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Ahortor EK, Gwira TM, Mahazu S, Erber AC, Ablordey A. Evaluation of an electricity-independent method for IS2404 Loop-mediated isothermal amplification (LAMP) diagnosis of Buruli ulcer in resource-limited settings. PLoS Negl Trop Dis 2024; 18:e0012338. [PMID: 39141676 DOI: 10.1371/journal.pntd.0012338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/04/2024] [Indexed: 08/16/2024] Open
Abstract
INTRODUCTION Buruli ulcer (BU) caused by Mycobacterium ulcerans (MU) is a devastating necrotic skin disease. PCR, recommended for confirmation of BU by WHO, requires an adequately equipped laboratory, therefore often delaying timely diagnosis and treatment of BU patients in remote settings. Loop-mediated isothermal amplification (LAMP) is a PCR-based protocol for isothermal amplification of DNA that has been suggested for diagnosis of BU in low-resource settings. STUDY AIMS AND METHODS This is an exploratory diagnostic test evaluation study, with an embedded qualitative sub-study. Its aims are two-fold: First, to evaluate a simple rapid syringe-based DNA extraction method (SM) in comparison with a more elaborate conventional DNA extraction method (CM), followed by a LAMP assay targeting IS2404 for the detection of MU, either using a commercially available pocket warmer (pw) or a heat block (hb) for incubation. Second, to complement this by exploring the diagnostic workflow for BU at a community-based health centre in an endemic area in rural Ghana as an example of a potential target setting, using interviews with researchers and health care workers (HCWs). Diagnostic test evaluation results are discussed in relation to the requirements of a target product profile (TPP) for BU diagnosis and the target setting. RESULTS A protocol using SM for DNA extraction followed by IS2404 PCR (IS2404 PCRSM) was able to identify MU DNA in 73 out of 83 BU clinical specimens submitted for diagnosis. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of IS2404 PCRSM were 90.12%, 100%, 100% and 65.21% respectively, as compared to the reference standard IS2404 PCR in combination with a standard extraction protocol for mycobacterial DNA. Evaluation of the LAMP assay on 64 SM DNA extracts showed a sensitivity, specificity, PPV and NPV of 83.6%, 100%, 100% and 50%, respectively, using either pocket warmer (pwLAMPSM) or heat block (hbLAMPSM) for incubation of the reaction, as compared to the same reference standard. The limit of detection of pwLAMPSM was found to be 30 copies of the IS2404 target. Interview findings explored barriers to BU diagnosis and treatment, including perceptions of the disease, costs, and availability of transport. Participants confirmed that a diagnosis at the PoC, in addition to screening based on clinical criteria, would be advantageous in order to prevent delays and loss to follow-up. DISCUSSION AND CONCLUSIONS The high diagnostic and analytic accuracy of the pwLAMP, evaluated by us in combination with a syringe-based DNA extraction method, supports its potential use for the rapid detection of MU in suspected BU samples at the community or primary health care level without reliable electricity supply. Further optimization needs include a lysis buffer, evaluation directly at the PoC and/or other sites, assessing staff training requirements and quality control.
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Affiliation(s)
- Evans K Ahortor
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- School of Pharmacy and Pharmaceutical Science, Cardiff University, Cardiff, Wales, United Kingdom
| | - Theresa Manful Gwira
- Department of Biochemistry, Cell and Molecular Biology & West African Centre for Cell Biology of Infectious Pathogens, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Samiratu Mahazu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Astrid C Erber
- Department of Epidemiology, Centre for Public Health, Medical University of Vienna, Vienna, Austria
- Infectious Diseases Data Observatory, Oxford, United Kingdom
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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2
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Pan CY, Kijamnajsuk P, Chen JJ. Portable loop-mediated isothermal amplification device with spectrometric detection for rapid pathogen identification. Anal Biochem 2024; 694:115615. [PMID: 39002745 DOI: 10.1016/j.ab.2024.115615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
With the rise in extreme weather due to global warming, coupled with globalization facilitating the spread of infectious diseases, there's a pressing need for portable testing platforms offering simplicity, low cost, and remote transmission, particularly beneficial in resource-limited and non-urban areas. We have developed a portable device using loop-mediated isothermal amplification (LAMP) with spectrometric detection to identify Salmonella Typhimurium DNA. The device utilizes the LinkIt 7697 microcontroller and a microspectrometer to capture and transmit spectral signals in real-time, allowing for improved monitoring and analysis of the reaction progress. We built a hand-held box containing a microspectrometer, thermoelectric cooler, ultraviolet LED, disposable reaction tube, and homemade thermal module, all powered by rechargeable batteries. Additionally, we conducted thorough experiments to ensure temperature accuracy within 1 °C under thermal control, developed a heating module with a LinkIt 7697 IoT development board to heat the DNA mixture to the reaction temperature within 3 min, and integrated foam insulation and a 3D-printed frame to enhance the device's thermal stability. We successfully demonstrated the amplification of Salmonella Typhimurium DNA with an impressive sensitivity of 2.83 × 10-4 ng/μL. A remote webpage interface allows for monitoring the temperature and fluorescence during the LAMP process, improving usability. This portable LAMP device with real-time detection offers a cost-effective solution for detecting Salmonella Typhimurium in food products. Its unique design and capabilities make it a promising tool for ensuring food safety.
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Affiliation(s)
- Chun Yu Pan
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
| | - Puchong Kijamnajsuk
- Department of Physics, Kasetsart University, 50 Ngamwongwan Rd, Lat Yao, Chatuchak, Bangkok, 10900, Thailand.
| | - Jyh Jian Chen
- Department of Biomechatronics Engineering, National Pingtung University of Science and Technology, 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
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3
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Zou Y, Mason MG, Botella JR. A low-cost, portable, dual-function readout device for amplification-based point-of-need diagnostics. Appl Environ Microbiol 2023; 89:e0090223. [PMID: 38047632 PMCID: PMC10734478 DOI: 10.1128/aem.00902-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/25/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE The first critical step in timely disease management is rapid disease identification, which is ideally on-site detection. Of all the technologies available for disease identification, nucleic acid amplification-based diagnostics are often used due to their specificity, sensitivity, adaptability, and speed. However, the modules to interpret amplification results rapidly, reliably, and easily in resource-limited settings at point-of-need (PON) are in high demand. Therefore, we developed a portable, low-cost, and easy-to-perform device that can be used for amplification readout at PON to enable rapid yet reliable disease identification by users with minimal training.
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Affiliation(s)
- Yiping Zou
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
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4
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Malpartida-Cardenas K, Moser N, Ansah F, Pennisi I, Ahu Prah D, Amoah LE, Awandare G, Hafalla JCR, Cunnington A, Baum J, Rodriguez-Manzano J, Georgiou P. Sensitive Detection of Asymptomatic and Symptomatic Malaria with Seven Novel Parasite-Specific LAMP Assays and Translation for Use at Point-of-Care. Microbiol Spectr 2023; 11:e0522222. [PMID: 37158750 PMCID: PMC10269850 DOI: 10.1128/spectrum.05222-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
Human malaria is a life-threatening parasitic disease with high impact in the sub-Saharan Africa region, where 95% of global cases occurred in 2021. While most malaria diagnostic tools are focused on Plasmodium falciparum, there is a current lack of testing non-P. falciparum cases, which may be underreported and, if undiagnosed or untreated, may lead to severe consequences. In this work, seven species-specific loop-mediated isothermal amplification (LAMP) assays were designed and evaluated against TaqMan quantitative PCR (qPCR), microscopy, and enzyme-linked immunosorbent assays (ELISAs). Their clinical performance was assessed with a cohort of 164 samples of symptomatic and asymptomatic patients from Ghana. All asymptomatic samples with a parasite load above 80 genomic DNA (gDNA) copies per μL of extracted sample were detected with the Plasmodium falciparum LAMP assay, reporting 95.6% (95% confidence interval [95% CI] of 89.9 to 98.5) sensitivity and 100% (95% CI of 87.2 to 100) specificity. This assay showed higher sensitivity than microscopy and ELISA, which were 52.7% (95% CI of 39.7 to 67%) and 67.3% (95% CI of 53.3 to 79.3%), respectively. Nine samples were positive for P. malariae, indicating coinfections with P. falciparum, which represented 5.5% of the tested population. No samples were detected as positive for P. vivax, P. ovale, P. knowlesi, or P. cynomolgi by any method. Furthermore, translation to the point-of-care was demonstrated with a subcohort of 18 samples tested locally in Ghana using our handheld lab-on-chip platform, Lacewing, showing comparable results to a conventional fluorescence-based instrument. The developed molecular diagnostic test could detect asymptomatic malaria cases, including submicroscopic parasitemia, and it has the potential to be used for point-of-care applications. IMPORTANCE The spread of Plasmodium falciparum parasites with Pfhrp2/3 gene deletions presents a major threat to reliable point-of-care diagnosis with current rapid diagnostic tests (RDTs). Novel molecular diagnostics based on nucleic acid amplification are needed to address this liability. In this work, we overcome this challenge by developing sensitive tools for the detection of Plasmodium falciparum and non-P. falciparum species. Furthermore, we evaluate these tools with a cohort of symptomatic and asymptomatic malaria patients and test a subcohort locally in Ghana. The findings of this work could lead to the implementation of DNA-based diagnostics to fight against the spread of malaria and provide reliable, sensitive, and specific diagnostics at the point of care.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Nicolas Moser
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Julius Clemence R. Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- School of Biomedical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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5
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Pallares-Rusiñol A, Bernuz M, Moura SL, Fernández-Senac C, Rossi R, Martí M, Pividori MI. Advances in exosome analysis. Adv Clin Chem 2022; 112:69-117. [PMID: 36642486 DOI: 10.1016/bs.acc.2022.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is growing demand for novel biomarkers that detect early stage disease as well as monitor clinical management and therapeutic strategies. Exosome analysis could provide the next advance in attaining that goal. Exosomes are membrane encapsulated biologic nanometric-sized particles of endocytic origin which are released by all cell types. Unfortunately, exosomes are exceptionally challenging to characterize with current technologies. Exosomes are between 30 and 200nm in diameter, a size that makes them out of the sensitivity range to most cell-oriented sorting or analysis platforms, i.e., traditional flow cytometers. The most common methods for targeting exosomes to date typically involve purification followed by the characterization and the specific determination of their cargo. The whole procedure is time consuming, requiring thus skilled personnel as well as laboratory facilities and benchtop instrumentation. The most relevant methodology for exosome isolation, characterization and quantification is addressed in this chapter, including the most up-to-date approaches to explore the potential usefulness of exosomes as biomarkers in liquid biopsies and in advanced nanomedicine.
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Affiliation(s)
- Arnau Pallares-Rusiñol
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mireia Bernuz
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Silio Lima Moura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Carolina Fernández-Senac
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Rosanna Rossi
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Mercè Martí
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - María Isabel Pividori
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain; Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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6
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Chen W, Wang W, Wang X, Li Z, Wu K, Li X, Li Y, Yi L, Zhao M, Ding H, Fan S, Chen J. Advances in the differential molecular diagnosis of vesicular disease pathogens in swine. Front Microbiol 2022; 13:1019876. [PMID: 36386633 PMCID: PMC9641196 DOI: 10.3389/fmicb.2022.1019876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV), Senecavirus A (SVA) and swine vesicular disease virus (SVDV) are members of the family Picornaviridae, which can cause similar symptoms - vesicular lesions in the tissues of the mouth, nose, feet, skin and mucous membrane of animals. Rapid and accurate diagnosis of these viruses allows for control measures to prevent the spread of these diseases. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR are traditional and reliable methods for pathogen detection, while their amplification reaction requires a thermocycler. Isothermal amplification methods including loop-mediated isothermal amplification and recombinase polymerase amplification developed in recent years are simple, rapid and do not require specialized equipment, allowing for point of care diagnostics. Luminex technology allows for simultaneous detection of multiple pathogens. CRISPR-Cas diagnostic systems also emerging nucleic acid detection technologies which are very sensitivity and specificity. In this paper, various nucleic acid detection methods aimed at vesicular disease pathogens in swine (including FMDV, SVA and SVDV) are summarized.
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Affiliation(s)
- Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Weijun Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xinyan Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
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7
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Xie R, Gao J, Li H, Yu W, Zhang J, Wang N, Chen A. Rapid detection of Arothron species by real-time fluorescence and colorimetric loop-mediated isothermal amplification assays targeting the mitochondrial cytochrome b gene. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Mota DS, Guimarães JM, Gandarilla AMD, Filho JCBS, Brito WR, Mariúba LAM. Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications. Can J Microbiol 2022; 68:383-402. [PMID: 35394399 DOI: 10.1139/cjm-2021-0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.
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Affiliation(s)
- D S Mota
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J M Guimarães
- Centro Multiusuário para Análises de Fenômenos Biomédicos, Universidade do Estado do Amazonas (UEA), Manaus, AM, 69065-00, Brazil
| | - A M D Gandarilla
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J C B S Filho
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - W R Brito
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - L A M Mariúba
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
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9
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Gomez-Gutierrez SV, Goodwin SB. Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2022; 13:857673. [PMID: 35371152 PMCID: PMC8965322 DOI: 10.3389/fpls.2022.857673] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 05/31/2023]
Abstract
Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate detection of wheat pathogens is essential in applying the most appropriate disease management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for detection of plant pathogens and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and alternative nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages compared with alternative isothermal approaches. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for detection of pathogens in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.
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10
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Hsieh K, Melendez JH, Gaydos CA, Wang TH. Bridging the gap between development of point-of-care nucleic acid testing and patient care for sexually transmitted infections. LAB ON A CHIP 2022; 22:476-511. [PMID: 35048928 PMCID: PMC9035340 DOI: 10.1039/d1lc00665g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The incidence rates of sexually transmitted infections (STIs), including the four major curable STIs - chlamydia, gonorrhea, trichomoniasis and, syphilis - continue to increase globally, causing medical cost burden and morbidity especially in low and middle-income countries (LMIC). There have seen significant advances in diagnostic testing, but commercial antigen-based point-of-care tests (POCTs) are often insufficiently sensitive and specific, while near-point-of-care (POC) instruments that can perform sensitive and specific nucleic acid amplification tests (NAATs) are technically complex and expensive, especially for LMIC. Thus, there remains a critical need for NAAT-based STI POCTs that can improve diagnosis and curb the ongoing epidemic. Unfortunately, the development of such POCTs has been challenging due to the gap between researchers developing new technologies and healthcare providers using these technologies. This review aims to bridge this gap. We first present a short introduction of the four major STIs, followed by a discussion on the current landscape of commercial near-POC instruments for the detection of these STIs. We present relevant research toward addressing the gaps in developing NAAT-based STI POCT technologies and supplement this discussion with technologies for HIV and other infectious diseases, which may be adapted for STIs. Additionally, as case studies, we highlight the developmental trajectory of two different POCT technologies, including one approved by the United States Food and Drug Administration (FDA). Finally, we offer our perspectives on future development of NAAT-based STI POCT technologies.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Johan H Melendez
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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11
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Erber AC, Sandler PJ, de Avelar DM, Swoboda I, Cota G, Walochnik J. Diagnosis of visceral and cutaneous leishmaniasis using loop-mediated isothermal amplification (LAMP) protocols: a systematic review and meta-analysis. Parasit Vectors 2022; 15:34. [PMID: 35073980 PMCID: PMC8785018 DOI: 10.1186/s13071-021-05133-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Sensitive, reliable and fast diagnostic tools that are applicable in low-resource settings, at the point of care (PoC), are seen as crucial in the fight against visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Addressing the need for a PoC test, several diagnostic tests, including serological and molecular methods, have been developed and evaluated in the past. One promising molecular method, already implemented for diagnosis of a range of diseases, is the loop-mediated isothermal amplification (LAMP) protocol. In this systematic review and meta-analysis, using a comprehensive search strategy, we focus on studies evaluating the performance of LAMP for the diagnosis of leishmaniasis in humans and other mammals such as dogs, compared with microscopy and/or any other molecular diagnostic method. A meta-analysis, pooling sensitivity and specificity rates and calculating areas under the curve (AUCs) in summary receiver operating characteristic (SROC) plots, was conducted on datasets extracted from studies, grouped by clinical condition and sample type. We found high sensitivity and specificity for LAMP when compared with microscopy and PCR using blood samples, with pooled estimate values of > 90% for all subgroups, corresponding to calculated AUC values > 0.96, except for LAMP compared to microscopy for diagnosis of CL. However, only a limited number of studies were truly comparable. Most of the observed heterogeneity is likely based on true differences between the studies rather than sampling error only. Due to simple readout methods and low laboratory equipment requirements for sample preparation compared to other molecular methods, LAMP is a promising candidate for a molecular (near-)PoC diagnostic method for VL and CL.
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Affiliation(s)
- Astrid Christine Erber
- Department of Epidemiology, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1st floor, 1090, Vienna, Austria. .,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LG, UK.
| | - Peter Julian Sandler
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Daniel Moreira de Avelar
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ines Swoboda
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Gláucia Cota
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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12
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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13
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Li RJ, Mauk MG, Seok Y, Bau HH. Electricity-free chemical heater for isothermal nucleic acid amplification with applications in COVID-19 home testing. Analyst 2021; 146:4212-4218. [PMID: 34075937 PMCID: PMC8238897 DOI: 10.1039/d1an00309g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Molecular detection of pathogenic nucleic acids from patient samples requires incubating biochemical reactions at specific temperatures to amplify DNA. This incubation is typically carried out with an electrical heater and a temperature controller. To reduce test cost, to eliminate the need for manufacturing incubators, which may require significant time, and to enable electricity-free operation, we use energetic compounds such as an Mg(Fe) alloy mixed with a phase-change material (PCM) that undergoes phase transformation at the desired incubation temperature. We dubbed this composite Energetic Phase Change Material (EPCM). When the EPCM is brought into contact with water, the magnesium alloy interacts with the water to produce heat. The EPCM heats up to its phase transition temperature. Any excess heat is absorbed as latent heat and the system is maintained at its desired incubation temperature, independent of ambient temperatures, long enough to facilitate enzymatic amplification. The EPCM together with colorimetric amplicon detection facilitates an inexpensive, disposable, point-of-need diagnostic test that does not require any electric power. We demonstrate the feasibility of our approach by detecting SARS-Cov-2 in saliva samples either without any instrumentation or with a palm-size CCD camera that enables us to follow the amplification process in real time.
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Affiliation(s)
- Rui Jie Li
- Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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14
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Sullivan BP, Bender AT, Ngyuen DN, Zhang JY, Posner JD. Nucleic acid sample preparation from whole blood in a paper microfluidic device using isotachophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1163:122494. [PMID: 33401049 DOI: 10.1016/j.jchromb.2020.122494] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023]
Abstract
Nucleic acid amplification tests (NAATs) are a crucial diagnostic and monitoring tool for infectious diseases. A key procedural step for NAATs is sample preparation: separating and purifying target nucleic acids from crude biological samples prior to nucleic acid amplification and detection. Traditionally, sample preparation has been performed with liquid- or solid-phase extraction, both of which require multiple trained user steps and significant laboratory equipment. The challenges associated with sample preparation have limited the dissemination of NAAT point-of-care diagnostics in low resource environments, including low- and middle-income countries. We report on a paper-based device for purification of nucleic acids from whole blood using isotachophoresis (ITP) for point-of-care NAATs. We show successful extraction and purification of target nucleic acids from large volumes (33 µL) of whole human blood samples with no moving parts and few user steps. Our device utilizes paper-based buffer reservoirs to fully contain the liquid ITP buffers and does not require complex filling procedures, instead relying on the natural wicking of integrated paper membranes. We perform on-device blood fractionation via filtration to remove leukocytes and erythrocytes from our sample, followed by integrated on-paper proteolytic digestion of endogenous plasma proteins to allow for successful isotachophoretic extraction. Paper-based isotachophoresis purifies and concentrates target nucleic acids that are added directly to recombinase polymerase amplification (RPA) reactions. We show consistent amplification of input copy concentrations of as low as 3 × 103 copies nucleic acid per mL input blood with extraction and purification taking only 30 min. By employing a paper architecture, we are able to incorporate these processes in a single, robust, low-cost design, enabling the direct processing of large volumes of blood, with the only intermediate user steps being the removal and addition of tape. Our device represents a step towards a simple, fully integrated sample preparation system for nucleic acid amplification tests at the point-of-care.
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Affiliation(s)
- Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Duy N Ngyuen
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Jane Yuqian Zhang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Jonathan D Posner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA; Department of Chemical Engineering, University of Washington, Seattle, WA, USA; Department of Family Medicine, University of Washington, Seattle, WA, USA.
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15
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McMahon DE, Oyesiku L, Semeere A, Kang D, Freeman EE. Novel Diagnostics for Kaposi Sarcoma and Other Skin Diseases in Resource-Limited Settings. Dermatol Clin 2020; 39:83-90. [PMID: 33228864 DOI: 10.1016/j.det.2020.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In resource-limited settings, point-of-care diagnostic devices have the potential to reduce diagnostic delays and improve epidemiologic surveillance of dermatologic conditions. We outline novel-point-of care diagnostics that have recently been developed for dermatologic conditions that primarily affect patients living in resource-limited settings, namely, Kaposi sarcoma, cutaneous leishmaniasis, leprosy, Buruli ulcer, yaws, onchocerciasis, and lymphatic filariasis. All of the technologies described in this article are prototypes, and some have undergone field testing. These devices still require validation in real-world settings and effective pricing to have a major impact on dermatologic care in resource-limited settings.
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Affiliation(s)
- Devon E McMahon
- Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, 50 Staniford Street, Boston, MA 02114, USA
| | - Linda Oyesiku
- Department of Dermatology, Massachusetts General Hospital, 50 Staniford Street, Boston, MA 02114, USA; University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | - Esther E Freeman
- Department of Dermatology, Harvard Medical School, Massachusetts General Hospital, 50 Staniford Street, Boston, MA 02114, USA.
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16
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Point-Of-Care or Point-Of-Need Diagnostic Tests: Time to Change Outbreak Investigation and Pathogen Detection. Trop Med Infect Dis 2020; 5:tropicalmed5040151. [PMID: 32992688 PMCID: PMC7709694 DOI: 10.3390/tropicalmed5040151] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022] Open
Abstract
In the recent years, the progress of international trade and travel has led to an increased risk of emerging infections. Around 75 percent of the pathogens causing these infections are of animal origin. Point-of-care tests (POCT) and point-of-need tests (PONT) have been established in order to directly provide accurate and rapid diagnostics at field level, the patient bed-side or at the site of outbreaks. These assays can help physicians and decision makers to take the right action without delay. Typically, POCT and PONT rely on genomic identification of pathogens or track their immunological fingerprint. Recently, protocols for metagenomic diagnostics in the field have been developed. In this review, we give an overview of the latest developments in portable diagnostic methods. In addition, four mobile platforms for the implementation of these techniques at point-of-care and point-of-need are described. These approaches can provide reliable diagnostics and surveillance, especially in low resource settings as well as at the level of one health.
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17
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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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18
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Moutsiopoulou A, Broyles D, Joda H, Dikici E, Kaur A, Kaifer A, Daunert S, Deo SK. Bioluminescent Protein-Inhibitor Pair in the Design of a Molecular Aptamer Beacon Biosensing System. Anal Chem 2020; 92:7393-7398. [PMID: 32410446 PMCID: PMC7955708 DOI: 10.1021/acs.analchem.0c00518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although bioluminescent molecular beacons designed around resonance quenchers have shown higher signal-to-noise ratios and increased sensitivity compared with fluorescent beacon systems, bioluminescence quenching is still comparatively inefficient. A more elegant solution to inefficient quenching can be realized by designing a competitive inhibitor that is structurally very similar to the native substrate, resulting in essentially complete substrate exclusion. In this work, we designed a conjugated anti-interferon-γ (IFN-γ) molecular aptamer beacon (MAB) attached to a bioluminescent protein, Gaussia luciferase (GLuc), and an inhibitor molecule with a similar structure to the native substrate coelenterazine. To prove that a MAB can be more sensitive and have a better signal-to-noise ratio, a bioluminescence-based assay was developed against IFN-γ and provided an optimized, physiologically relevant detection limit of 1.0 nM. We believe that this inhibitor approach may provide a simple alternative strategy to standard resonance quenching in the development of high-performance molecular beacon-based biosensing systems.
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Affiliation(s)
- Angeliki Moutsiopoulou
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
- University of Miami, Department of Chemistry, Coral Gables, Florida 33146, United States
| | - David Broyles
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Hamdi Joda
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Emre Dikici
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Avinash Kaur
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
| | - Angel Kaifer
- University of Miami, Department of Chemistry, Coral Gables, Florida 33146, United States
| | - Sylvia Daunert
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
- Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Miami, Florida 33136, United States
- University of Miami Clinical and Translational Science Institute, Miami, Florida 33136, United States
| | - Sapna K Deo
- University of Miami, Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, Miami, Florida 33136, United States
- Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute of the University of Miami, Miami, Florida 33136, United States
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19
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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20
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Vidal L, Ben Aissa A, Salabert J, Jara JJ, Vallribera A, Pividori MI, Sebastián RM. Biotinylated Phosphorus Dendrimers as Control Line in Nucleic Acid Lateral Flow Tests. Biomacromolecules 2020; 21:1315-1323. [PMID: 32067443 DOI: 10.1021/acs.biomac.0c00161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lateral flow assays (LFA) are an affordable, easy-to-use, qualitative rapid test for clinical diagnosis in nonlaboratory environments and low-resource facilities. The control line of these tests is very important to provide a valid result, confirming that the platform operates correctly. A clear, nondiffused line is desirable. The number of colored nanoparticles that reach the control line in a positive test can be very small, and they should all be trapped efficiently by the molecules adsorbed there. In this work, we proposed the use of robust biotinylated dendrimers of two different generations as signal amplifiers in control lines of LFA, able to react with streptavidin-modified gold nanoparticles. Besides the synthesis and characterization, the analytical performance as control lines will be studied, and their response will be compared with other commercially available biotinylated molecules. Finally, the utility of the dendrimer implemented in a NALF (Nucleic Acid Lateral Flow) strip was also demonstrated for detection of the amplicons obtained by double-tagging PCR (polymerase chain reaction) for the detection of E. coli as a model of foodborne pathogen.
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Affiliation(s)
- Laura Vidal
- Department of Chemistry, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, 08193 Cerdanyola del Vallès, Barcelona Spain
| | | | - Jordi Salabert
- Department of Chemistry, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, 08193 Cerdanyola del Vallès, Barcelona Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Campus UAB, Cerdanyola del Vallès, 08193-Barcelona, Spain
| | - José Juan Jara
- Department of Chemistry, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, 08193 Cerdanyola del Vallès, Barcelona Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Campus UAB, Cerdanyola del Vallès, 08193-Barcelona, Spain
| | - Adelina Vallribera
- Department of Chemistry, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, 08193 Cerdanyola del Vallès, Barcelona Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Campus UAB, Cerdanyola del Vallès, 08193-Barcelona, Spain
| | - María Isabel Pividori
- Department of Chemistry, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, 08193 Cerdanyola del Vallès, Barcelona Spain
| | - Rosa María Sebastián
- Department of Chemistry, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, 08193 Cerdanyola del Vallès, Barcelona Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Campus UAB, Cerdanyola del Vallès, 08193-Barcelona, Spain
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22
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Tunable and precise miniature lithium heater for point-of-care applications. Proc Natl Acad Sci U S A 2020; 117:4632-4641. [PMID: 32071225 DOI: 10.1073/pnas.1916562117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Point-of-care diagnostic assays often involve multistep reactions, requiring a wide range of precise temperatures. Although precise heating is critical to performing these assays, it is challenging to provide it in an electricity-free format away from established infrastructure. Chemical heaters are electricity-free and use exothermic reactions. However, they are unsuitable for point-of-care multistep reactions because they sacrifice portability, have a narrow range of achievable temperatures, and long ramp-up times. Here we developed a miniature heater by modulating the lithium-water reaction kinetics using bubbles in a channel. Our heaters are up to 8,000 times smaller than current devices and can provide precise (within 5 °C) and tunable heating from 37 °C to 65 °C (∆TRT = 12 °C to 40 °C) with ramp-up times of a minute. We demonstrate field portablity and stability and show their use in an electricity-free multistep workflow that needs a range of temperatures. Ultimately, we envision providing better access to cutting edge biochemical techniques, including diagnostics, by making portable and electricity-free heating available at any location.
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Waema MW, Misinzo G, Kagira JM, Agola EL, Ngowi HA. DNA-Detection Based Diagnostics for Taenia solium Cysticercosis in Porcine. J Parasitol Res 2020; 2020:5706981. [PMID: 32395335 PMCID: PMC7199576 DOI: 10.1155/2020/5706981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/02/2019] [Indexed: 11/17/2022] Open
Abstract
Porcine cysticercosis is a neglected and underestimated disease caused by metacestode stage of the tapeworm, Taenia solium (T. solium). Pigs are the intermediate hosts of T. solium while human are the only known definitive host. The disease has an economic consequence because the affected farmers lose 50-100 percent of the value of pigs if they are infected. Lack of affordable, easy to use, sensitive, and specific molecular diagnostic tools for detection of infections at the farm level hinders the control of porcine cysticercosis in endemic areas. A number of DNA based diagnostic assays for the detection of T. solium infections in pigs have been developed and evaluated but none is applicable at low-resource areas where this disease is an endemic. This review focuses mainly on DNA based diagnostic methods, their sensitivity, specificity, and utilization at low-resource areas. We summarized data from 65 studies on the current DNA-detection based diagnostic techniques for T. solium cysticercosis in porcine, published in English between the years 2000-2018, identified through PubMed search engine. Of the different polymerase chain reaction (PCR) assays developed for identification of T. solium, the most sensitive (97-100%) and specific (100%) one is nested PCR. One study utilized loop-mediated isothermal amplification (LAMP) as a diagnostic tool for the detection of T. solium infections though its field use was never determined. Recombinase polymerase amplification (RPA) has been evaluated as a diagnostic tool for a variety of diseases, but has never been exploited for the diagnosis of cysticercosis/taeniasis. In conclusion, several molecular methods have been developed and evaluated in lab settings. However, there is need to validate these methods as a diagnostic tool to diagnose porcine cysticercosis in low-resource areas.
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Affiliation(s)
- Maxwell W. Waema
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, P.O Box 3297, Chuo Kikuu, Morogoro, Tanzania
| | - Gerald Misinzo
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Sokoine University of Agriculture, P.O Box 3297, Chuo Kikuu, Morogoro, Tanzania
| | - John M. Kagira
- Department of Animal Health and Production, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000-00200, Nairobi, Kenya
| | - Eric L. Agola
- Centre of Biotechnology Research and Development, Kenya Medical Research Institute, P.O Box 3297, Nairobi, Kenya
| | - Helena A. Ngowi
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, P.O Box 3021, Chuo Kikuu, Morogoro, Tanzania
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24
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Nzelu CO, Kato H, Peters NC. Loop-mediated isothermal amplification (LAMP): An advanced molecular point-of-care technique for the detection of Leishmania infection. PLoS Negl Trop Dis 2019; 13:e0007698. [PMID: 31697673 PMCID: PMC6837287 DOI: 10.1371/journal.pntd.0007698] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Leishmaniasis, caused by protozoan parasites of the Leishmania genus, represents an important health problem in many regions of the world. Lack of effective point-of-care (POC) diagnostic tests applicable in resources-limited endemic areas is a critical barrier to effective treatment and control of leishmaniasis. The development of the loop-mediated isothermal amplification (LAMP) assay has provided a new tool towards the development of a POC diagnostic test based on the amplification of pathogen DNA. LAMP does not require a thermocycler, is relatively inexpensive, and is simple to perform with high amplification sensitivity and specificity. In this review, we discuss the current technical developments, applications, diagnostic performance, challenges, and future of LAMP for molecular diagnosis and surveillance of Leishmania parasites. Studies employing the LAMP assay to diagnose human leishmaniasis have reported sensitivities of 80% to 100% and specificities of 94% to 100%. These observations suggest that LAMP offers a good molecular POC technique for the diagnosis of leishmaniasis and is also readily applicable to screening at-risk populations and vector sand flies for Leishmania infection in endemic areas.
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Affiliation(s)
- Chukwunonso O. Nzelu
- Snyder Institute for Chronic Diseases, Departments of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine and Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
- * E-mail: (CON); (NCP)
| | - Hirotomo Kato
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
| | - Nathan C. Peters
- Snyder Institute for Chronic Diseases, Departments of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine and Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
- * E-mail: (CON); (NCP)
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25
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Ciesielski D, Özay B, McCalla S, Gedeon T. A mathematical model for a biphasic DNA amplification reaction. J R Soc Interface 2019; 16:20190143. [PMID: 31138090 DOI: 10.1098/rsif.2019.0143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Isothermal DNA amplification reactions are a prevalent tool with many applications, ranging from analyte detection to DNA circuits. Exponential amplification reaction (EXPAR) is a popular isothermal DNA amplification method that exponentially amplifies short DNA oligonucleotides. A recent modification of this technique using an energetically stable looped template with palindromic binding regions demonstrated unexpected biphasic amplification and much higher DNA yield than EXPAR. This ultrasensitive DNA amplification reaction (UDAR) shows high-gain, switch-like DNA output from low concentrations of DNA input. Here we present the first mathematical model of UDAR based on four reaction mechanisms and show the model can reproduce the experimentally observed biphasic behaviour. Furthermore, we show that three of these mechanisms are necessary to reproduce biphasic experimental results. The reaction mechanisms are (i) positively cooperative multistep binding spurred by two trigger binding sites on the template; (ii) gradual template deactivation; (iii) recycling of deactivated templates into active templates; and (iv) polymerase sequestration. These mechanisms can potentially illuminate the behaviour of EXPAR as well as other nucleic acid amplification reactions.
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Affiliation(s)
- Danielle Ciesielski
- 1 Department of Mathematical Sciences, Montana State University , Bozeman, MT 59715 , USA
| | - Burcu Özay
- 2 Department of Chemical and Biological Engineering, Montana State University , Bozeman, MT 59715 , USA
| | - Stephanie McCalla
- 2 Department of Chemical and Biological Engineering, Montana State University , Bozeman, MT 59715 , USA
| | - Tomas Gedeon
- 1 Department of Mathematical Sciences, Montana State University , Bozeman, MT 59715 , USA
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26
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Simultaneous Detection of Different Zika Virus Lineages via Molecular Computation in a Point-of-Care Assay. Viruses 2018; 10:v10120714. [PMID: 30558136 PMCID: PMC6316447 DOI: 10.3390/v10120714] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/08/2018] [Accepted: 12/11/2018] [Indexed: 02/06/2023] Open
Abstract
We have developed a generalizable “smart molecular diagnostic” capable of accurate point-of-care (POC) detection of variable nucleic acid targets. Our isothermal assay relies on multiplex execution of four loop-mediated isothermal amplification reactions, with primers that are degenerate and redundant, thereby increasing the breadth of targets while reducing the probability of amplification failure. An easy-to-read visual answer is computed directly by a multi-input Boolean OR logic gate (gate output is true if either one or more gate inputs is true) signal transducer that uses degenerate strand exchange probes to assess any combination of amplicons. We demonstrate our methodology by using the same assay to detect divergent Asian and African lineages of the evolving Zika virus (ZIKV), while maintaining selectivity against non-target viruses. Direct analysis of biological specimens proved possible, with crudely macerated ZIKV-infected Aedes aegypti mosquitoes being identified with 100% specificity and sensitivity. The ease-of-use with minimal instrumentation, broad programmability, and built-in fail-safe reliability make our smart molecular diagnostic attractive for POC use.
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REASSURED diagnostics to inform disease control strategies, strengthen health systems and improve patient outcomes. Nat Microbiol 2018; 4:46-54. [PMID: 30546093 PMCID: PMC7097043 DOI: 10.1038/s41564-018-0295-3] [Citation(s) in RCA: 402] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 10/18/2018] [Indexed: 01/27/2023]
Abstract
Lack of access to quality diagnostics remains a major contributor to health burden in resource-limited settings. It has been more than 10 years since ASSURED (affordable, sensitive, specific, user-friendly, rapid, equipment-free, delivered) was coined to describe the ideal test to meet the needs of the developing world. Since its initial publication, technological innovations have led to the development of diagnostics that address the ASSURED criteria, but challenges remain. From this perspective, we assess factors contributing to the success and failure of ASSURED diagnostics, lessons learnt in the implementation of ASSURED tests over the past decade, and highlight additional conditions that should be considered in addressing point-of-care needs. With rapid advances in digital technology and mobile health (m-health), future diagnostics should incorporate these elements to give us REASSURED diagnostic systems that can inform disease control strategies in real-time, strengthen the efficiency of health care systems and improve patient outcomes.
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Warkad SD, Nimse SB, Song KS, Kim T. HCV Detection, Discrimination, and Genotyping Technologies. SENSORS (BASEL, SWITZERLAND) 2018; 18:E3423. [PMID: 30322029 PMCID: PMC6210034 DOI: 10.3390/s18103423] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.
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Affiliation(s)
- Shrikant Dashrath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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29
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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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Choi JR, Hu J, Gong Y, Feng S, Wan Abas WAB, Pingguan-Murphy B, Xu F. An integrated lateral flow assay for effective DNA amplification and detection at the point of care. Analyst 2018; 141:2930-9. [PMID: 27010033 DOI: 10.1039/c5an02532j] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lateral flow assays (LFAs) have been extensively explored in nucleic acid testing (NAT) for medical diagnostics, food safety analysis and environmental monitoring. However, the amount of target nucleic acid in a raw sample is usually too low to be directly detected by LFAs, necessitating the process of amplification. Even though cost-effective paper-based amplification techniques have been introduced, they have always been separately performed from LFAs, hence increasing the risk of reagent loss and cross-contaminations. To date, integrating paper-based nucleic acid amplification into colorimetric LFA in a simple, portable and cost-effective manner has not been introduced. Herein, we developed an integrated LFA with the aid of a specially designed handheld battery-powered system for effective amplification and detection of targets in resource-poor settings. Interestingly, using the integrated paper-based loop-mediated isothermal amplification (LAMP)-LFA, we successfully performed highly sensitive and specific target detection, achieving a detection limit of as low as 3 × 10(3) copies of target DNA, which is comparable to the conventional tube-based LAMP-LFA in an unintegrated format. The device may serve in conjunction with a simple paper-based sample preparation to create a fully integrated paper-based sample-to-answer diagnostic device for point-of-care testing (POCT) in the near future.
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Affiliation(s)
- Jane Ru Choi
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia. and The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Yan Gong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Shangsheng Feng
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China. and MOE Key Laboratory for Multifunctional Materials and Structures (LMMS), School of Aerospace, Xi'an Jiaotong University, Xi'an, PR China and State Key Laboratory of Mechanical Structure Strength and Vibration, School of Aerospace, Xi'an Jiaotong University, Xi'an, PR China
| | - Wan Abu Bakar Wan Abas
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Belinda Pingguan-Murphy
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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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: 38] [Impact Index Per Article: 6.3] [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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Liu L, Wang J, Zhang R, Lin M, Shi R, Han Q, Wang J, Yuan W. Visual and equipment-free reverse transcription recombinase polymerase amplification method for rapid detection of foot-and-mouth disease virus. BMC Vet Res 2018; 14:263. [PMID: 30170587 PMCID: PMC6119248 DOI: 10.1186/s12917-018-1594-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/24/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Foot-and-mouth disease (FMD), which is caused by foot-and-mouth disease virus (FMDV), is a highly contagious tansboundary disease of cloven-hoofed animals and causes devastating economic damages. Accurate, rapid and simple detection of FMDV is critical to containing an FMD outbreak. Recombinase polymerase amplification (RPA) has been explored for detection of diverse pathogens because of its accuracy, rapidness and simplicity. A visible and equipment-free reverse-transcription recombinase polymerase amplification assay combined with lateral flow strip (LFS RT-RPA) was developed to detect the FMDV using primers and LF probe specific for the 3D gene. RESULTS The FMDV LFS RT-RPA assay was performed successfully in a closed fist using body heat for 15 min, and the products were visible on the LFS inspected by the naked eyes within 2 min. The assay could detect FMDV serotypes O, A and Asia1, and there were no cross-reactions with vesicular stomatitis virus (VSV), encephalomyocarditis virus (EMCV), classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus 2 (PCV2) and pseudorabies virus (PRV). The analytical sensitivity was 1.0 × 102 copies in vitro transcribed FMDV RNA per reaction, which was the same as a real-time RT-PCR. For the 55 samples, FMDV RNA positive rate was 45.5% (25/55) by LFS RT-RPA and 52.7% (29/55) by real-time RT-PCR. For the LFS RT-RPA assay, the positive and negative predicative values were 100% and 80%, respectively. CONCLUSIONS The performance of the LFS RT-RPA assay was comparable to real-time RT-PCR, while the LFS RT-RPA assay was much faster and easier to be performed. The developed FMDV LFS RT-RPA assay provides an attractive and promising tool for rapid and reliable detection of FMDV in under-equipped laboratory and at point-of-need facility, which is of great significance in FMD control in low resource settings.
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Affiliation(s)
- Libing Liu
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China
| | - Jinfeng Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China
| | - Ruoxi Zhang
- Hebei Animal Disease Control Center, Shijiazhuang, 050050, People's Republic of China
| | - Mi Lin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, People's Republic of China
| | - Ruihan Shi
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China.,Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang, 050051, People's Republic of China
| | - Qingan Han
- Hebei Animal Disease Control Center, Shijiazhuang, 050050, People's Republic of China
| | - Jianchang Wang
- Center of Inspection and Quarantine, Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, 050051, People's Republic of China. .,Hebei Academy of Science and Technology for Inspection and Quarantine, Shijiazhuang, 050051, People's Republic of China.
| | - Wanzhe Yuan
- College of Veterinary Medicine, Agricultural University of Hebei, No.38 Lingyusi Street, Baoding, Hebei, 071001, People's Republic of China.
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33
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Waller AW, Lotton JL, Gaur S, Andrade JM, Andrade JE. Evaluation of Micronutrient Sensors for Food Matrices in Resource-Limited Settings: A Systematic Narrative Review. J Food Sci 2018; 83:1792-1804. [PMID: 29928780 DOI: 10.1111/1750-3841.14202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/01/2018] [Indexed: 11/29/2022]
Abstract
In resource-limited settings, mass food fortification is a common strategy to ensure the population consumes appropriate quantities of essential micronutrients. Food and government organizations in these settings, however, lack tools to monitor the quality and compliance of fortified products and their efficacy to enhance nutrient status. The World Health Organization has developed general guidelines known as ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable to end-users) to aid the development of useful diagnostic tools for these settings. These guidelines assume performance aspects such as sufficient accuracy, reliability, and validity. The purpose of this systematic narrative review is to examine the micronutrient sensor literature on its adherence towards the ASSURED criteria along with accuracy, reliability, and validation when developing micronutrient sensors for resource-limited settings. Keyword searches were conducted in three databases: Web of Science, PubMed, and Scopus and were based on 6-point inclusion criteria. A 16-question quality assessment tool was developed to determine the adherence towards quality and performance criteria. Of the 2,365 retrieved studies, 42 sensors were included based on inclusion/exclusion criteria. Results showed that improvements to the current sensor design are necessary, especially their affordability, user-friendliness, robustness, equipment-free, and deliverability within the ASSURED criteria, and accuracy and validity of the additional criteria to be useful in resource-limited settings. Although it requires further validation, the 16-question quality assessment tool can be used as a guide in the development of sensors for resource-limited settings.
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Affiliation(s)
- Anna W Waller
- Dept. of Food Science and Human Nutrition, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, U.S.A
| | - Jennifer L Lotton
- Dept. of Food Science and Human Nutrition, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, U.S.A
| | - Shashank Gaur
- Dept. of Food Science and Human Nutrition, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Innovations, John I. Haas, Yakima, WA, 98902
| | - Jeanette M Andrade
- Dept. of Food Science and Human Nutrition, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, U.S.A.,School of Family and Consumer Sciences, Eastern Illinois Univ., Charleston, IL, 61920, U.S.A
| | - Juan E Andrade
- Div. of Nutritional Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, U.S.A
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34
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Natoli ME, Rohrman BA, De Santiago C, van Zyl GU, Richards-Kortum RR. Paper-based detection of HIV-1 drug resistance using isothermal amplification and an oligonucleotide ligation assay. Anal Biochem 2018; 544:64-71. [PMID: 29229373 PMCID: PMC5854266 DOI: 10.1016/j.ab.2017.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 01/17/2023]
Abstract
Regular HIV-1 viral load monitoring is the standard of care to assess antiretroviral therapy effectiveness in resource-rich settings. Persistently elevated viral loads indicate virologic failure (VF), which warrants HIV drug resistance testing (HIVDRT) to allow individualized regimen switches. However, in settings lacking access to HIVDRT, clinical decisions are often made based on symptoms, leading to unnecessary therapy switches and increased costs of care. This work presents a proof-of-concept assay to detect M184V, the most common drug resistance mutation after first-line antiretroviral therapy failure, in a paper format. The first step isothermally amplifies a section of HIV-1 reverse transcriptase containing M184V using a recombinase polymerase amplification (RPA) assay. Then, an oligonucleotide ligation assay (OLA) is used to selectively label the mutant and wild type amplified sequences. Finally, a lateral flow enzyme-linked immunosorbent assay (ELISA) differentiates between OLA-labeled products with or without M184V. Our method shows 100% specificity and 100% sensitivity when tested with samples that contained 200 copies of mutant DNA and 800 copies of wild type DNA prior to amplification. When integrated with sample preparation, this method may detect HIV-1 drug resistance at a low cost and at a rural hospital laboratory.
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Affiliation(s)
- Mary E Natoli
- Department of Bioengineering, Rice University, 6100 Main St MS-142, Houston, TX 77005, USA
| | | | - Carolina De Santiago
- Department of Bioengineering, Rice University, 6100 Main St MS-142, Houston, TX 77005, USA
| | - Gert U van Zyl
- National Health Laboratory Service, Tygerberg Business Unit, Coastal Branch, South Africa; Division of Medical Virology, Stellenbosch University, Parow, South Africa
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35
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Mauk MG, Song J, Liu C, Bau HH. Simple Approaches to Minimally-Instrumented, Microfluidic-Based Point-of-Care Nucleic Acid Amplification Tests. BIOSENSORS 2018; 8:E17. [PMID: 29495424 PMCID: PMC5872065 DOI: 10.3390/bios8010017] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/10/2023]
Abstract
Designs and applications of microfluidics-based devices for molecular diagnostics (Nucleic Acid Amplification Tests, NAATs) in infectious disease testing are reviewed, with emphasis on minimally instrumented, point-of-care (POC) tests for resource-limited settings. Microfluidic cartridges ('chips') that combine solid-phase nucleic acid extraction; isothermal enzymatic nucleic acid amplification; pre-stored, paraffin-encapsulated lyophilized reagents; and real-time or endpoint optical detection are described. These chips can be used with a companion module for separating plasma from blood through a combined sedimentation-filtration effect. Three reporter types: Fluorescence, colorimetric dyes, and bioluminescence; and a new paradigm for end-point detection based on a diffusion-reaction column are compared. Multiplexing (parallel amplification and detection of multiple targets) is demonstrated. Low-cost detection and added functionality (data analysis, control, communication) can be realized using a cellphone platform with the chip. Some related and similar-purposed approaches by others are surveyed.
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Affiliation(s)
- Michael G Mauk
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Jinzhao Song
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Changchun Liu
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
| | - Haim H Bau
- Mechanical Engineering and Applied Mechanics (MEAM), School of Engineering and Applied Science, University of Pennsylvania, Towne Building, 220 33rd Street, Philadelphia, PA 19104, USA.
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36
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Duchesne L, Lacombe K. Innovative technologies for point-of-care testing of viral hepatitis in low-resource and decentralized settings. J Viral Hepat 2018; 25:108-117. [PMID: 29134742 DOI: 10.1111/jvh.12827] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 09/18/2017] [Indexed: 12/13/2022]
Abstract
According to the Global Burden of Diseases, chronic viral hepatitis B and C are one of the most challenging global health conditions that rank among the first causes of morbidity and mortality worldwide. Low- and middle-income countries are particularly affected by the health burden associated with HBV or HCV infection. One major gap in efficiently addressing the issue of viral hepatitis is universal screening. However, the costs and chronic lack of human resources for using traditional screening strategies based on serology and molecular biology preclude any scaling-up. Point-of-care tests have been deemed a powerful potential solution to fill the current diagnostics gap in low-resource and decentralized settings. Despite high interest resulting from their development in recent years, very few point-of-care devices have reached the market. Scaling down and automating all testing steps in 1 single device (eg, sample preparation, detection and readout) is indeed challenging. But innovations in multiple disciplines such as nanotechnologies, microfluidics, biosensors and synthetic biology have led to the creation of chip-sized laboratory systems called "lab-on-a-chip" devices. This review aims to explain how these innovations can overcome technological barriers that usually arise for each testing step while developing integrated point-of-care tests. Point-of-care test prototypes rarely meet the requirements for mass production, which also hinders their large-scale production. In addition to logistical hurdles, legal and economic constraints specific to the commercialization of in vitro diagnostics, which have also participated in the low transfer of innovative point-of-care tests to the field, are discussed.
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Affiliation(s)
- L Duchesne
- Sorbonne Universités, UPMC Univ Paris, Paris, France.,Inserm, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - K Lacombe
- Sorbonne Universités, UPMC Univ Paris, Paris, France.,Inserm, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.,Service de maladies infectieuses et tropicales, Hôpital Saint-Antoine, Paris, France
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37
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Chan K, Wong PY, Parikh C, Wong S. Moving toward rapid and low-cost point-of-care molecular diagnostics with a repurposed 3D printer and RPA. Anal Biochem 2018; 545:4-12. [PMID: 29339059 DOI: 10.1016/j.ab.2018.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
Traditionally, the majority of nucleic acid amplification-based molecular diagnostic tests are done in centralized settings. In recent years, point-of-care tests have been developed for use in low-resource settings away from central laboratories. While most experts agree that point-of-care molecular tests are greatly needed, their availability as cost-effective and easy-to-operate tests remains an unmet goal. In this article, we discuss our efforts to develop a recombinase polymerase amplification reaction-based test that will meet these criteria. First, we describe our efforts in repurposing a low-cost 3D printer as a platform that can carry out medium-throughput, rapid, and high-performing nucleic acid extraction. Next, we address how these purified templates can be rapidly amplified and analyzed using the 3D printer's heated bed or the deconstructed, low-cost thermal cycler we have developed. In both approaches, real-time isothermal amplification and detection of template DNA or RNA can be accomplished using a low-cost portable detector or smartphone camera. Last, we demonstrate the capability of our technologies using foodborne pathogens and the Zika virus. Our low-cost approach does not employ complicated and high-cost components, making it suitable for resource-limited settings. When integrated and commercialized, it will offer simple sample-to-answer molecular diagnostics.
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Affiliation(s)
- Kamfai Chan
- AI Biosciences, Inc., College Station, TX 77845, USA
| | - Pui-Yan Wong
- AI Biosciences, Inc., College Station, TX 77845, USA
| | | | - Season Wong
- AI Biosciences, Inc., College Station, TX 77845, USA.
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38
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Shah K, Bentley E, Tyler A, Richards KSR, Wright E, Easterbrook L, Lee D, Cleaver C, Usher L, Burton JE, Pitman JK, Bruce CB, Edge D, Lee M, Nazareth N, Norwood DA, Moschos SA. Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood. Chem Sci 2017; 8:7780-7797. [PMID: 29163915 PMCID: PMC5694917 DOI: 10.1039/c7sc03281a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log-linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource-limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats.
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Affiliation(s)
- Kavit Shah
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- BGResearch Ltd. , 6 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Emma Bentley
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Adam Tyler
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Kevin S R Richards
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Edward Wright
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Linda Easterbrook
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Diane Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Claire Cleaver
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Louise Usher
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Jane E Burton
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - James K Pitman
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Christine B Bruce
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - David Edge
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Martin Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Nelson Nazareth
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - David A Norwood
- Diagnostic Systems Division and Virology Division , United States Army Medical Research Institute of Infectious Diseases , Fort Detrick , MD 21701-5011 , USA
| | - Sterghios A Moschos
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Applied Sciences , Faculty of Health and Life Sciences , Northumbria University , C4.03 Ellison Building, Ellison Place , Newcastle Upon Tyne , Tyne and Wear NE1 8ST , UK . ; Tel: +44(0) 191 215 6623
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39
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Kumar Y, Bansal S, Jaiswal P. Loop-Mediated Isothermal Amplification (LAMP): A Rapid and Sensitive Tool for Quality Assessment of Meat Products. Compr Rev Food Sci Food Saf 2017; 16:1359-1378. [DOI: 10.1111/1541-4337.12309] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yogesh Kumar
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Sangita Bansal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Pranita Jaiswal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
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40
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Scherr TF, Markwalter CF, Bauer WS, Gasperino D, Wright DW, Haselton FR. Application of mass transfer theory to biomarker capture by surface functionalized magnetic beads in microcentrifuge tubes. Adv Colloid Interface Sci 2017; 246:275-288. [PMID: 28595937 DOI: 10.1016/j.cis.2017.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/15/2017] [Accepted: 02/15/2017] [Indexed: 12/11/2022]
Abstract
In many diagnostic assays, specific biomarker extraction and purification from a patient sample is performed in microcentrifuge tubes using surface-functionalized magnetic beads. Although assay binding times are known to be highly dependent on sample viscosity, sample volume, capture reagent, and fluid mixing, the theoretical mass transport framework that has been developed and validated in engineering has yet to be applied in this context. In this work, we adapt this existing framework for simultaneous mass transfer and surface reaction and apply it to the binding of biomarkers in clinical samples to surface-functionalized magnetic beads. We discuss the fundamental fluid dynamics of vortex mixing within microcentrifuge tubes as well as describe how particles and biomolecules interact with the fluid. The model is solved over a wide range of parameters, and we present scenarios when a simplified analytical expression would be most accurate. Next, we review of some relevant techniques for model parameter estimation. Finally, we apply the mass transfer theory to practical use-case scenarios of immediate use to clinicians and assay developers. Throughout, we highlight where further characterization is necessary to bridge the gap between theory and practical application.
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41
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Kolm C, Martzy R, Brunner K, Mach RL, Krska R, Heinze G, Sommer R, Reischer GH, Farnleitner AH. A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7028-7035. [PMID: 28541661 PMCID: PMC5573901 DOI: 10.1021/acs.est.7b01074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of U.S. Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci. The limit of detection was 25 target copies per reaction, only 3 times higher than that of qPCR. The applicability of the assay was tested on 30 environmental water sample DNA extracts, simulating a gradient of fecal pollution. Despite the isothermal nature of the reaction, the HDA results were consistent with those of the qPCR reference. Given this performance, we conclude that the developed Enterococcus HDA assay has great potential as a qualitative molecular screening method for resource-limited settings when combined with compatible up- and downstream processes. This amplification strategy can pave the way for developing a new generation of rapid, low-cost, and field-deployable molecular diagnostic tools for water quality monitoring.
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Affiliation(s)
- Claudia Kolm
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Molecular Diagnostics Group, Department
IFA-Tulln, Konrad-Lorenz-Straße
20, 3430 Tulln, Austria
- ICC
Interuniversity
Cooperation Centre Water & Health, Vienna, Austria (ICC Interuniversity
Cooperation Center Water & Health, Vienna, Austria (www.waterandhealth.at)
| | - Roland Martzy
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Molecular Diagnostics Group, Department
IFA-Tulln, Konrad-Lorenz-Straße
20, 3430 Tulln, Austria
- ICC
Interuniversity
Cooperation Centre Water & Health, Vienna, Austria (ICC Interuniversity
Cooperation Center Water & Health, Vienna, Austria (www.waterandhealth.at)
| | - Kurt Brunner
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Molecular Diagnostics Group, Department
IFA-Tulln, Konrad-Lorenz-Straße
20, 3430 Tulln, Austria
| | - Robert L. Mach
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Research Group of Environmental Microbiology
and Molecular Diagnostics 166/5/4, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Rudolf Krska
- University
of Natural Resources and Life Sciences, Vienna (BOKU), Department IFA-Tulln, Center for Analytical Chemistry, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Georg Heinze
- Medical
University Vienna, Center for Medical Statistics,
Informatics and Intelligent Systems, Section for Clinical Biometrics, Spitalgasse 23, 1090 Vienna, Austria
| | - Regina Sommer
- Medical
University Vienna, Institute for Hygiene
and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, 1090 Vienna, Austria
- ICC
Interuniversity
Cooperation Centre Water & Health, Vienna, Austria (ICC Interuniversity
Cooperation Center Water & Health, Vienna, Austria (www.waterandhealth.at)
| | - Georg H. Reischer
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Molecular Diagnostics Group, Department
IFA-Tulln, Konrad-Lorenz-Straße
20, 3430 Tulln, Austria
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Research Group of Environmental Microbiology
and Molecular Diagnostics 166/5/4, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Andreas H. Farnleitner
- TU
Wien, Institute of Chemical, Environmental
& Biological Engineering, Research Group of Environmental Microbiology
and Molecular Diagnostics 166/5/4, Gumpendorferstraße 1a, 1060 Vienna, Austria
- Karl Landsteiner
University of Health Sciences, Research Unit Water Quality and Health, Dr.-Karl-Dorrek-Straße 30, 3500 Krems, Austria
- ICC
Interuniversity
Cooperation Centre Water & Health, Vienna, Austria (ICC Interuniversity
Cooperation Center Water & Health, Vienna, Austria (www.waterandhealth.at)
- Telephone: +43-664-605882244. E-mail:
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42
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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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43
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Fu E, Downs C. Progress in the development and integration of fluid flow control tools in paper microfluidics. LAB ON A CHIP 2017; 17:614-628. [PMID: 28119982 DOI: 10.1039/c6lc01451h] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Paper microfluidics is a rapidly growing subfield of microfluidics in which paper-like porous materials are used to create analytical devices. There is a need for higher performance field-use tests for many application domains including human disease diagnosis, environmental monitoring, and veterinary medicine. A key factor in creating high performance paper-based devices is the ability to manipulate fluid flow within the devices. This critical review is focused on the progress that has been made in (i) the development of fluid flow control tools and (ii) the integration of those tools into paper microfluidic devices. Further, we strive to be comprehensive in our presentation and provide historical context through discussion and performance comparisons, when possible, of both relevant earlier work and recent work. Finally, we discuss the major areas of focus for fluid flow methods development to advance the potential of paper microfluidics for high-performance field applications.
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Affiliation(s)
- Elain Fu
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, USA.
| | - Corey Downs
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, USA.
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44
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Martineau RL, Murray SA, Ci S, Gao W, Chao SH, Meldrum DR. Improved Performance of Loop-Mediated Isothermal Amplification Assays via Swarm Priming. Anal Chem 2016; 89:625-632. [PMID: 27809497 DOI: 10.1021/acs.analchem.6b02578] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed "swarm primers" based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites. Thus, despite the addition of a new primer set to an already complex assay, no significant increase in assay complexity is incurred. Swarm priming is presented for three DNA templates: Lambda phage, Synechocystis sp. PCC 6803 rbcL gene, and human HFE. The results of adding swarm primers to conventional LAMP reactions include increased amplification speed, increased indicator contrast, and increased reaction products. For at least one template, minor improvements in assay repeatability are also shown. In addition, swarm priming is shown to be effective at increasing the reaction speed for RNA amplification via RT-LAMP. Collectively, these results suggest that the addition of swarm primers will likely benefit most if not all existing LAMP assays based on state-of-the-art, six-primer reactions.
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Affiliation(s)
- Rhett L Martineau
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Sarah A Murray
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shufang Ci
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Weimin Gao
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shih-Hui Chao
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Deirdre R Meldrum
- Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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Tram DTN, Wang H, Sugiarto S, Li T, Ang WH, Lee C, Pastorin G. Advances in nanomaterials and their applications in point of care (POC) devices for the diagnosis of infectious diseases. Biotechnol Adv 2016; 34:1275-1288. [PMID: 27686397 PMCID: PMC7127209 DOI: 10.1016/j.biotechadv.2016.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 01/17/2023]
Abstract
Nanotechnology has gained much attention over the last decades, as it offers unique opportunities for the advancement of the next generation of sensing tools. Point-of-care (POC) devices for the selective detection of biomolecules using engineered nanoparticles have become a main research thrust in the diagnostic field. This review presents an overview on how the POC-associated nanotechnology, currently applied for the identification of nucleic acids, proteins and antibodies, might be further exploited for the detection of infectious pathogens: although still premature, future integrations of nanoparticles with biological markers that target specific microorganisms will enable timely therapeutic intervention against life-threatening infectious diseases.
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Affiliation(s)
- Dai Thien Nhan Tram
- Pharmacy Department National University of Singapore, Singapore 117543, Singapore.
| | - Hao Wang
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering, Drive 3, Singapore 117576, Singapore.
| | - Sigit Sugiarto
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Tao Li
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering, Drive 3, Singapore 117576, Singapore.
| | - Giorgia Pastorin
- Pharmacy Department National University of Singapore, Singapore 117543, Singapore; NanoCore, Faculty of Engineering, National University of Singapore, Singapore 117576, Singapore; NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences (CeLS), Singapore 117456, Singapore.
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Lafleur LK, Bishop JD, Heiniger EK, Gallagher RP, Wheeler MD, Kauffman P, Zhang X, Kline EC, Buser JR, Kumar S, Byrnes SA, Vermeulen NMJ, Scarr NK, Belousov Y, Mahoney W, Toley BJ, Ladd PD, Lutz BR, Yager P. A rapid, instrument-free, sample-to-result nucleic acid amplification test. LAB ON A CHIP 2016; 16:3777-87. [PMID: 27549897 DOI: 10.1039/c6lc00677a] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The prototype demonstrated here is the first fully integrated sample-to-result diagnostic platform for performing nucleic acid amplification tests that requires no permanent instrument or manual sample processing. The multiplexable autonomous disposable nucleic acid amplification test (MAD NAAT) is based on two-dimensional paper networks, which enable sensitive chemical detection normally reserved for laboratories to be carried out anywhere by untrained users. All reagents are stored dry in the disposable test device and are rehydrated by stored buffer. The paper network is physically multiplexed to allow independent isothermal amplification of multiple targets; each amplification reaction is also chemically multiplexed with an internal amplification control. The total test time is less than one hour. The MAD NAAT prototype was used to characterize a set of human nasal swab specimens pre-screened for methicillin-resistant Staphylococcus aureus (MRSA) bacteria. With qPCR as the quantitative reference method, the lowest input copy number in the range where the MAD NAAT prototype consistently detected MRSA in these specimens was ∼5 × 10(3) genomic copies (∼600 genomic copies per biplexed amplification reaction).
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Affiliation(s)
- Lisa K Lafleur
- Department of Bioengineering, University of Washington, Seattle, USA.
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Xu G, Zhao H, Cooper JM, Reboud J. A capillary-based multiplexed isothermal nucleic acid-based test for sexually transmitted diseases in patients. Chem Commun (Camb) 2016; 52:12187-12190. [PMID: 27722490 PMCID: PMC5058349 DOI: 10.1039/c6cc05679b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 09/08/2016] [Indexed: 11/21/2022]
Abstract
We demonstrate a multiplexed loop mediated isothermal amplification (LAMP) assay for infectious disease diagnostics, where the analytical process flow of target pathogens genomic DNA is performed manually by moving magnetic beads through a series of plugs in a capillary. Heat is provided by a water bath and the results are read by the naked eye, enabling applications in low resource settings.
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Affiliation(s)
- Gaolian Xu
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Rankine Building, G12 8LT Glasgow, UK.
| | - Hang Zhao
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Rankine Building, G12 8LT Glasgow, UK.
| | - Jonathan M Cooper
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Rankine Building, G12 8LT Glasgow, UK.
| | - Julien Reboud
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Rankine Building, G12 8LT Glasgow, UK.
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48
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Mohon AN, Lee LDY, Bayih AG, Folefoc A, Guelig D, Burton RA, LaBarre P, Chan W, Meatherall B, Pillai DR. NINA-LAMP compared to microscopy, RDT, and nested PCR for the detection of imported malaria. Diagn Microbiol Infect Dis 2016; 85:149-53. [PMID: 27017271 PMCID: PMC4862928 DOI: 10.1016/j.diagmicrobio.2015.11.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/06/2015] [Accepted: 11/08/2015] [Indexed: 01/08/2023]
Abstract
Microscopy and field adaptable rapid diagnostic tests (RDTs) are not sensitive and specific in certain conditions such as poor training of microscopists, lack of electricity, or lower sensitivity in the detection of non-falciparum malaria. More sensitive point-of-care testing (POCT) would reduce delays in diagnosis and initiation of therapy. In the current study, we have evaluated the efficacy of noninstrumented nucleic acid amplification (NINA) coupled with loop-mediated isothermal amplification (LAMP) for detection of traveler's malaria (n=140) in comparison with microscopy, nested PCR, and the only Food and Drug Administration-approved rapid diagnostic test. NINA-LAMP was 100% sensitive and 98.6% specific when compared to nested PCR. For non-falciparum detection, NINA-LAMP sensitivity was 100% sensitive compared to nested PCR, whereas RDT sensitivity was 71%. LAMP is highly sensitive and specific for symptomatic malaria diagnosis regardless of species.
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Affiliation(s)
- Abu Naser Mohon
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, AB, Canada; Department of Pathology and Laboratory Medicine, University of Calgary, AB, Canada
| | - Lydia Da-Yeong Lee
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, AB, Canada
| | - Abebe Genetu Bayih
- Department of Pathology and Laboratory Medicine, University of Calgary, AB, Canada
| | - Asongna Folefoc
- Department of Pathology and Laboratory Medicine, University of Calgary, AB, Canada
| | | | | | | | - Wilson Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, AB, Canada
| | | | - Dylan R Pillai
- Department of Microbiology, Immunology and Infectious Disease, University of Calgary, AB, Canada; Department of Pathology and Laboratory Medicine, University of Calgary, AB, Canada; Department of Medicine, University of Calgary, Calgary, AB, Canada.
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Daher RK, Stewart G, Boissinot M, Bergeron MG. Recombinase Polymerase Amplification for Diagnostic Applications. Clin Chem 2016; 62:947-58. [PMID: 27160000 PMCID: PMC7108464 DOI: 10.1373/clinchem.2015.245829] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/15/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND First introduced in 2006, recombinase polymerase amplification (RPA) has stirred great interest, as evidenced by 75 publications as of October 2015, with 56 of them just in the last 2 years. The widespread adoption of this isothermal molecular tool in many diagnostic fields represents an affordable (approximately 4.3 USD per test), simple (few and easy hands-on steps), fast (results within 5–20 min), and sensitive (single target copy number detected) method for the identification of pathogens and the detection of single nucleotide polymorphisms in human cancers and genetically modified organisms. CONTENT This review summarizes the current knowledge on RPA. The molecular diagnostics of various RNA/DNA pathogens is discussed while highlighting recent applications in clinical settings with focus on point-of-care (POC) bioassays and on automated fluidic platforms. The strengths and limitations of this isothermal method are also addressed. SUMMARY RPA is becoming a molecular tool of choice for the rapid, specific, and cost-effective identification of pathogens. Owing to minimal sample-preparation requirements, low operation temperature (25–42 °C), and commercial availability of freeze-dried reagents, this method has been applied outside laboratory settings, in remote areas, and interestingly, onboard automated sample-to-answer microfluidic devices. RPA is undoubtedly a promising isothermal molecular technique for clinical microbiology laboratories and emergence response in clinical settings.
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Affiliation(s)
- Rana K Daher
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada
| | - Gale Stewart
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Maurice Boissinot
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada.
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50
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Mughal TI, Radich JP, Deininger MW, Apperley JF, Hughes TP, Harrison CJ, Gambacorti-Passerini C, Saglio G, Cortes J, Daley GQ. Chronic myeloid leukemia: reminiscences and dreams. Haematologica 2016; 101:541-58. [PMID: 27132280 PMCID: PMC5004358 DOI: 10.3324/haematol.2015.139337] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/20/2016] [Indexed: 12/26/2022] Open
Abstract
With the deaths of Janet Rowley and John Goldman in December 2013, the world lost two pioneers in the field of chronic myeloid leukemia. In 1973, Janet Rowley, unraveled the cytogenetic anatomy of the Philadelphia chromosome, which subsequently led to the identification of the BCR-ABL1 fusion gene and its principal pathogenetic role in the development of chronic myeloid leukemia. This work was also of major importance to support the idea that cytogenetic changes were drivers of leukemogenesis. John Goldman originally made seminal contributions to the use of autologous and allogeneic stem cell transplantation from the late 1970s onwards. Then, in collaboration with Brian Druker, he led efforts to develop ABL1 tyrosine kinase inhibitors for the treatment of patients with chronic myeloid leukemia in the late 1990s. He also led the global efforts to develop and harmonize methodology for molecular monitoring, and was an indefatigable organizer of international conferences. These conferences brought together clinicians and scientists, and accelerated the adoption of new therapies. The abundance of praise, tributes and testimonies expressed by many serve to illustrate the indelible impressions these two passionate and affable scholars made on so many people's lives. This tribute provides an outline of the remarkable story of chronic myeloid leukemia, and in writing it, it is clear that the historical triumph of biomedical science over this leukemia cannot be considered without appreciating the work of both Janet Rowley and John Goldman.
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MESH Headings
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Cytogenetic Analysis/history
- Cytogenetic Analysis/methods
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/genetics
- History, 20th Century
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Molecular Targeted Therapy/history
- Molecular Targeted Therapy/methods
- Mutation
- Philadelphia Chromosome
- Prognosis
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Research/history
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Affiliation(s)
| | - Jerald P Radich
- Fredrick Hutchinson Cancer Center, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | | | | | - George Q Daley
- Boston Children's Hospital, Harvard Medicine, School, Boston, MA, USA
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