1
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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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2
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Knox A, Zerna G, Beddoe T. Current and Future Advances in the Detection and Surveillance of Biosecurity-Relevant Equine Bacterial Diseases Using Loop-Mediated Isothermal Amplification (LAMP). Animals (Basel) 2023; 13:2663. [PMID: 37627456 PMCID: PMC10451754 DOI: 10.3390/ani13162663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Horses play an important role throughout the world, whether for work, culture, or leisure, providing an ever-growing significant contribution to the economy. The increase in importation and movement of horses, both nationally and internationally, has inevitably allowed for the global equine industry to grow. Subsequently, however, the potential for transmission of fatal equine bacterial diseases has also escalated, and devasting outbreaks continue to occur. To prevent such events, disease surveillance and diagnosis must be heightened throughout the industry. Current common, or "gold-standard" techniques, have shown to be inadequate at times, thus requiring newer technology to impede outbreaks. Loop-mediated isothermal amplification (LAMP) has proven to be a reliable, rapid, and accessible tool in both diagnostics and surveillance. This review will discuss equine bacterial diseases of biosecurity relevance and their current diagnostic approaches, as well as their respective LAMP assay developments. Additionally, we will provide insight regarding newer technology and advancements associated with this technique and their potential use for the outlined diseases.
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Affiliation(s)
| | | | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscience, La Trobe University, Bundoora, VIC 3082, Australia; (A.K.); (G.Z.)
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3
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Kundrod KA, Barra M, Wilkinson A, Smith CA, Natoli ME, Chang MM, Coole JB, Santhanaraj A, Lorenzoni C, Mavume C, Atif H, Montealegre JR, Scheurer ME, Castle PE, Schmeler KM, Richards-Kortum RR. An integrated isothermal nucleic acid amplification test to detect HPV16 and HPV18 DNA in resource-limited settings. Sci Transl Med 2023; 15:eabn4768. [PMID: 37343083 PMCID: PMC10566637 DOI: 10.1126/scitranslmed.abn4768] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
High-risk human papillomavirus (HPV) DNA testing is widely acknowledged as the most sensitive cervical cancer screening method but has limited availability in resource-limited settings, where the burden of cervical cancer is highest. Recently, HPV DNA tests have been developed for use in resource-limited settings, but they remain too costly for widespread use and require instruments that are often limited to centralized laboratories. To help meet the global need for low-cost cervical cancer screening, we developed a prototype, sample-to-answer, point-of-care test for HPV16 and HPV18 DNA. Our test relies on isothermal DNA amplification and lateral flow detection, two technologies that reduce the need for complex instrumentation. We integrated all test components into a low-cost, manufacturable platform, and performance of the integrated test was evaluated with synthetic samples, provider-collected clinical samples in a high-resource setting in the United States, and self-collected clinical samples in a low-resource setting in Mozambique. We demonstrated a clinically relevant limit of detection of 1000 HPV16 or HPV18 DNA copies per test. The test requires six user steps, yields results in 45 min, and can be performed using a benchtop instrument and minicentrifuge by minimally trained personnel. The projected per-test cost is <$5, and the projected instrumentation cost is <$1000. These results show the feasibility of a sample-to-answer, point-of-care HPV DNA test. With the inclusion of other HPV types, this test has the potential to fill a critical gap for decentralized and globally accessible cervical cancer screening.
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Affiliation(s)
- Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mary E Natoli
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jackson B Coole
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Cesaltina Lorenzoni
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Celda Mavume
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Hira Atif
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | | | - Michael E Scheurer
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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4
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Zingg JM, Yang YP, Seely S, Joshi P, Roshid MHO, Iribarren Latasa F, O'Connor G, Alfaro J, Riquelme E, Bernales S, Dikici E, Deo S, Daunert S. Rapid isothermal point-of-care test for screening of SARS-CoV-2 (COVID-19). ASPECTS OF MOLECULAR MEDICINE 2023; 1:100002. [PMID: 37519861 PMCID: PMC9890548 DOI: 10.1016/j.amolm.2023.100002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
Rapid on-site diagnosis of emerging pathogens is key for early identification of infected individuals and for prevention of further spreading in a population. Currently available molecular diagnostic tests are instrument-based whereas rapid antibody and antigen tests are often not sufficiently sensitive for detection in pre-symptomatic subjects. There is a need for rapid point of care molecular screening tests that can be easily adapted to emerging pathogens and are selective, sensitive, reliable in different settings around the world. We have developed a simple, rapid (<30 min), and inexpensive test for SARS-CoV-2 that is based on combination of isothermal reverse transcription recombinase polymerase amplification (RT-RPA) using modified primers and visual detection with paper-based microfluidics. Our test (CoRapID) is specific for SARS-CoV-2 (alpha to omicron variants) and does not detect other coronaviruses and pathogens by in silico and in vitro analysis. A two-step test protocol was developed with stable lyophilized reagents that reduces handling by using portable and disposable components (droppers, microapplicators/swabs, paper-strips). After optimization of assay components and conditions, we have achieved a limit of detection (LoD) of 1 copy/reaction by adding a blocking primer to the lateral flow assay. Using a set of 138 clinical samples, a sensitivity of 88.1% (P < 0.05, CI: 78.2-93.8%) and specificity of 93.9% (P < 0.05, CI: 85.4-97.6%) was determined. The lack of need for instrumentation for our CoRapID makes it an ideal on-site primary screening tool for local hospitals, doctors' offices, senior homes, workplaces, and in remote settings around the world that often do not have access to clinical laboratories.
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Affiliation(s)
- Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
| | - Yu-Ping Yang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
| | - Spencer Seely
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
| | - Pratibha Joshi
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
- Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Fabiola Iribarren Latasa
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
- Universidad Francisco de Vitoria, Madrid, Spain
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
| | | | | | - Sebastian Bernales
- Merken Biotech SpA, Zañartu, 1482, Santiago, Chile
- Centro Ciencia & Vida, Zañartu, 1482, Santiago, Chile
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136-6129, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136-6129, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136-6129, USA
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136-6129, USA
- University of Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33136-6129, USA
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5
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Cheng XR, Wang F, Liu CY, Li J, Shan C, Wang K, Wang Y, Li PF, Li XM. Sensitive naked-eye detection of telomerase activity based on exponential amplification reaction and lateral flow assay. Anal Bioanal Chem 2022; 414:6139-6147. [PMID: 35715586 DOI: 10.1007/s00216-022-04179-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/27/2022]
Abstract
Telomerase is a promising diagnostic and prognostic biomarker for cancers. Sensitive, simple, and reliable telomerase activity detection is vital for cancer diagnosis. Herein, we developed an ultrasensitive visualized assay for telomerase activity that combined the exponential amplification reaction (EXPAR) and lateral flow assay for easy and quick signal readout, which we termed as a lateral flow readout-EXPAR (LFR-EXPAR) assay. In the LFR-EXPAR assay, telomerase elongation products initiate the exponential amplification reaction, the generated trigger hybridizes with the reporter to form the recognition site of the nicking enzyme, and the nicking enzyme cuts the reporter strand. The degradation of the reporter can be detected with a universal lateral flow dipstick and read out with the naked eye. After conducting a series of proof-of-concept investigations, the LFR-EXPAR assay was found to achieve a sensitivity comparable to that of a TRAP (telomere repeat amplification protocol) assay. The LFR-EXPAR assay can be used to realize ultrasensitive and point-of-care detection of telomerase without requiring specialized instruments, holding great promise for early cancer diagnosis.
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Affiliation(s)
- Xue-Ru Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Chan Shan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China.
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China.
| | - Xin-Min Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao, 266073, China.
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6
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Zhang Y, Farwin A, Ying JY. Directly interface microreaction tube and test strip for the Detection of Salmonella in food with combined isothermal amplification and lateral flow assay. Food Microbiol 2022; 107:104062. [DOI: 10.1016/j.fm.2022.104062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/04/2022]
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7
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Borri C, Centi S, Chioccioli S, Bogani P, Micheletti F, Gai M, Grandi P, Laschi S, Tona F, Barucci A, Zoppetti N, Pini R, Ratto F. Paper-based genetic assays with bioconjugated gold nanorods and an automated readout pipeline. Sci Rep 2022; 12:6223. [PMID: 35418671 PMCID: PMC9007582 DOI: 10.1038/s41598-022-10227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/21/2022] [Indexed: 01/10/2023] Open
Abstract
Paper-based biosensors featuring immunoconjugated gold nanoparticles have gained extraordinary momentum in recent times as the platform of choice in key cases of field applications, including the so-called rapid antigen tests for SARS-CoV-2. Here, we propose a revision of this format, one that may leverage on the most recent advances in materials science and data processing. In particular, we target an amplifiable DNA rather than a protein analyte, and we replace gold nanospheres with anisotropic nanorods, which are intrinsically brighter by a factor of ~ 10, and multiplexable. By comparison with a gold-standard method for dot-blot readout with digoxigenin, we show that gold nanorods entail much faster and easier processing, at the cost of a higher limit of detection (from below 1 to 10 ppm in the case of plasmid DNA containing a target transgene, in our current setup). In addition, we test a complete workflow to acquire and process photographs of dot-blot membranes with custom-made hardware and regression tools, as a strategy to gain more analytical sensitivity and potential for quantification. A leave-one-out approach for training and validation with as few as 36 sample instances already improves the limit of detection reached by the naked eye by a factor around 2. Taken together, we conjecture that the synergistic combination of new materials and innovative tools for data processing may bring the analytical sensitivity of paper-based biosensors to approach the level of lab-grade molecular tests.
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Affiliation(s)
- Claudia Borri
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Sonia Centi
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy.
| | - Sofia Chioccioli
- Dipartimento di Biologia, Università degli Studi di Firenze, 50019, Sesto Fiorentino, FI, Italy
| | - Patrizia Bogani
- Dipartimento di Biologia, Università degli Studi di Firenze, 50019, Sesto Fiorentino, FI, Italy
| | - Filippo Micheletti
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Marco Gai
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Paolo Grandi
- Laboratori Victoria S.R.L, 51100, Pistoia, Italy
| | - Serena Laschi
- Ecobioservices & Researches S.R.L, 50019, Sesto Fiorentino, FI, Italy
| | - Francesco Tona
- Ecobioservices & Researches S.R.L, 50019, Sesto Fiorentino, FI, Italy
| | - Andrea Barucci
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Nicola Zoppetti
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Roberto Pini
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
| | - Fulvio Ratto
- Istituto di Fisica Applicata "Nello Carrara", Consiglio Nazionale delle Ricerche, 50019, Sesto Fiorentino, FI, Italy
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8
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Wang Y, Chen H, Wei H, Rong Z, Wang S. Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader. LAB ON A CHIP 2022; 22:1531-1541. [PMID: 35266944 DOI: 10.1039/d1lc01167g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Several virulent variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged along with the spread of this virus throughout the population. Some variants can exhibit increased transmissibility and reduced immune neutralization reactivity. These changes are deeply concerning issues that may hinder the ongoing effort of epidemic control measures, especially mass vaccination campaigns. The accurate discrimination of SARS-CoV-2 and its emerging variants is essential to contain the coronavirus disease 2019 pandemic. Herein, we report a low-cost, facile, and highly sensitive diagnostic platform that can simultaneously distinguish wild-type (WT) SARS-CoV-2 and its two mutations, namely, D614G and N501Y, within 2 h. WT or mutant (M) nucleic acid fragments at each allelic locus were selectively amplified by the tetra-primer amplification refractory mutation system (ARMS)-PCR assay. Allele-specific amplicons were simultaneously detected by two test lines on a quantum dot nanobead (QB)-based dual-color fluorescent test strip, which could be interpreted by the naked eye or by a home-made fluorescent strip readout device that was wirelessly connected to a smartphone for quantitative data analysis and result presentation. The WT and M viruses were indicated and were strictly discriminated by the presence of a green or red band on test line 1 for the D614G site and test line 2 for the N501Y site. The limits of detection (LODs) for the WT and M D614G were estimated as 78.91 and 33.53 copies per μL, respectively. This assay was also modified for the simultaneous detection of the N and ORF1ab genes of SARS-CoV-2 with LODs of 1.90 and 6.07 copies per μL, respectively. The proposed platform can provide a simple, accurate, and affordable diagnostic approach for the screening of SARS-CoV-2 and its variants of concern even in resource-limited settings.
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Affiliation(s)
- Yunxiang Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Hong Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Hongjuan Wei
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Zhen Rong
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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10
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Bengtson M, Bharadwaj M, Franch O, van der Torre J, Meerdink V, Schallig H, Dekker C. CRISPR-dCas9 based DNA detection scheme for diagnostics in resource-limited settings. NANOSCALE 2022; 14:1885-1895. [PMID: 35044397 PMCID: PMC8812997 DOI: 10.1039/d1nr06557b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 05/17/2023]
Abstract
Nucleic-acid detection is crucial for basic research as well as for applications in medicine such as diagnostics. In resource-limited settings, however, most DNA-detection diagnostic schemes are inapplicable since they rely on expensive machinery, electricity, and trained personnel. Here, we present an isothermal DNA detection scheme for the diagnosis of pathogenic DNA in resource-limited settings. DNA was extracted from urine and blood samples using two different instrument-free methods, and amplified using Recombinase Polymerase Amplification with a sensitivity of <10 copies of DNA within 15 minutes. Target DNA was bound by dCas9/sgRNA that was labelled with a DNA oligomer to subsequently induce Rolling Circle Amplification. This second amplification step produced many copies of a G-quadruplex DNA structure that facilitates a colorimetric readout that is visible to the naked eye. This isothermal DNA-detection scheme can be performed at temperatures between 20-45 °C. As an example of the applicability of the approach, we isothermally (23 °C) detected DNA from a parasite causing visceral leishmaniasis that was spiked into buffer and resulted in a sensitivity of at least 1 zeptomole. For proof of principle, DNA spiked into blood was coupled to the CRISPR-dCas9-based detection scheme yielding a colorimetric readout visible to the naked eye. Given the versatility of the guide-RNA programmability of targets, we envision that this DNA detection scheme can be adapted to detect any DNA with minimal means, which facilitates applications such as point-of-care diagnostics in resource-limited settings.
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Affiliation(s)
- Michel Bengtson
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Mitasha Bharadwaj
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Oskar Franch
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Veronique Meerdink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Henk Schallig
- Amsterdam University Medical Centers, Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory for Experimental Parasitology, Amsterdam institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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12
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Banerjee S, Biswas SK, Kedia N, Sarkar R, De A, Mitra S, Roy S, Chowdhury R, Samaddar S, Bandopadhyay A, Banerjee I, Jana S, Goswami R, Dutta S, Chawla-Sarkar M, Chakraborty S, Mondal A. Piecewise Isothermal Nucleic Acid Testing (PINAT) for Infectious Disease Detection with Sample-to-Result Integration at the Point-of-Care. ACS Sens 2021; 6:3753-3764. [PMID: 34582171 DOI: 10.1021/acssensors.1c01573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed a piecewise isothermal nucleic acid test (PINAT) as a platform technology for diagnosing pathogen-associated infections, empowered by an illustrative novel methodology that embeds an exclusive DNA-mediated specific probing reaction with the backbone of an isothermal reverse transcription cum amplification protocol for detecting viral RNA. In a point-of-care format, this test is executable in a unified single-step, single-chamber procedure, leading to seamless sample-to-result integration in an inexpensive, scalable, pre-programmable, and customizable portable device, with mobile-app-integrated interpretation and analytics involving minimal manually operative procedures. The test exhibited a high sensitivity and specificity of detection when assessed using 200 double-blind patient samples for detecting SARS-CoV-2 infection by the Indian Council of Medical Research (ICMR), and subsequently using 170 double-blind patient samples in a point-of-care format outside controlled laboratory settings as performed by unskilled technicians in an organized clinical trial. We also established its efficacy in detecting Influenza A infection by performing the diagnosis at the point of collection with uncompromised detection rigor. The envisaged trade-off between advanced laboratory-based molecular diagnostic procedures and the elegance of common rapid tests renders the method ideal for deployment in resource-limited settings towards catering the needs of the underserved.
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Affiliation(s)
- Saptarshi Banerjee
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Sujay Kumar Biswas
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, India
| | - Nandita Kedia
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Rakesh Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Aratrika De
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Suvrotoa Mitra
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Subhanita Roy
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Ranjini Chowdhury
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | | | - Aditya Bandopadhyay
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Indranath Banerjee
- B.C. Roy Technology Hospital, Indian Institute of Technology, Kharagpur 721302, India
| | - Subhasis Jana
- Purba Medinipur District Hospital, Tamluk, Purba Medinipur, West Bengal 721636, India
| | - Ritobrata Goswami
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Mamta Chawla-Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Arindam Mondal
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
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13
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Astatke M, Tiburzi O, Connolly A. A novel RNA detection technique for point-of-care identification of pathogens. J Immunoassay Immunochem 2021; 43:1955380. [PMID: 34355634 DOI: 10.1080/15321819.2021.1955380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Despite significant progress in recent years to improve capabilities to diagnose infections at point-of-care (POC), there are still technical hurdles that need to be overcome to ensure proper medical interventions. Current microbial POC tests involve polymerase chain reaction (PCR) or sandwich immunoassay (IA) based detection formats. PCR is highly sensitive but requires complex instrumentation, whereas lateral flow (LF) based IA tests are handheld but lack sensitivity. We present here a portable and sensitive technique by integrating an isothermal RNA amplification approach with IA detection format. The technique comprises i) Nucleic Acid Sequence Based isothermal Amplification (NASBA), ii) amplicon tagging with hapten labeled probes, iii) capturing the amplicon and iv) formation of a sandwich complex with an antibody (Ab) that selectively recognizes the DNA-RNA duplex. The results can be extended to develop an automated, portable and highly sensitive diagnostic platform suitable for POC applications.
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Affiliation(s)
- Mekbib Astatke
- Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, Laurel, United States
| | - Olivia Tiburzi
- Applied Biological Sciences, The Johns Hopkins University Applied Physics Laboratory, Laurel, United States
| | - Amy Connolly
- Fina Biosolutions, LLC, Rockville, United States
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14
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Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
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Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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15
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Nucleic acid lateral flow assay for simultaneous detection of hygiene indicator bacteria. Anal Bioanal Chem 2021; 413:5003-5011. [PMID: 34132819 DOI: 10.1007/s00216-021-03462-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/29/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023]
Abstract
A simple and rapid polymerase chain reaction (PCR)-based lateral flow assay (LFA) was developed for multiplex detection of hygiene indicator bacteria. Specifically, new PCR primers were designed for accurately detecting Escherichia coli, coliform bacteria, and total bacteria, and the results obtained as a colorimetric signal (generated by the accumulation of gold nanoparticles at distinct test zones on flow strips) could be identified by the naked eye in <10 min after the completion of PCR. The proposed LFA system did not exhibit any cross-reactivities with 8 distinct bacterial strains and can detect down to 1 colony forming unit (CFU)/mL. Furthermore, three species of cultured bacteria (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) inoculated onto sterilized ham were successfully analyzed using the LFA system, which demonstrated that this system shows sufficient sensitivity and specificity for food hygiene monitoring. The speed and simplicity of this LFA make it suitable for use in the food industry as part of routine screening analysis.
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16
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Kumar S, Gallagher R, Bishop J, Kline E, Buser J, Lafleur L, Shah K, Lutz B, Yager P. Long-term dry storage of enzyme-based reagents for isothermal nucleic acid amplification in a porous matrix for use in point-of-care diagnostic devices. Analyst 2021; 145:6875-6886. [PMID: 32820749 DOI: 10.1039/d0an01098g] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nucleic acid amplification test (NAAT)-based point-of-care (POC) devices are rapidly growing for use in low-resource settings. However, key challenges are the ability to store the enzyme-based reagents in dry form in the device and the long-term stability of those reagents at elevated temperatures, especially where ambient temperatures could be as high as 45 °C. Here, we describe a set of excipients including a combination of trehalose, polyethylene glycol and dextran, and a method for using them that allows long-term dry storage of enzyme-based reagents for an isothermal strand displacement amplification (iSDA) reaction in a porous matrix. Various porous materials, including nitrocellulose, cellulose, and glass fiber, were tested. Co-dried reagents for iSDA always included those that amplified the ldh1 gene in Staphylococcus aureus (a polymerase and a nicking enzyme, 4 primers, dNTPs and a buffer). Reagents also either included a capture probe and a streptavidin-Au label required for lateral flow (LF) detection after amplification, or a fluorescent probe used for real-time detection. The reagents showed the best stability in a glass fiber matrix when stored in the presence of 10% trehalose and 2.5% dextran. The reagents were stable for over a year at ∼22 °C as determined by lateral flow detection and gel electrophoresis. The reagents also exhibited excellent stability after 360 h at 45 °C; the assay still detected as few as 10 copies of ldh1 gene target by lateral flow detection, and 50 copies with real-time fluorescence detection. These results demonstrate the potential for incorporation of amplification reagents in dry form in point-of-care devices for use in a wide range of settings.
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Affiliation(s)
- Sujatha Kumar
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, Washington, USA.
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17
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Wang X, Wang G, Wang Y, Quan S, Qi H, Sun L, Shen C, Huang H, Jiao W, Shen A. Development and Preliminary Application of Multiplex Loop-Mediated Isothermal Amplification Coupled With Lateral Flow Biosensor for Detection of Mycobacterium tuberculosis Complex. Front Cell Infect Microbiol 2021; 11:666492. [PMID: 33987108 PMCID: PMC8110928 DOI: 10.3389/fcimb.2021.666492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to develop a simple and reliable method to detect Mycobacterium tuberculosis complex (MTBC) and verify its clinical application preliminarily. A loop-mediated isothermal amplification method coupled with lateral flow biosensor (LAMP-LFB) assay, was developed and evaluated for detection of MTBC. Two sets of primers, which targeted IS6110 and IS1081 sequences of MTBC, were designed for establishment of multiplex LAMP-LFB assay. The amplicons were labelled with biotin and fluorescein isothiocyanate (FITC) by adding FITC labelled primer and biotin-14-dATP and biotin-14-dCTP and could be visualized using LFB. The optimal reaction conditions of multiplex LAMP-LFB assay confirmed were 66°C for 50 min. The analytical sensitivity of multiplex LAMP-LFB is 10 fg of genomic templates using pure culture, and no cross-reactivity with other common bacteria and non-tuberculous mycobacteria strains was obtained. A total of 143 clinical samples collected from 100 TB patients (62 definite TB cases and 38 probable TB cases) and 43 non-TB patients were used for evaluating the feasibility of multiplex LAMP-LFB assay. The multiplex LAMP-LFB (82.0%, 82/100) showed higher sensitivity than culture (47.0%, 47/100, P < 0.001) and Xpert MTB/RIF (54.0%, 54/100, P < 0.001). Importantly, the multiplex LAMP-LFB assay detected additional 28 probable TB cases, which increased the percentage of definite TB cases from 62.0% (62/100) to 90.0% (90/100). The specificity of multiplex LAMP-LFB assay in patients without TB was 97.7% (42/43). Therefore, multiplex LAMP-LFB assay is a simple, reliable, and sensitive method for MTBC detection, especially in probable TB cases and resource limited settings.
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Affiliation(s)
- Xingyun Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Guirong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yacui Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shuting Quan
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hairong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weiwei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Adong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
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18
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Wang C, Liu M, Wang Z, Li S, Deng Y, He N. Point-of-care diagnostics for infectious diseases: From methods to devices. NANO TODAY 2021; 37:101092. [PMID: 33584847 PMCID: PMC7864790 DOI: 10.1016/j.nantod.2021.101092] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 05/04/2023]
Abstract
The current widespread of COVID-19 all over the world, which is caused by SARS-CoV-2 virus, has again emphasized the importance of development of point-of-care (POC) diagnostics for timely prevention and control of the pandemic. Compared with labor- and time-consuming traditional diagnostic methods, POC diagnostics exhibit several advantages such as faster diagnostic speed, better sensitivity and specificity, lower cost, higher efficiency and ability of on-site detection. To achieve POC diagnostics, developing POC detection methods and correlated POC devices is the key and should be given top priority. The fast development of microfluidics, micro electro-mechanical systems (MEMS) technology, nanotechnology and materials science, have benefited the production of a series of portable, miniaturized, low cost and highly integrated POC devices for POC diagnostics of various infectious diseases. In this review, various POC detection methods for the diagnosis of infectious diseases, including electrochemical biosensors, fluorescence biosensors, surface-enhanced Raman scattering (SERS)-based biosensors, colorimetric biosensors, chemiluminiscence biosensors, surface plasmon resonance (SPR)-based biosensors, and magnetic biosensors, were first summarized. Then, recent progresses in the development of POC devices including lab-on-a-chip (LOC) devices, lab-on-a-disc (LOAD) devices, microfluidic paper-based analytical devices (μPADs), lateral flow devices, miniaturized PCR devices, and isothermal nucleic acid amplification (INAA) devices, were systematically discussed. Finally, the challenges and future perspectives for the design and development of POC detection methods and correlated devices were presented. The ultimate goal of this review is to provide new insights and directions for the future development of POC diagnostics for the management of infectious diseases and contribute to the prevention and control of infectious pandemics like COVID-19.
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Affiliation(s)
- Chao Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, PR China
| | - Mei Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, PR China
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19
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Boyle AG, Rankin SC, O'Shea K, Stefanovski D, Peng J, Song J, Bau HH. Detection of Streptococcus equi subsp. equi in guttural pouch lavage samples using a loop-mediated isothermal nucleic acid amplification microfluidic device. J Vet Intern Med 2021; 35:1597-1603. [PMID: 33728675 PMCID: PMC8163136 DOI: 10.1111/jvim.16105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/01/2023] Open
Abstract
Background Rapid point‐of‐care (POC) detection of Streptococcus equi subsp. equi (S. equi) would theoretically reduce the spread of strangles by identifying index and carrier horses. Hypothesis That the eqbE isothermal amplification (LAMP) assay, and the same eqbE LAMP assay tested in a microfluidic device format, are comparable to a triplex real‐time quantitative polymerase chain reaction (qPCR) assay that is commonly used in diagnostic labs. Samples Sixty‐eight guttural pouch lavage (GPL) specimens from horses recovering from strangles. Methods Guttural pouch lavage specimens were tested for S. equi retrospectively using the benchtop eqbE LAMP, the eqbE LAMP microfluidic device, and compared to the triplex qPCR, that detects 2 S. equi‐specific genes, eqbE and SEQ2190, as the reference standard using the receiver operating characteristic area under the curve (ROC). Results The 27/68 specimens were positive by benchtop eqbE LAMP, 31/64 by eqbE LAMP microfluidic device, and 12/67 by triplex qPCR. Using the triplex PCR as the reference, the benchtop eqbE LAMP showed excellent discrimination (ROC Area = 0.813, 95% confidence interval [CI] = 0.711‐0.915) as did the LAMP microfluidic device (ROC Area = 0.811, 95% CI = 0.529‐0.782). There was no significant difference between the benchtop LAMP and LAMP microfluidic device (ROC Area 0.813 ± 0.055 vs 0.811 ± 0.034, P = .97). Conclusions The eqbE LAMP microfluidic device detected S. equi in GPL specimens from convalescent horses. This assay shows potential for development as a POC device for rapid, sensitive, accurate, and cost‐efficient detection of S. equi.
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Affiliation(s)
- Ashley G Boyle
- Department of Clinical Studies-New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - Shelley C Rankin
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen O'Shea
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Darko Stefanovski
- Department of Clinical Studies-New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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20
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Rodriguez-Manzano J, Malpartida-Cardenas K, Moser N, Pennisi I, Cavuto M, Miglietta L, Moniri A, Penn R, Satta G, Randell P, Davies F, Bolt F, Barclay W, Holmes A, Georgiou P. Handheld Point-of-Care System for Rapid Detection of SARS-CoV-2 Extracted RNA in under 20 min. ACS CENTRAL SCIENCE 2021; 7:307-317. [PMID: 33649735 PMCID: PMC7839415 DOI: 10.1021/acscentsci.0c01288] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 05/02/2023]
Abstract
The COVID-19 pandemic is a global health emergency characterized by the high rate of transmission and ongoing increase of cases globally. Rapid point-of-care (PoC) diagnostics to detect the causative virus, SARS-CoV-2, are urgently needed to identify and isolate patients, contain its spread and guide clinical management. In this work, we report the development of a rapid PoC diagnostic test (<20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. The developed LAMP assay was tested on a real-time benchtop instrument (RT-qLAMP) showing a lower limit of detection of 10 RNA copies per reaction. It was validated against extracted RNA from 183 clinical samples including 127 positive samples (screened by the CDC RT-qPCR assay). Results showed 91% sensitivity and 100% specificity when compared to RT-qPCR and average positive detection times of 15.45 ± 4.43 min. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n = 52), showing average detection times of 12.68 ± 2.56 min for positive samples (n = 34), demonstrating a comparable performance to a benchtop commercial instrument. Paired with a smartphone for results visualization and geolocalization, this portable diagnostic platform with secure cloud connectivity will enable real-time case identification and epidemiological surveillance.
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Affiliation(s)
- Jesus Rodriguez-Manzano
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kenny Malpartida-Cardenas
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nicolas Moser
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ivana Pennisi
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Matthew Cavuto
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Luca Miglietta
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ahmad Moniri
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rebecca Penn
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Giovanni Satta
- Imperial
College Healthcare NHS Trust, Hammersmith Hospital, London W12 0HS, United Kingdom
| | - Paul Randell
- Imperial
College Healthcare NHS Trust, Hammersmith Hospital, London W12 0HS, United Kingdom
| | - Frances Davies
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Frances Bolt
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Wendy Barclay
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alison Holmes
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial
College Healthcare NHS Trust, Hammersmith Hospital, London W12 0HS, United Kingdom
| | - Pantelis Georgiou
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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21
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Dong T, Ma X, Sheng N, Qi X, Chu Y, Song Q, Zou B, Zhou G. Point-of-care DNA testing by automatically and sequentially performing extraction, amplification and identification in a closed-type cassette. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 327:128919. [PMID: 32963421 PMCID: PMC7497388 DOI: 10.1016/j.snb.2020.128919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 05/06/2023]
Abstract
Nucleic acid detection is important for clinical diagnostics; however, it is challenging to perform genetic testing at the point-of-care due to the tedious steps involved in DNA extraction and the risk of cross-contamination from amplicons. To achieve a fully-automated and contamination-free nucleic acid detection, we propose a closed-type cassette system which enables the following steps to be operated automatically and sequentially: sample preparation based on magnetic beads, target amplification using multiplex polymerase chain reaction, and colorimetric detection of amplicons using a serial invasive reaction coupled with the aggregation of gold nanoparticle probes. The cassette was designed to be round and closed, and 10 targets in a sample could be simultaneously detected by the naked eye or using a spectrophotometer in the system. In addition, a cassette-driven device was fabricated to transfer reagents between wells, to control the temperature of each reaction, and to sense the colour in the detection wells. The cassette system was sensitive enough to detect 10 genotypes at 5 single nucleotide polymorphism sites related to the anticoagulant's usage, by using a 0.5 μL blood sample. The accuracy of the system was evaluated by detecting 12 whole blood samples, and the results obtained were consistent with those obtained using pyrosequencing. The cassette is airtight and the whole system is fully automatic; the only manual operation is the addition of the sample to the cassette, performing point-of-care genetic testing in a sample-in/answer-out way.
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Affiliation(s)
- Tianhui Dong
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Nan Sheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Qinxin Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Guohua Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, China
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22
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Das D, Namboodiri S. Selection of a suitable paper membrane for Loop Mediated Isothermal DNA amplification reaction (LAMP) in a point-of-care diagnostic kit – Experimental and CFD analysis. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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23
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Lu HW, Sakamuri R, Kumar P, Ferguson TM, Doebler RW, Herrington KD, Talbot RP, Weigel KM, Nguyen FK, Cangelosi GA, Narita M, Boyle DS, Niemz A. Integrated nucleic acid testing system to enable TB diagnosis in peripheral settings. LAB ON A CHIP 2020; 20:4071-4081. [PMID: 33021611 PMCID: PMC7787164 DOI: 10.1039/d0lc00445f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To facilitate treatment and limit transmission of tuberculosis (TB), new methods are needed to enable rapid and affordable diagnosis of the disease in high-burden low-resource settings. We have developed a prototype integrated nucleic acid testing device to detect Mycobacterium tuberculosis (M.tb) in sputum. The device consists of a disposable cartridge and compact, inexpensive instrument that automates pathogen lysis, nucleic acid extraction, isothermal DNA amplification and lateral flow detection. A liquefied and disinfected sputum sample is manually injected into the cartridge, and all other steps are automated, with a result provided in <1.5 h. Cell disruption and DNA extraction is executed within a four-port active valve containing a miniature bead blender (based on PureLyse® technology, Claremont BioSolutions LLC). The DNA-containing eluate is combined with dry master-mix reagents and target DNA is isothermally amplified. Amplified master-mix is then pumped into a lateral flow strip chamber for detection. The entire process is performed in a single-use closed-system cartridge to prevent amplicon carryover. For testing of M.tb-spiked sputum the system provided a limit of detection of 5 × 103 colony forming units (CFU) per mL. None of the negative sputum-only controls yielded a false-positive result. Testing of 45 clinical sputum specimens from TB cases and controls relative to a validated manual qPCR-based comparator method revealed a preliminary sensitivity of 90% and specificity of 96%. With further development, the herein described integrated nucleic acid testing device can enable TB diagnosis and treatment initiation in the same clinical encounter in near-patient low-resource settings of high TB burden countries.
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Affiliation(s)
- Hsiang-Wei Lu
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Rama Sakamuri
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Pranav Kumar
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Tanya M Ferguson
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Robert W Doebler
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Keith D Herrington
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Ryan P Talbot
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Kris M Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Felicia K Nguyen
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Masahiro Narita
- Seattle & King County Tuberculosis Control Clinic, Harborview Medical Center, 325 9th Ave, Seattle, WA 98104, USA
| | | | - Angelika Niemz
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
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24
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Development of a polymerase chain reaction - Nucleic acid sensor assay for the rapid detection of chicken adulteration. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Improvement of Loop-Mediated Isothermal Amplification Combined with Chromatographic Flow Dipstick Assay for Salmonella in Food Samples. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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27
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Yee EH, Sikes HD. Polymerization-Based Amplification for Target-Specific Colorimetric Detection of Amplified Mycobacterium tuberculosis DNA on Cellulose. ACS Sens 2020; 5:308-312. [PMID: 31970983 DOI: 10.1021/acssensors.9b02424] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an appealing method for low-cost, point-of-care nucleic acid diagnostic assays due to high sensitivity, minimal equipment requirements, and compatibility with user-friendly colorimetric detection methods. The enhanced sensitivity LAMP offers comes with vulnerability to cross-contamination, where negative samples are exposed to minute amounts of nucleic acids from positive samples. These amounts are insignificant in less sensitive amplification methods, but visible when LAMP is paired with common colorimetric methods. Here, we examined the use of eosin photopolymerization, a tunable reaction, for colorimetric detection of LAMP products to reduce this false positive risk. Using eosin and biotin end-labeled primers, we successfully amplified target regions of the Mycobacterium tuberculosis (MTB) genome using PCR and LAMP, captured amplicons on streptavidin-coated cellulose, and detected DNA targets via eosin photopolymerization, producing a bright pink color only if MTB DNA was present in the sample. Consistent with previous reports, the LAMP-based method exhibited high background signal, but tuning the illumination time for the photopolymerization reaction allowed readouts from samples with no added MTB DNA to remain blank and visually distinct from pink positives. This method yielded limits of detection of 30 and 300 copies/μL for LAMP and PCR amplification, respectively. When confronted with boiled MTB culture samples, this method gave clear positive readouts, compared to negligible signal from other Mycobacterium boiled culture samples. This new method of LAMP colorimetric detection has the potential to increase the utility of LAMP as a nucleic acid assay technique by mitigating sensitivity to cross-contamination.
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Affiliation(s)
| | - Hadley D. Sikes
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
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28
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Liu L, Yang D, Liu G. Signal amplification strategies for paper-based analytical devices. Biosens Bioelectron 2019; 136:60-75. [DOI: 10.1016/j.bios.2019.04.043] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022]
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29
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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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30
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Nurul Najian A, Foo PC, Ismail N, Kim-Fatt L, Yean CY. Probe-specific loop-mediated isothermal amplification magnetogenosensor assay for rapid and specific detection of pathogenic Leptospira. Mol Cell Probes 2019; 44:63-68. [DOI: 10.1016/j.mcp.2019.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/28/2019] [Accepted: 03/10/2019] [Indexed: 12/13/2022]
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31
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Yu J, Wang F, Zhan X, Wang X, Zuo F, Wei Y, Qi J, Liu Y. Improvement and evaluation of loop-mediated isothermal amplification combined with a chromatographic flow dipstick assay and utilization in detection of Vibrio cholerae. Anal Bioanal Chem 2018; 411:647-658. [PMID: 30506503 DOI: 10.1007/s00216-018-1472-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/25/2018] [Accepted: 11/02/2018] [Indexed: 01/27/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a specific, sensitive, and easy-to-perform nucleic acid analytical technique with wide application for diagnosis of disease. Recently, LAMP combined with use of a lateral chromatographic flow dipstick (LFD) has been widely used in nucleic acid detection. However, the LFD mechanism has not been systematically analyzed, and the optimal combination of labeled primers has not been adequately evaluated. We analyzed the LAMP mechanism and discovered that the labeled loop primers played a significant role in the LFD assay. To verify our hypothesis, we developed two LFD assays for Vibrio cholerae to detect the ctxA gene and the 16S-23S ribosomal DNA internal transcribed spacer (ITS). We labeled the inner primers [forward inner primer (FIP) and backward inner primer (BIP)] and loop primers [forward loop primer (LF) and backward loop primer (LB)]. Then the labeled and unlabeled primers were combined to form ten different primer sets. We assessed the specificity, sensitivity, and efficiency of LFD assays with use of different primer compositions. All triple-labeled primer sets resulted in false positive results in the LFD assay, as did the FIP and BIP double-labeled primer set. Other double-labeled-primer sets used in LFD assays showed higher sensitivity than the LAMP assays. Moreover, FIP and LF double-labeled and BIP and LB double-labeled sets had the highest sensitivity. In both cases, assays could be performed in 20 min. We also applied the ITS LFD assays in food samples. The enrichment broths of 112 oyster samples were tested, and the proportion that tested positive by the LFD assays was 6.25%, which was not lower than the rate for the conventional PCR method (5.36%). Graphical abstract ᅟ.
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Affiliation(s)
- Jia Yu
- College of Life Sciences, Qingdao University, Qingdao, 266071, Shandong, China
| | - Feixue Wang
- School of Medicine, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Xijing Zhan
- Tianjin International Travel Health Care Center, Tianjin, 300456, China
| | - Xin Wang
- Tianjin International Travel Health Care Center, Tianjin, 300456, China
| | - Feng Zuo
- Tianjin International Travel Health Care Center, Tianjin, 300456, China
| | - Yuxi Wei
- College of Life Sciences, Qingdao University, Qingdao, 266071, Shandong, China
| | - Jun Qi
- Tianjin International Travel Health Care Center, Tianjin, 300456, China.
| | - Yin Liu
- School of Medicine, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin, 300071, China.
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32
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Luo K, Kim HY, Oh MH, Kim YR. Paper-based lateral flow strip assay for the detection of foodborne pathogens: principles, applications, technological challenges and opportunities. Crit Rev Food Sci Nutr 2018; 60:157-170. [PMID: 30311773 DOI: 10.1080/10408398.2018.1516623] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As a representative colorimetic biosnesor, paper-based LFSA have emerged as a promising and robust tool that can easily and instansly detect the presence of target biological components in food sample. Recently, LFSAs have gained a considerable attention as an alternative method for rapid diagnosis of foodborne pathogens to the conventional culture-based assays such as plate counting and PCR. One major drawback of the current LFSAs for the detection of pathogenic bacteria is the low sensitivity, limiting its practical applications in POCT. Not like many other protein-based biomarkers that are present in nM or pM range, the number of pathogenic bacteria that cause disease can be as low as few CFU/ml. Here, we review current advances in LFSAs for the detection of pathogenic bacteria in terms of chromatic agents and analyte types. Furthermore, recent approaches for signal enhancement and modifications of the LFSA architecture for multiplex detection of pathogenic bacteria are included in this review, together with the advantages and limitations of each techniques. Finally, the technological challenges and future prospect of LFSA-based POCT for the detection of pathogenic bacteria are discussed.
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Affiliation(s)
- Ke Luo
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104 Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104 Korea
| | - Mi-Hwa Oh
- National Institute of Animal Science, Rural Development Administration, Wanju 55365 Korea
| | - Young-Rok Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 17104 Korea
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33
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Reid MS, Le XC, Zhang H. Die exponentielle isotherme Amplifikation von Nukleinsäuren und Assays zur Detektion von Proteinen, Zellen, kleinen Molekülen und Enzymaktivitäten: Anwendungen für EXPAR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Michael S. Reid
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
| | - X. Chris Le
- Department of Chemistry; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
- Department of Laboratory Medicine and Pathology; Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology; Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building; University of Alberta; Edmonton Alberta T6G 2G3 Kanada
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34
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Reid MS, Le XC, Zhang H. Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example. Angew Chem Int Ed Engl 2018; 57:11856-11866. [PMID: 29704305 DOI: 10.1002/anie.201712217] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/09/2018] [Indexed: 12/30/2022]
Abstract
Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in situ assay applications. These amplification techniques eliminate the need for temperature cycling, as required for the polymerase chain reaction (PCR), while achieving comparable amplification yields. We highlight here recent advances in the exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. The incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables the highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from nonspecific template interactions, must be addressed to further improve isothermal and exponential amplification techniques.
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Affiliation(s)
- Michael S Reid
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, 10-102 Clinical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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35
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Bender AT, Borysiak MD, Levenson AM, Lillis L, Boyle DS, Posner JD. Semiquantitative Nucleic Acid Test with Simultaneous Isotachophoretic Extraction and Amplification. Anal Chem 2018; 90:7221-7229. [PMID: 29761701 DOI: 10.1021/acs.analchem.8b00185] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid amplification tests (NAATs) provide high diagnostic accuracy for infectious diseases and quantitative results for monitoring viral infections. The majority of NAATs require complex equipment, cold chain dependent reagents, and skilled technicians to perform the tests. This largely confines NAATs to centralized laboratories and can significantly delay appropriate patient care. Low-cost, point-of-care (POC) NAATs are especially needed in low-resource settings to provide patients with diagnosis and treatment planning in a single visit to improve patient care. In this work, we present a rapid POC NAAT with integrated sample preparation and amplification using electrokinetics and paper substrates. We use simultaneous isotachophoresis (ITP) and recombinase polymerase amplification (RPA) to rapidly extract, amplify, and detect target nucleic acids from serum and whole blood in a paper-based format. We demonstrate simultaneous ITP and RPA can consistently detect 5 copies per reaction in buffer and 10 000 copies per milliliter of human serum with no intermediate user steps. We also show preliminary extraction and amplification of DNA from whole blood samples. Our test is rapid (results in less than 20 min) and made from low-cost materials, indicating its potential for detecting infectious diseases and monitoring viral infections at the POC in low resource settings.
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Affiliation(s)
- Andrew T Bender
- Mechanical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Mark D Borysiak
- Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | - Amanda M Levenson
- Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
| | | | | | - Jonathan D Posner
- Mechanical Engineering , University of Washington , Seattle , Washington 98195 , United States.,Chemical Engineering , University of Washington , Seattle , Washington 98195 , United States
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36
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Özay B, Robertus CM, Negri JL, McCalla SE. First characterization of a biphasic, switch-like DNA amplification. Analyst 2018; 143:1820-1828. [PMID: 29577124 PMCID: PMC5969907 DOI: 10.1039/c8an00130h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1 pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.
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Affiliation(s)
- Burcu Özay
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT 59717, USA.
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37
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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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38
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Poulton K, Webster B. Development of a lateral flow recombinase polymerase assay for the diagnosis of Schistosoma mansoni infections. Anal Biochem 2018; 546:65-71. [PMID: 29425749 DOI: 10.1016/j.ab.2018.01.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 12/14/2022]
Abstract
Infection with Schistosoma mansoni causes intestinal schistosomiasis, a major health problem across Africa. The accurate diagnosis of intestinal schistosomiasis is vital to inform surveillance/control programs. Diagnosis mainly relies on microscopic detection of eggs in faecal samples but many factors affect sensitivity. Molecular diagnostics are sensitive and specific but application is limited as necessary infrastructure, financial resources and skilled personnel are often lacking in endemic settings. Recombinase Polymerase Amplification (RPA) is an isothermal DNA amplification/detection technology that is practical in nearly any setting. Here we developed a RPA lateral flow (LF) assay targeting the 28S rDNA region of S. mansoni. The 28S LF-RPA assay's lower limit of detection was 10pg DNA with the lower test parameters permitting sufficient amplification being 6 min and 25°C. Optimal assay parameters were 40-45°C and 10 min with an analytical sensitivity of 102 copies of DNA. Additionally the PCRD3 lateral flow detection cassettes proved more robust and sensitive compared to the Milenia HybriDetect strips. This 28S LF-RPA assay produces quick reproducible results that are easy to interpret, require little infrastructure and is a promising PON test for the field molecular diagnosis of intestinal schistosomiasis.
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Affiliation(s)
- Kate Poulton
- The London School of Hygiene and Tropical Medicine, Keppel Street, London, UK; The Natural History Museum, Cromwell Road, London, UK
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39
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Li S, Gu Y, Lyu Y, Jiang Y, Liu P. Integrated Graphene Oxide Purification-Lateral Flow Test Strips (iGOP-LFTS) for Direct Detection of PCR Products with Enhanced Sensitivity and Specificity. Anal Chem 2017; 89:12137-12144. [PMID: 29072445 DOI: 10.1021/acs.analchem.7b02769] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An integrated graphene oxide purification-lateral flow test strip (iGOP-LFTS) was developed for on-strip purifying and visually detecting polymerase chain reaction (PCR) products with an improved sensitivity as well as a more stringent specificity. PCR products amplified with a pair of biotin- and digoxin-labeled primers were directly pipetted onto GO pads, on which graphene oxide selectively adsorbed residual primers and primer-dimers with the aid of a running buffer containing MgCl2 and Tween 20. By stacking up three GO pads to increase the surface area for adsorption, 83.4% of double-stranded DNA with a length of 30 bp and 98.6% of 20-nt primers could be removed from a 10-μL DNA mixture. Since no primers interfered with detection, the increase of the sample loading volume from 5 to 20 μL could improve the signal-to-noise ratio of the test line 1.6 fold using the iGOP-LFTS while no changes were observed using the conventional LFTS. The limit of detection of the iGOP-LFTS was determined to be 30 copies of bacteriophage λ-DNA with naked eyes and this limit could be further decreased to 3 copies by loading 20 μL of the sample, which corresponded to a 1000-fold improvement compared to that of the LFTS detected by naked eyes. When the ImageJ analysis was employed, a 100-fold decrease of the detection limit can be obtained. In addition, due to the removal of the primer-dimers, the dim test line observed in the negative control of the LFTS was eliminated using the iGOP-LFTS. A mock clinical specimen spiked with defective HIV-1 (human immunodeficiency virus) viruses was successfully analyzed using a two-step reverse transcription-PCR with 30 amplification cycles followed by the iGOP-LFTS detection. These significant improvements were achieved without introducing any additional hands-on operations and instrumentations.
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Affiliation(s)
- Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing, 100084, China
| | - Yin Gu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing, 100084, China
| | - Yi Lyu
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, 102206, China
| | - Yan Jiang
- National HIV/HCV Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, 102206, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University , Beijing, 100084, China
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40
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Sun Y, Chen J, Li J, Xu Y, Jin H, Xu N, Yin R, Hu G. Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis. PLoS One 2017; 12:e0186985. [PMID: 29084241 PMCID: PMC5662171 DOI: 10.1371/journal.pone.0186985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/11/2017] [Indexed: 12/24/2022] Open
Abstract
Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb) in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM), but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST), was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC) microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation.
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Affiliation(s)
- Yajuan Sun
- Department of Neurology, the Second Hospital of Jilin University, Changchun, Jilin, China
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Jiajun Chen
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Jia Li
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yawei Xu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Hui Jin
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Na Xu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Rui Yin
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- College of Biological Engineering, Jilin College of Agricultural Science and Technology, Jilin, Jilin, China
- * E-mail: (GHH); (RY)
| | - Guohua Hu
- Department of Neurology, the Second Hospital of Jilin University, Changchun, Jilin, China
- * E-mail: (GHH); (RY)
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41
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Mauk M, Song J, Bau HH, Gross R, Bushman FD, Collman RG, Liu C. Miniaturized devices for point of care molecular detection of HIV. LAB ON A CHIP 2017; 17:382-394. [PMID: 28092381 PMCID: PMC5285266 DOI: 10.1039/c6lc01239f] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The HIV pandemic affects 36.7 million people worldwide, predominantly in resource-poor settings. Nucleic acid-based molecular detection of HIV plays a significant role in antiretroviral treatment monitoring for HIV patients, as well as diagnosis of HIV infection in infants. Currently available molecular diagnostic methods are complex, time-consuming and relatively expensive, thus limiting their use in resource-poor settings. Recent advances in microfluidics technology have made possible low-cost integrated miniaturized devices for molecular detection and quantification of HIV at the point of care. We review recent technical advances in molecular testing of HIV using microfluidic technology, with a focus on assays based on isothermal nucleic acid amplification. Microfluidic components for sample preparation, isothermal amplification and result detection are discussed and compared. We also discuss the challenges and future directions for developing an integrated "sample-to-result" microfluidic platform for HIV molecular detection.
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Affiliation(s)
- Michael Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Robert Gross
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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42
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Ultrasensitive, rapid and inexpensive detection of DNA using paper based lateral flow assay. Sci Rep 2016; 6:37732. [PMID: 27886248 PMCID: PMC5123575 DOI: 10.1038/srep37732] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/31/2016] [Indexed: 01/07/2023] Open
Abstract
Sensitive, specific, rapid, inexpensive and easy-to-use nucleic acid tests for use at the point-of-need are critical for the emerging field of personalised medicine for which companion diagnostics are essential, as well as for application in low resource settings. Here we report on the development of a point-of-care nucleic acid lateral flow test for the direct detection of isothermally amplified DNA. The recombinase polymerase amplification method is modified slightly to use tailed primers, resulting in an amplicon with a duplex flanked by two single stranded DNA tails. This tailed amplicon facilitates detection via hybridisation to a surface immobilised oligonucleotide capture probe and a gold nanoparticle labelled reporter probe. A detection limit of 1 × 10-11 M (190 amol), equivalent to 8.67 × 105 copies of DNA was achieved, with the entire assay, both amplification and detection, being completed in less than 15 minutes at a constant temperature of 37 °C. The use of the tailed primers obviates the need for hapten labelling and consequent use of capture and reporter antibodies, whilst also avoiding the need for any post-amplification processing for the generation of single stranded DNA, thus presenting an assay that can facilely find application at the point of need.
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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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Li J, Macdonald J. Multiplexed lateral flow biosensors: Technological advances for radically improving point-of-care diagnoses. Biosens Bioelectron 2016; 83:177-92. [DOI: 10.1016/j.bios.2016.04.021] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/22/2022]
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Zhang J, Shen Z, Xiang Y, Lu Y. Integration of Solution-Based Assays onto Lateral Flow Device for One-Step Quantitative Point-of-Care Diagnostics Using Personal Glucose Meter. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00270] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- JingJing Zhang
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Zhe Shen
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yu Xiang
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yi Lu
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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46
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Comparison of isothermal helicase-dependent amplification and PCR for the detection of Mycobacterium tuberculosis by an electrochemical genomagnetic assay. Anal Bioanal Chem 2016; 408:8603-8610. [DOI: 10.1007/s00216-016-9514-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 01/09/2023]
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Safavieh M, Kanakasabapathy MK, Tarlan F, Ahmed MU, Zourob M, Asghar W, Shafiee H. Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection. ACS Biomater Sci Eng 2016; 2:278-294. [PMID: 28503658 PMCID: PMC5425166 DOI: 10.1021/acsbiomaterials.5b00449] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.
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Affiliation(s)
- Mohammadali Safavieh
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Manoj K. Kanakasabapathy
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Farhang Tarlan
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
| | - Minhaz U. Ahmed
- Biosensors and Biotechnology Laboratory, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, Negara Brunei Darussalam
| | - Mohammed Zourob
- Department of Chemistry, College of Science, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Waseem Asghar
- Department of Computer Engineering & Electrical Engineering and Computer Science, Florida Atlantic University, 777 Glades Road, Boca Raton, Florida 33431, United States
| | - Hadi Shafiee
- Division of Biomedical Engineering, Division of Renal Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 65 Lansdowne Street, Cambridge, Massachusetts 02139, United States
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48
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Ferguson TM, Weigel KM, Lakey Becker A, Ontengco D, Narita M, Tolstorukov I, Doebler R, Cangelosi GA, Niemz A. Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis. Sci Rep 2016; 6:19541. [PMID: 26785769 PMCID: PMC4726292 DOI: 10.1038/srep19541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/16/2015] [Indexed: 11/23/2022] Open
Abstract
Nucleic acid amplification testing (NAAT) enables rapid and sensitive diagnosis of tuberculosis (TB), which facilitates treatment and mitigates transmission. Nucleic acid extraction from sputum constitutes the greatest technical challenge in TB NAAT for near-patient settings. This report presents preliminary data for a semi-automated sample processing method, wherein sputum is disinfected and liquefied, followed by PureLyse® mechanical lysis and solid-phase nucleic acid extraction in a miniaturized, battery-operated bead blender. Sputum liquefaction and disinfection enabled a >104 fold reduction in viable load of cultured Mycobacterium tuberculosis (M.tb) spiked into human sputum, which mitigates biohazard concerns. Sample preparation via the PureLyse® method and a clinically validated manual method enabled positive PCR-based detection for sputum spiked with 104 and 105 colony forming units (cfu)/mL M.tb. At 103 cfu/mL sputum, four of six and two of six samples amplified using the comparator and PureLyse® method, respectively. For clinical specimens from TB cases and controls, the two methods provided 100% concordant results for samples with 1 mL input volume (N = 41). The semi-automated PureLyse® method therefore performed similarly to a validated manual comparator method, but is faster, minimally instrumented, and can be integrated into TB molecular diagnostic platforms designed for near-patient low-resource settings.
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Affiliation(s)
| | - Kris M Weigel
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, WA.,Seattle Biomedical Research Institute, Seattle, WA
| | - Annie Lakey Becker
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, WA.,Seattle Biomedical Research Institute, Seattle, WA
| | - Delia Ontengco
- Seattle Biomedical Research Institute, Seattle, WA.,University of Santo Tomas Graduate School, Manila, Philippines
| | - Masahiro Narita
- Public Health - Seattle &King County, TB Control Program, Seattle, WA
| | | | | | - Gerard A Cangelosi
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, WA.,Seattle Biomedical Research Institute, Seattle, WA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA
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50
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Nurul Najian A, Engku Nur Syafirah E, Ismail N, Mohamed M, Yean CY. Development of multiplex loop mediated isothermal amplification (m-LAMP) label-based gold nanoparticles lateral flow dipstick biosensor for detection of pathogenic Leptospira. Anal Chim Acta 2016; 903:142-8. [DOI: 10.1016/j.aca.2015.11.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/25/2015] [Accepted: 11/05/2015] [Indexed: 01/21/2023]
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