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De Falco M, De Felice M, Rota F, Zappi D, Antonacci A, Scognamiglio V. Next-generation diagnostics: augmented sensitivity in amplification-powered biosensing. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yilmaz T, Goluch ED. A comprehensive review of conventional techniques and biosensor systems developed for in situ detection of vibrio cholerae. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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Zhao F, Niu L, Yan L, Nong J, Wang C, Wang J, Gao N, Zhu X, Wu L, Zheng F, Hu S. Establishment and Application of Multiple Cross Displacement Amplification Coupled With Lateral Flow Biosensor (MCDA-LFB) for Visual and Rapid Detection of Candida albicans in Clinical Samples. Front Cell Infect Microbiol 2019; 9:102. [PMID: 31058099 PMCID: PMC6477880 DOI: 10.3389/fcimb.2019.00102] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/25/2019] [Indexed: 12/24/2022] Open
Abstract
Candida albicans is an opportunistic pathogenic yeast that predominantly causes invasive candidiasis. The conventional diagnosis of C. albicans infection depends on time-consuming, culture-based gold-standard methods. Here, a multiple cross displacement amplification (MCDA) assay, combined with a gold nanoparticle-based lateral flow biosensor (LFB) visualization method, was developed for the rapid detection of C. albicans. The internal transcribed spacer II, a region between 5.8 and 28 S fungal ribosomal DNA, is a C. albicans species-specific sequence that was used as the MCDA assay target. As an isothermal amplification method, the MCDA reaction with optimized conditions could be completed within only 40 min at a constant temperature (64°C). Then, the amplification reaction products could be visibly detected by a LFB without special equipment. The developed MCDA-LFB assay for C. albicans detection was a specific and accurate method, and could distinguish C. albicans from other pathogens. Just 200 fg of genomic DNA template from pure cultures of C. albicans could be detected using the MCDA-LFB method. The limit of detection (LOD) of the new method was more sensitive than that of both qPCR and loop-mediated isothermal amplification (LAMP). Of 240 clinical sputum samples, all of the C. albicans-positive (87/240) samples identified by the gold-standard method were successfully detected by the MCDA-LFB assay. Moreover, the true positive rate of the newly developed assay was not only higher than that of qPCR (100 vs. 86.2%), but also higher than that of LAMP (100 vs. 94.3%). Thus, the MCDA-LFB assay might be a simple, specific, and sensitive method for the rapid diagnosis of C. albicans in clinical samples.
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Affiliation(s)
- Fan Zhao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Lina Niu
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, China.,Key Laboratory of Translation Medicine Tropical Diseases, Haikou, China.,Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou, China
| | - Linlin Yan
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jinqing Nong
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Chunmei Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jing Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Naishu Gao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Xiaoxue Zhu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Lei Wu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Fengzhi Zheng
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Shoukui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
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Lyalina TA, Goncharova EA, Prokofeva NY, Voroshilina ES, Kolpashchikov DM. A DNA minimachine for selective and sensitive detection of DNA. Analyst 2019; 144:416-420. [DOI: 10.1039/c8an02274g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic molecular machines have been explored to manipulate matter at the molecular level.
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Affiliation(s)
- Tatiana A. Lyalina
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
| | - Ekaterina A. Goncharova
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
| | - Nadezhda Y. Prokofeva
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
| | - Ekaterina S. Voroshilina
- Ural State Medical University
- Department of Microbiology
- Virology and immunology
- Ekaterinburg
- Russian Federation
| | - Dmitry M. Kolpashchikov
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
- Chemistry Department
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Da-Silva E, Baudart J, Barthelmebs L. Biosensing platforms for Vibrio bacteria detection based on whole cell and nucleic acid analysis: A review. Talanta 2018; 190:410-422. [DOI: 10.1016/j.talanta.2018.07.092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/27/2018] [Accepted: 07/31/2018] [Indexed: 11/15/2022]
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Niu L, Zhao F, Chen J, Nong J, Wang C, Wang J, Gao N, Zhu X, Wu L, Hu S. Isothermal amplification and rapid detection of Klebsiella pneumoniae based on the multiple cross displacement amplification (MCDA) and gold nanoparticle lateral flow biosensor (LFB). PLoS One 2018; 13:e0204332. [PMID: 30273362 PMCID: PMC6166938 DOI: 10.1371/journal.pone.0204332] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/06/2018] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a frequent pathogen causing nosocomial infections and outbreaks. We developed a multiple cross displacement amplification (MCDA) assay for the detection of K. pneumoniae, which can get the positive results within 40 minutes’ isothermal amplification. Gold-nanoparticle lateral flow biosensor (LFB) and colorimetric indicators were used for the rapid readouts of MCDA amplification. The detection limit of this assay was 100 fg per reaction at 65°C, which was confirmed to be the optimal amplification temperature according to the real time turbidimeters. For specificity, all of the 30 clinical-source K. pneumoniae strains were positive for the MCDA, and all of the non-K. pneumoniae strains belonging to 31 different species were negative for this MCDA assay. To evaluate the practical applicability of this method, we assessed its detection limit for K. pneumoniae strains in sputum samples (24 CFU per reaction), and DNA templates of 100 sputum samples further underwent the MCDA-LFB tests. All of the sputum samples being positive for K. pneumoniae (30/100) with the culture method were successfully identified with the MCDA assay, the detection power of which was higher than that of polymerase chain reaction (PCR) (25/100). Thus, the MCDA test for K. pneumoniae combined with the gold nanoparticle LFB as the results readout scheme, are simple, specific, and sensitive methods for the rapid diagnosis of K. pneumoniae in clinical samples.
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Affiliation(s)
- Lina Niu
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, Hainan, China
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Fan Zhao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jinlong Chen
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, Hainan, China
| | - Jinqing Nong
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Chunmei Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jing Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Naishu Gao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Xiaoxue Zhu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Lei Wu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Shoukui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
- * E-mail:
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Engku Nur Syafirah E, Nurul Najian A, Foo PC, Mohd Ali MR, Mohamed M, Yean CY. An ambient temperature stable and ready-to-use loop-mediated isothermal amplification assay for detection of toxigenic Vibrio cholerae in outbreak settings. Acta Trop 2018; 182:223-231. [PMID: 29545156 DOI: 10.1016/j.actatropica.2018.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 11/26/2022]
Abstract
Cholera, caused by Vibrio cholerae is a foodborne disease that frequently reported in food and water related outbreak. Rapid diagnosis of cholera infection is important to avoid potential spread of disease. Among available diagnostic platforms, loop-mediated isothermal amplification (LAMP) is regarded as a potential diagnostic tool due to its rapidity, high sensitivity and specificity and independent of sophisticated thermalcycler. However, the current LAMP often requires multiple pipetting steps, hence is susceptible to cross contamination. Besides, the strict requirement of cold-chain during transportation and storage make its application in low resource settings to be inconvenient. To overcome these problems, the present study is aimed to develop an ambient-temperature-stable and ready-to-use LAMP assay for the detection of toxigenic Vibrio cholerae in low resource settings. A set of specific LAMP primers were designed and tested against 155 V. cholerae and non-V. cholerae strains. Analytical specifity showed that the developed LAMP assay detected 100% of pathogenic V. cholerae and did not amplified other tested bacterial strains. Upon testing against stool samples spiked with toxigenic V. cholerae outbreak isolates, the LAMP assay detected all of the spiked samples (n = 76/76, 100%), in contrast to the conventional PCR which amplified 77.6% (n = 59/76) of the tested specimens. In term of sensitivity, the LAMP assay was 100-fold more sensitive as compared to the conventional PCR method, with LOD of 10 fg per μL and 10 CFU per mL. Following lyophilisation with addition of lyoprotectants, the dry-reagent LAMP mix has an estimated shelf-life of 90.75 days at room temperature.
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Bao H, Yang B, Zhang X, Lei L, Li Z. Bacteria-templated fabrication of a charge heterogeneous polymeric interface for highly specific bacterial recognition. Chem Commun (Camb) 2017; 53:2319-2322. [DOI: 10.1039/c6cc09242j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using bacteria-templated polymerization, a novel bacteria-imprinted polymer (BIP) was fabricated for bacterial recognition.
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Affiliation(s)
- Han Bao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- Zhejiang University
- Hangzhou 310027
- P. R. China
- College of Chemical and Biological Engineering
| | - Bin Yang
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou 310027
- P. R. China
| | - Xingwang Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- Zhejiang University
- Hangzhou 310027
- P. R. China
- College of Chemical and Biological Engineering
| | - Lecheng Lei
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- Zhejiang University
- Hangzhou 310027
- P. R. China
- College of Chemical and Biological Engineering
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- Zhejiang University
- Hangzhou 310027
- P. R. China
- College of Chemical and Biological Engineering
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Cecchini F, Fajs L, Cosnier S, Marks RS. Vibrio cholerae detection: Traditional assays, novel diagnostic techniques and biosensors. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Fountoglou N, Petropoulou M, Iliadi A, Christopoulos TK, Ioannou PC. Τwo-panel molecular testing for genetic predisposition for thrombosis using multi-allele visual biosensors. Anal Bioanal Chem 2016; 408:1943-52. [DOI: 10.1007/s00216-016-9310-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/25/2015] [Accepted: 01/04/2016] [Indexed: 01/29/2023]
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