel tool in the development of molecular-based analytical systems for rapid pathogen detection. Anal Bioanal Chem 2017; 410:679-693. [PMID: 28932883 PMCID: PMC7079856 DOI: 10.1007/s00216-017-0620-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/18/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022]
Abstract
Highly sensitive testing of nucleic acids is essential to improve the detection of pathogens, which pose a major threat for public health worldwide. Currently available molecular assays, mainly based on PCR, have a limited utility in point-of-need control or resource-limited settings. Consequently, there is a strong interest in developing cost-effective, robust, and portable platforms for early detection of these harmful microorganisms. Since its description in 2004, isothermal helicase-dependent amplification (HDA) has been successfully applied in the development of novel molecular-based technologies for rapid, sensitive, and selective detection of viruses and bacteria. In this review, we highlight relevant analytical systems using this simple nucleic acid amplification methodology that takes place at a constant temperature and that is readily compatible with microfluidic technologies. Different strategies for monitoring HDA amplification products are described. In addition, we present technological advances for integrating sample preparation, HDA amplification, and detection. Future perspectives and challenges toward point-of-need use not only for clinical diagnosis but also in food safety testing and environmental monitoring are also discussed. Expanding the analytical toolbox for the detection of DNA sequences specific of pathogens with isothermal helicase dependent amplification (HDA) ![]()
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Affiliation(s)
- Susana Barreda-García
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - Rebeca Miranda-Castro
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | | | - Arturo J Miranda-Ordieres
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - María Jesús Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain.
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Zhang L, Ding B, Chen Q, Feng Q, Lin L, Sun J. Point-of-care-testing of nucleic acids by microfluidics. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.013] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Basha IHK, Ho ETW, Yousuff CM, Hamid NHB. Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies. MICROMACHINES 2017; 8:E266. [PMID: 30400456 PMCID: PMC6190060 DOI: 10.3390/mi8090266] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/30/2017] [Accepted: 07/16/2017] [Indexed: 12/21/2022]
Abstract
Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
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Affiliation(s)
- Ismail Hussain Kamal Basha
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Eric Tatt Wei Ho
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Caffiyar Mohamed Yousuff
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Nor Hisham Bin Hamid
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
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New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings. Eur J Clin Microbiol Infect Dis 2017; 36:1717-1731. [PMID: 28573472 DOI: 10.1007/s10096-017-3013-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/08/2017] [Indexed: 12/20/2022]
Abstract
Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification. Access to electricity is often difficult in resource-limited areas, so the amplification step needs to be equipment-free. Consequently, the reaction has to be isothermal to alleviate the need for a thermocycler. LAMP, NASBA, HDA, and RPA are examples of the technologies available. Nucleic acid detection techniques are currently based on fluorescence, colorimetry, or chemiluminescence. For point-of-care diagnostics, the results should be readable with the naked eye. Nowadays, interpretation and communication of results to health professionals could rely on a smartphone, used as a telemedicine device. The major challenge of creating an "all-in-one" diagnostic test involves the design of an optimal solution and a sequence for each analytical step, as well as combining the execution of all these steps on a single device. This review provides an overview of available materials and technologies which seem to be adapted to point-of-care nucleic acid-based diagnosis, in low-resource areas.
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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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Nicolini AM, McCracken KE, Yoon JY. Future developments in biosensors for field-ready Zika virus diagnostics. J Biol Eng 2017; 11:7. [PMID: 28127399 PMCID: PMC5260080 DOI: 10.1186/s13036-016-0046-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/27/2016] [Indexed: 12/11/2022] Open
Abstract
Since early reports of the recent Zika virus outbreak in May 2015, much has been learned and discussed regarding Zika virus infection and transmission. However, many opportunities still remain for translating these findings into field-ready sensors and diagnostics. In this brief review, we discuss current diagnostic methods, consider the prospects of translating other flavivirus biosensors directly to Zika virus sensing, and look toward the future developments needed for high-sensitivity and high-specificity biosensors to come.
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Affiliation(s)
- Ariana M. Nicolini
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721 USA
| | - Katherine E. McCracken
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
| | - Jeong-Yeol Yoon
- Biomedical Engineering Graduate Interdisciplinary Program and Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721 USA
- Department of Agricultural and Biosystems Engineering, The University of Arizona, Tucson, AZ 85721 USA
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Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA. Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Front Microbiol 2016; 7:1321. [PMID: 27667984 PMCID: PMC5017214 DOI: 10.3389/fmicb.2016.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/10/2016] [Indexed: 01/09/2023] Open
Abstract
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
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Affiliation(s)
- Mina Bashir
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Division of Endocrinology and Diabetology, Medical University of GrazGraz, Austria
| | - Mahjabeen Ahmed
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Department of Biological Sciences, California State Polytechnic UniversityPomona, CA, USA
| | - Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Doina Ciobanu
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Thomas R Pieber
- Division of Endocrinology and Diabetology, Medical University of Graz Graz, Austria
| | - Parag A Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, USA
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Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J Microbiol Methods 2015; 119:223-7. [PMID: 26554941 DOI: 10.1016/j.mimet.2015.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/04/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used for point-of-care nucleic acid based diagnostics. LAMP can be monitored in real-time by measuring the increase in fluorescence of DNA binding dyes. However, there is little information comparing the effect of various fluorescent dyes on signal to noise ratio (SNR) or threshold time (Tt). This information is critical for implementation with field deployable diagnostic tools that require small, low power consumption, robust, and inexpensive optical components with reagent saving low volume reactions. In this study, SNR and Tt during real-time LAMP was evaluated with eleven fluorescent dyes. Of all dyes tested, SYTO-82, SYTO-84, and SYTOX Orange resulted in the shortest Tt, and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10 min, 10 copies of Giardia intestinalis in ~20 min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15 min. Results demonstrate that reaction efficiency depends on both dye type and concentration and the selected polymerase. The optimized protocol was evaluated in the Gene-Z™ device, a hand-held battery operated platform characterized via simple and low cost optics, and a multiple assay microfluidic chip with micron volume reaction wells. Compared to the more conventional intercalating dye (SYBR Green), reliable amplification was only observed in the Gene-Z™ when using higher concentrations of SYTO-81.
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