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Peng K, Wu Z, Feng Z, Deng R, Ma X, Fan B, Liu H, Tang Z, Zhao Z, Li Y. A highly integrated digital PCR system with on-chip heating for accurate DNA quantitative analysis. Biosens Bioelectron 2024; 253:116167. [PMID: 38422813 DOI: 10.1016/j.bios.2024.116167] [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: 09/27/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Digital polymerase chain reaction (dPCR) is extensively used for highly sensitive disease diagnosis due to its single-molecule detection ability. However, current dPCR systems require intricate DNA sample distribution, rely on cumbersome external heaters, and exhibit sluggish thermal cycling, hampering efficiency and speed of the dPCR process. Herein, we presented the development of a microwell array based dPCR system featuring an integrated self-heating dPCR chip. By utilizing hydrodynamic and electrothermal simulations, the chip's structure is optimized, resulting in improved partitioning within microwells and uniform thermal distribution. Through strategic hydrophilic/hydrophobic modifications on the chip's surface, we effectively secured the compartmentalization of sample within the microwells by employing an overlaying oil phase, which renders homogeneity and independence of samples in the microwells. To achieve precise, stable, uniform, and rapid self-heating of the chip, the ITO heating layer and the temperature control algorithm are deliberately designed. With a capacity of 22,500 microwells that can be easily expanded, the system successfully quantified EGFR plasmid solutions, exhibiting a dynamic linear range of 105 and a detection limit of 10 copies per reaction. To further validate its performance, we employed the dPCR platform for quantitative detection of BCR-ABL1 mutation gene fragments, where its performance was compared against the QuantStudio 3D, and the self-heating dPCR system demonstrated similar analytical accuracy to the commercial dPCR system. Notably, the individual chip is produced on a semiconductor manufacturing line, benefiting from mass production capabilities, so the chips are cost-effective and conducive to widespread adoption and accessibility.
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Affiliation(s)
- Kang Peng
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhihong Wu
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhongxin Feng
- Affiliated Hospital of Guizhou Medical University, Guiyang, 550002, Guizhou, PR China
| | - Ruijun Deng
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Xiangguo Ma
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Beiyuan Fan
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Haonan Liu
- BOE Technology Group Co Ltd., Beijing, 100176, PR China
| | - Zhuzhu Tang
- Affiliated Hospital of Guizhou Medical University, Guiyang, 550002, Guizhou, PR China
| | - Zijian Zhao
- BOE Technology Group Co Ltd., Beijing, 100176, PR China.
| | - Yanzhao Li
- BOE Technology Group Co Ltd., Beijing, 100176, PR China.
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2
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Sepahi N, Samsami S, Mansoori Y, Chenari M, Namavari N, Yazdanpanah A, Ghasemian A, Montaseri Z, Sharifzadeh M, Ranjbar R, Namavari S, Ghanbariasad A. Development of a novel Colorimetric Assay for the rapid diagnosis of Coronavirus disease 2019 from nasopharyngeal samples. Sci Rep 2024; 14:12125. [PMID: 38802360 PMCID: PMC11130264 DOI: 10.1038/s41598-024-53747-0] [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: 11/14/2023] [Accepted: 02/04/2024] [Indexed: 05/29/2024] Open
Abstract
Emergence of Coronavirus disease 2019 (COVID-19) pandemic has posed a huge threat to public health. Rapid and reliable test to diagnose infected subjects is crucial for disease spread control. We developed a colorimetric test for COVID-19 detection using a Colorimetric Assay based on thiol-linked RNA modified gold nanoparticles (AuNPs) and oligonucleotide probes. This method was conducted on RNA from 200 pharyngeal swab samples initially tested by Real-Time polymerase chain reaction (RT-PCR) as gold standard. A specific oligonucleotide probe designed based on ORF1ab of COVID-19 was functionalized with AuNPs-probe conjugate. The exposure of AuNP-probe to isolated RNA samples was tested using hybridization. In this comparative study, the colorimetric functionalized AuNPs assay exhibited a detection limit of 25 copies/µL. It was higher in comparison to the RT-PCR method, which could only detect 15 copies/µL. The results demonstrated 100% specificity and 96% sensitivity for the developed method. Herein, we developed an incredibly rapid, simple and cost-effective Colorimetric Assay lasting approximately 30 min which could process considerably higher number of COVID-19 samples compared to the RT-PCR. This AuNP-probe conjugate colorimetric method could be considered the optimum alternatives for conventional diagnostic tools especially in over-populated and/or low-income countries.
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Affiliation(s)
- Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Sahar Samsami
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Maryam Chenari
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Negin Namavari
- School of Medicine Grenada, St. George's University, St. George's, West Indies, Grenada
| | - Ava Yazdanpanah
- Student Research Committee, Fasa University of Medical Sciences, Fasa, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Zahra Montaseri
- Department of Infectious Diseases, School of Medicine, Fasa University of Medical Science, Fasa, Iran
| | - Mahboobeh Sharifzadeh
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Razie Ranjbar
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Sahar Namavari
- Department of Medical Biotechnologies, School of Advanced Technologies, Fasa University of Medical Sciences, Avicenna Square, Fasa, Fars, Islamic Republic of Iran
| | - Ali Ghanbariasad
- Department of Medical Biotechnologies, School of Advanced Technologies, Fasa University of Medical Sciences, Avicenna Square, Fasa, Fars, Islamic Republic of Iran.
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3
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Lewis JD, Salipante SJ. Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests. J Clin Microbiol 2024; 62:e0024324. [PMID: 38629844 DOI: 10.1128/jcm.00243-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.
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Affiliation(s)
- Janessa D Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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4
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Hussain M, He X, Wang C, Wang Y, Wang J, Chen M, Kang H, Yang N, Ni X, Li J, Zhou X, Liu B. Recent advances in microfluidic-based spectroscopic approaches for pathogen detection. BIOMICROFLUIDICS 2024; 18:031505. [PMID: 38855476 PMCID: PMC11162289 DOI: 10.1063/5.0204987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024]
Abstract
Rapid identification of pathogens with higher sensitivity and specificity plays a significant role in maintaining public health, environmental monitoring, controlling food quality, and clinical diagnostics. Different methods have been widely used in food testing laboratories, quality control departments in food companies, hospitals, and clinical settings to identify pathogens. Some limitations in current pathogens detection methods are time-consuming, expensive, and laborious sample preparation, making it unsuitable for rapid detection. Microfluidics has emerged as a promising technology for biosensing applications due to its ability to precisely manipulate small volumes of fluids. Microfluidics platforms combined with spectroscopic techniques are capable of developing miniaturized devices that can detect and quantify pathogenic samples. The review focuses on the advancements in microfluidic devices integrated with spectroscopic methods for detecting bacterial microbes over the past five years. The review is based on several spectroscopic techniques, including fluorescence detection, surface-enhanced Raman scattering, and dynamic light scattering methods coupled with microfluidic platforms. The key detection principles of different approaches were discussed and summarized. Finally, the future possible directions and challenges in microfluidic-based spectroscopy for isolating and detecting pathogens using the latest innovations were also discussed.
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Affiliation(s)
| | - Xu He
- Engineering Research Center of Intelligent Theranostics Technology and Instruments, Ministry of Education, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Chao Wang
- Engineering Research Center of Intelligent Theranostics Technology and Instruments, Ministry of Education, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Yichuan Wang
- Engineering Research Center of Intelligent Theranostics Technology and Instruments, Ministry of Education, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Jingjing Wang
- Engineering Research Center of Intelligent Theranostics Technology and Instruments, Ministry of Education, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Mingyue Chen
- Engineering Research Center of Intelligent Theranostics Technology and Instruments, Ministry of Education, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Haiquan Kang
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | | | - Xinye Ni
- The Affiliated Changzhou Second People’s Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou 213161, China
| | | | - Xiuping Zhou
- Department of Laboratory Medicine, The Peoples Hospital of Rugao, Rugao Hospital Affiliated to Nantong University, Nantong 226500, China
| | - Bin Liu
- Author to whom correspondence should be addressed:
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5
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Barra M, Chang M, Salcedo MP, Schmeler K, Scheurer M, Maza M, Lopez L, Alfaro K, Richards-Kortum R. Single-tube four-target lateral flow assay detects human papillomavirus types associated with majority of cervical cancers. Anal Biochem 2024; 688:115480. [PMID: 38331373 DOI: 10.1016/j.ab.2024.115480] [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: 12/20/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Isothermal nucleic acid amplification methods have many advantages for use at the point of care. However, there is a lack of multiplexed isothermal amplification tests to detect multiple targets in a single reaction, which would be valuable for many diseases, such as infection with high-risk human papillomavirus (hrHPV). In this study, we developed a multiplexed loop-mediated isothermal amplification (LAMP) reaction to detect the three most common hrHPV types that cause cervical cancer (HPV16, HPV18, and HPV45) and a cellular control for sample adequacy. First, we characterized the assay limit of detection (LOD) in a real-time reaction with fluorescence readout; after 30 min of amplification the LOD was 100, 10, and 10 copies/reaction of HPV16, HPV18, and HPV45, respectively, and 0.1 ng/reaction of human genomic DNA (gDNA). Next, we implemented the assay on lateral flow strips, and the LOD was maintained for HPV16 and HPV18, but increased to 100 copies/reaction for HPV45 and to 1 ng/reaction for gDNA. Lastly, we used the LAMP test to evaluate total nucleic acid extracted from 38 clinical samples; compared to qPCR, the LAMP test had 89% sensitivity and 95% specificity. When integrated with sample preparation, this multiplexed LAMP assay could be useful for point-of-care testing.
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Affiliation(s)
- Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Megan Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mila P Salcedo
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Scheurer
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Mauricio Maza
- Basic Health International, San Salvador, El Salvador
| | - Leticia Lopez
- Basic Health International, San Salvador, El Salvador
| | - Karla Alfaro
- Basic Health International, San Salvador, El Salvador
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6
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Ruszova E, Vanek D, Stühmer W, Khaznadar Z, Subhashini N. The Utilization of the SaLux19-Based Loop-Mediated Isothermal Amplification (LAMP) Assay for the Rapid and Sensitive Identification of Minute Amounts of a Biological Specimen. Life (Basel) 2024; 14:579. [PMID: 38792600 PMCID: PMC11122329 DOI: 10.3390/life14050579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Our research has developed a highly sensitive and simple assay to detect small amounts of animal and human biological material in less than 40 min. The handheld SaLux19 device developed at the Max Planck Institute of Experimental Medicine in Göttingen, Germany, was used to validate our concept. The proposed system uses isothermal amplification of DNA in a rapid assay format. Our results show that the assay can detect Sus scrofa nucleic acids with very high sensitivity and specificity. This detection system has potential for forensic scenarios.
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Affiliation(s)
- Ema Ruszova
- Bulovka University Hospital, 180 81 Prague, Czech Republic
- Forensic DNA Service, Budinova 2, 180 81 Prague, Czech Republic
| | - Daniel Vanek
- Bulovka University Hospital, 180 81 Prague, Czech Republic
- Forensic DNA Service, Budinova 2, 180 81 Prague, Czech Republic
- Institute for Environmental Sciences, Charles University, 110 00 Prague, Czech Republic
- Department of Forensic Medicine, Second Faculty of Medicine, Charles University, 110 00 Prague, Czech Republic
| | - Walter Stühmer
- Max Planck Institute of Multidisciplinary Sciences, Hermann-Rein-Str. 3, 37075 Göttingen, Germany
| | - Ziad Khaznadar
- Bulovka University Hospital, 180 81 Prague, Czech Republic
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7
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Tran DH, Tran HT, Vo B, Than TT, Nguyen VT, Le VP, Phung H. Enhancing classical swine fever virus identification: the advantages of Field-LAMP testing. Aust Vet J 2024; 102:67-73. [PMID: 37875328 DOI: 10.1111/avj.13297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/22/2023] [Accepted: 10/07/2023] [Indexed: 10/26/2023]
Abstract
Classical swine fever virus (CSFV) identification has witnessed significant advancements with the development of rapid reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assays. However, conventional RT-LAMP assays for CSFV diagnosis are hindered by a laborious RNA extraction step. Moreover, the need for thermal incubators and expensive micropipettes has limited their application in field settings. Addressing these challenges, our study presents a groundbreaking solution-an electro-free and point-of-care (POC) tool known as the field-LAMP assay-for the rapid clinical detection of CSFV. By eliminating the RNA extraction requirement, advancing the colorimetric read-out and lyophilized reaction reagents, our field-LAMP assay streamlines the diagnostic process, saving valuable time and effort. This novel approach also overcomes the dependency on electric-dependent thermal incubators and expensive micropipettes, making it practical and accessible for use in the field. The successful development of the field-LAMP assay marks a significant milestone in CSFV detection. This electro-free and POC tool offers several advantages, including its ability to deliver rapid results without compromising accuracy, facilitating prompt response and containment measures.
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Affiliation(s)
- D H Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - H T Tran
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Btt Vo
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - T T Than
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - V T Nguyen
- Institute of Veterinary Science and Technology, Hanoi, Vietnam
| | - V P Le
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Htt Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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8
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Manzo M, Serra A, Pedone E, Pirone L, Scognamiglio V, De Felice M, De Falco M. DNA Polymerase I Large Fragment from Deinococcus radiodurans, a Candidate for a Cutting-Edge Room-Temperature LAMP. Int J Mol Sci 2024; 25:1392. [PMID: 38338670 PMCID: PMC10855757 DOI: 10.3390/ijms25031392] [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: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
In recent years, the loop-mediated isothermal amplification (LAMP) technique, designed for microbial pathogen detection, has acquired fundamental importance in the biomedical field, providing rapid and precise responses. However, it still has some drawbacks, mainly due to the need for a thermostatic block, necessary to reach 63 °C, which is the BstI DNA polymerase working temperature. Here, we report the identification and characterization of the DNA polymerase I Large Fragment from Deinococcus radiodurans (DraLF-PolI) that functions at room temperature and is resistant to various environmental stress conditions. We demonstrated that DraLF-PolI displays efficient catalytic activity over a wide range of temperatures and pH, maintains its activity even after storage under various stress conditions, including desiccation, and retains its strand-displacement activity required for isothermal amplification technology. All of these characteristics make DraLF-PolI an excellent candidate for a cutting-edge room-temperature LAMP that promises to be very useful for the rapid and simple detection of pathogens at the point of care.
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Affiliation(s)
- Marilena Manzo
- Institute of Bioscience and BioResources, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Assunta Serra
- Institute of Bioscience and BioResources, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Viviana Scognamiglio
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, Monterotondo, 00015 Rome, Italy
| | - Mariarita De Felice
- Institute of Bioscience and BioResources, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mariarosaria De Falco
- Institute of Bioscience and BioResources, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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9
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Camacho MJ, Albuquerque DC, Inácio ML, Martins VC, Mota M, Freitas PP, de Andrade E. FTA-LAMP based biosensor for a rapid in-field detection of Globodera pallida-the pale potato cyst nematode. Front Bioeng Biotechnol 2024; 12:1337879. [PMID: 38303911 PMCID: PMC10830618 DOI: 10.3389/fbioe.2024.1337879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
The combination of a sensitive and specific magnetoresistive sensing device with an easy DNA extraction method and a rapid isothermal amplification is presented here targeting the on-site detection of Globodera pallida, a potato endoparasitic nematode. FTA-cards were used for DNA extraction, LAMP was the method developed for DNA amplification and a nanoparticle functionalized magnetic-biosensor was used for the detection. The combinatorial effect of these three emerging technologies has the capacity to detect G. pallida with a detection limit of one juvenile, even when mixed with other related species. This combined system is far more interesting than what a single technology can provide. Magnetic biosensors can be combined with any DNA extraction protocol and LAMP forming a new solution to target G. pallida. The probe designed in this study consistently distinguished G. pallida (∆Vac binding/Vac sensor above 1%) from other cyst nematodes (∆Vac binding/Vac sensor below 1%). It was confirmed that DNA either extracted with FTA-cards or Lab extraction Kit was of enough quantity and quality to detect G. pallida whenever present (alone or in mixed samples), ensuring probe specificity and sensitivity. This work provides insights for a new strategy to construct advanced devices for pathogens in-field diagnostics. LAMP runs separately but can be easily integrated into a single device.
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Affiliation(s)
- Maria João Camacho
- INIAV—National Institute for Agriculture and Veterinary Research, Oeiras, Portugal
- NemaLab/ MED—Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal
- INESC Microsistemas e Nanotecnologias, Lisbon, Portugal
| | - Débora C. Albuquerque
- INESC Microsistemas e Nanotecnologias, Lisbon, Portugal
- IST—Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Maria L. Inácio
- INIAV—National Institute for Agriculture and Veterinary Research, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
| | | | - Manuel Mota
- NemaLab/ MED—Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal
| | - Paulo P. Freitas
- INESC Microsistemas e Nanotecnologias, Lisbon, Portugal
- INL—International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Eugénia de Andrade
- INIAV—National Institute for Agriculture and Veterinary Research, Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
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10
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Tao J, Yan H, Chen S, Du J, Zhou S, Guo H, Lu L, Fang J, Jin X, Wang Z, Ying H, Han W, Dai F. Establishment and application of a loop-mediated isothermal amplification-lateral flow dipstick (LAMP-LFD) method for detecting Clostridium piliforme. Vet Med Sci 2024; 10:e1318. [PMID: 37922247 PMCID: PMC10949940 DOI: 10.1002/vms3.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/21/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023] Open
Abstract
BACKGROUND Clostridium piliforme (causative agent of Tyzzer disease) infects various animals, including primates, and hence a threat to animal and human health worldwide. At present, it is detected using traditional methods, such as path morphology, polymerase chain reaction and enzyme-linked immunosorbent assay. Therefore, it is necessary to develop convenient, efficient visual molecular biological methods for detecting C. piliforme. OBJECTIVES To establish a method with good specificity, high sensitivity and simple operation for the detection of C. piliforme. METHODS In this study, we designed internal and external primers based on the conserved 23S rRNA region of C. piliforme to develop a biotin-labelled diarrhoea-suffered loop-mediated isothermal amplification (LAMP) system for detecting of C. piliforme and assessed the specificity, sensitivity and repeatability of the LAMP system. RESULTS The LAMP system did not exhibit cross-reactivity with 24 other common pathogenic species, indicating that it had good specificity. The minimum concentration of sensitivity was 1 × 10-7 ng/μL. Mouse models (Meriones unguiculatus) of Tyzzer disease were established and a LAMP-lateral flow dipstick (LAMP-LFD) was developed for detecting C. piliforme. The detection rate of C. piliforme was 5.08% in clean-grade animals and 9.96% in specific-pathogen-free-grade animals from Jiangsu, Zhejiang and Shanghai. In addition, the detection rates of C. piliforme were 10.1%, 8.6% and 20%, in animals from Hangzhou, Wenzhou and Shaoxing, respectively. The detection rate of C. piliforme was higher in experimental animals used in schools than in those used in companies and research institutes. CONCLUSIONS The LAMP-LFD method established in this study can be used to detect C. piliforme in animals handled in laboratory facilities of universities, pharmaceutical enterprises and research and development institutions.
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Affiliation(s)
- Junhao Tao
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Huiqiong Yan
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Sisi Chen
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Jiangtao Du
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Shasang Zhou
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Honggang Guo
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Lingqun Lu
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
| | - Jie Fang
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Xiaoyin Jin
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Zhiyuan Wang
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
| | - Huazhong Ying
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
- Engineering Research Center of Novel Vaccine of Zhejiang ProvinceHangzhou Medical CollegeHangzhouChina
| | - Wei Han
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
- Engineering Research Center of Novel Vaccine of Zhejiang ProvinceHangzhou Medical CollegeHangzhouChina
| | - Fangwei Dai
- Center of Laboratory AnimalHangzhou Medical CollegeHangzhouChina
- Zhejiang Provincial Key Laboratory of Laboratory Animals and Safety ResearchHangzhou Medical CollegeHangzhouChina
- Engineering Research Center of Novel Vaccine of Zhejiang ProvinceHangzhou Medical CollegeHangzhouChina
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11
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Grammatikos S, Svoliantopoulos I, Gizeli E. Naked-Eye Detection of LAMP-Produced Nucleic Acids in Saliva Using Chitosan-Capped AuNPs in a Single-Tube Assay. Anal Chem 2023; 95:18514-18521. [PMID: 38065570 PMCID: PMC10733902 DOI: 10.1021/acs.analchem.3c03878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a low-technology molecular assay that is highly adaptable to point-of-care (POC) applications. However, achieving sensitive naked-eye detection of the amplified target in a crude sample is challenging. Herein, we report a simple yet highly efficient and sensitive methodology for the colorimetric visualization of a single target copy in saliva using chitosan-capped gold nanoparticles (Chit-AuNPs) synthesized via a green chemistry approach. The presence or absence of free Chit in the Chit-AuNPs solution was shown to affect LAMP colorimetric detection oppositely: the observed stabilization in the negative samples and aggregation in the positive samples in the presence of free Chit were reversed in the case of neat Chit-AuNPs. The mechanism of the two assays was investigated and attributed to electrostatic and depletion effects exerted between the Chit-AuNPs, free Chit, and the solution components. The developed contamination-free, one-tube assay successfully amplified and detected down to 1-5 cfu of Salmonella and 10 copies of SARS-CoV-2 per reaction (25 μL) used, respectively, as model DNA and RNA targets in the presence of 20% saliva, making the method suitable for POC applications. Compared to the commonly used pH-sensitive dyes, Chit-AuNPs are shown to have an enhanced sensitivity toward naked-eye colorimetric observation owing to the direct detection of DNA amplicons. Thus, this is a simple, highly sensitive, fast, and versatile naked-eye detection methodology that could be coupled to any LAMP or RT-LAMP assay, avoiding the need of using complicated sample pretreatments and/or AuNPs long and laborious functionalization processes.
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Affiliation(s)
- Stylianos Grammatikos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Biology, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Ioannis Svoliantopoulos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Biology, University of Crete, Voutes, 70013 Heraklion, Greece
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12
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Kaur M, Ayarnah K, Duanis-Assaf D, Alkan N, Eltzov E. Paper-based colorimetric loop-mediated isothermal amplification (LAMP) assay for the identification of latent Colletotrichum in harvested fruit. Anal Chim Acta 2023; 1267:341394. [PMID: 37257967 DOI: 10.1016/j.aca.2023.341394] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Paper-based analytical devices (PADs) have gained enormous attention because of their low-cost, simple fabrication, and portability. Here, we propose a paper-based device for performing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with real-time simultaneous detection of C. gloeosporioides latent infections in tomatoes. RT-LAMP-based PAD platform comprises a paper substrate on which the DNA amplification reaction occurs. Among different types of tested papers, cellulose membrane (grade 4) enabled effective visualization of the amplification result. The assay was found highly selective for the latent stage of C. gloeosporioides with lower limit of detection (LOD) of 0.5 pg of total extracted RNA. The developed assay generated the results within 40 min and hence can be efficiently employed for identifying C. gloeosporioides in resource-limited settings.
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Affiliation(s)
- Manpreet Kaur
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Khadijah Ayarnah
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Danielle Duanis-Assaf
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Institute of Biochemistry, Food Science and Nutrition, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Noam Alkan
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - Evgeni Eltzov
- Department of Postharvest Science, Institute of Postharvest and Food Sciences, The Volcani Institute, Agricultural Research Organization, Bet Dagan, 50250, Israel; Agro-Nanotechnology and Advanced Materials Research Center, Institute of Postharvest and Food Science, Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, 7505101, Israel.
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13
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Bacon A, Wang W, Lee H, Umrao S, Sinawang PD, Akin D, Khemtonglang K, Tan A, Hirshfield S, Demirci U, Wang X, Cunningham BT. Review of HIV Self Testing Technologies and Promising Approaches for the Next Generation. BIOSENSORS 2023; 13:298. [PMID: 36832064 PMCID: PMC9954708 DOI: 10.3390/bios13020298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 05/28/2023]
Abstract
The ability to self-test for HIV is vital to preventing transmission, particularly when used in concert with HIV biomedical prevention modalities, such as pre-exposure prophylaxis (PrEP). In this paper, we review recent developments in HIV self-testing and self-sampling methods, and the potential future impact of novel materials and methods that emerged through efforts to develop more effective point-of-care (POC) SARS-CoV-2 diagnostics. We address the gaps in existing HIV self-testing technologies, where improvements in test sensitivity, sample-to-answer time, simplicity, and cost are needed to enhance diagnostic accuracy and widespread accessibility. We discuss potential paths toward the next generation of HIV self-testing through sample collection materials, biosensing assay techniques, and miniaturized instrumentation. We discuss the implications for other applications, such as self-monitoring of HIV viral load and other infectious diseases.
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Affiliation(s)
- Amanda Bacon
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weijing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hankeun Lee
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Umrao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| | - Prima Dewi Sinawang
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Demir Akin
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kodchakorn Khemtonglang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anqi Tan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sabina Hirshfield
- Special Treatment and Research (STAR) Program, Department of Medicine, SUNY Downstate Health Sciences University, Brooklyn, New York, NY 11203, USA
| | - Utkan Demirci
- Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Genomic Diagnostics, Woese Institute for Genomic Biology, Urbana, IL 61801, USA
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14
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Marangoni JM, Ng KKS, Emadi A. Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification. MICROMACHINES 2023; 14:472. [PMID: 36838172 PMCID: PMC9960872 DOI: 10.3390/mi14020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.
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Affiliation(s)
- Jesse M. Marangoni
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kenneth K. S. Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Arezoo Emadi
- Department of Electrical and Computer Engineering, University of Windsor, Windsor, ON N9B 3P4, Canada
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