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Liu J, Fu R, Zhang S, Hou J, Ma H, Hu S, Li H, Zhang Y, Wang W, Qiao B, Zang B, Min X, Zhang F, Du J, Yan S. Rapid and multi-target genotyping of Helicobacter pylori with digital microfluidics. Biosens Bioelectron 2024; 256:116282. [PMID: 38626615 DOI: 10.1016/j.bios.2024.116282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/18/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Helicobacter pylori (H. pylori) infection correlates closely with gastric diseases such as gastritis, ulcers, and cancer, influencing more than half of the world's population. Establishing a rapid, precise, and automated platform for H. pylori diagnosis is an urgent clinical need and would significantly benefit therapeutic intervention. Recombinase polymerase amplification (RPA)-CRISPR recently emerged as a promising molecular diagnostic assay due to its rapid detection capability, high specificity, and mild reaction conditions. In this work, we adapted the RPA-CRISPR assay on a digital microfluidics (DMF) system for automated H. pylori detection and genotyping. The system can achieve multi-target parallel detection of H. pylori nucleotide conservative genes (ureB) and virulence genes (cagA and vacA) across different samples within 30 min, exhibiting a detection limit of 10 copies/rxn and no false positives. We further conducted tests on 80 clinical saliva samples and compared the results with those derived from real-time quantitative polymerase chain reaction, demonstrating 100% diagnostic sensitivity and specificity for the RPA-CRISPR/DMF method. By automating the assay process on a single chip, the DMF system can significantly reduce the usage of reagents and samples, minimize the cross-contamination effect, and shorten the reaction time, with the additional benefit of losing the chance of experiment failure/inconsistency due to manual operations. The DMF system together with the RPA-CRISPR assay can be used for early detection and genotyping of H. pylori with high sensitivity and specificity, and has the potential to become a universal molecular diagnostic platform.
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Affiliation(s)
- Jinsong Liu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563006, China; College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563000, China
| | - Rongxin Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China; Engineering Research Center of Integrated Acousto-opto-electronic Microsystems, Ministry of Education of China, Beijing, 100081, China
| | - Shuailong Zhang
- School of Integrated Circuits and Electronic, Beijing Institute of Technology, Beijing, 100081, China; Engineering Research Center of Integrated Acousto-opto-electronic Microsystems, Ministry of Education of China, Beijing, 100081, China.
| | - Jialu Hou
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Hanbin Ma
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Siyi Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Hang Li
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China; Engineering Research Center of Integrated Acousto-opto-electronic Microsystems, Ministry of Education of China, Beijing, 100081, China
| | - Yanli Zhang
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Weian Wang
- Department of Gastroenterology, The Third Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, 100039, China
| | - Bokang Qiao
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China; Beijing Institute of Heart, Lung and Vascular Diseases, Key Laboratory of Remodeling-Related Cardiovascular Diseases, Beijing, 100029, China
| | - Baisheng Zang
- Zhejiang Anji GeneDetective Medical Technology Co. Ltd., Anji, 313300, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563006, China; College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563000, China
| | - Feng Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563006, China; College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563000, China
| | - Jie Du
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China; Beijing Institute of Heart, Lung and Vascular Diseases, Key Laboratory of Remodeling-Related Cardiovascular Diseases, Beijing, 100029, China.
| | - Shengkai Yan
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, 563006, China; College of Laboratory Medicine, Zunyi Medical University, Zunyi, 563000, China.
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Nguyen HQ, Nguyen VD, Phan VM, Seo TS. Development of a self-contained microfluidic chip and an internet-of-things-based point-of-care device for automated identification of respiratory viruses. Lab Chip 2024; 24:2485-2496. [PMID: 38587207 DOI: 10.1039/d3lc00933e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The COVID-19 pandemic greatly impacted the in vitro diagnostic market, leading to the development of new technologies such as point-of-care testing (POCT), multiplex testing, and digital health platforms. In this study, we present a self-contained microfluidic chip integrated with an internet-of-things (IoT)-based point-of-care (POC) device for rapid and sensitive diagnosis of respiratory viruses. Our platform enables sample-to-answer diagnostics within 70 min by automating RNA extraction, reverse transcription-loop-mediated isothermal amplification (RT-LAMP), and fluorescence detection. The microfluidic chip is designed to store all the necessary reagents for the entire diagnostic assay, including a lysis buffer, a washing buffer, an elution buffer, and a lyophilized RT-LAMP cocktail. It can perform nucleic acid extraction, aliquoting, and gene amplification in multiple reaction chambers without cross-contamination. The IoT-based POC device consists of a Raspberry Pi 4 for device control and data processing, a CMOS sensor for measuring fluorescence signals, a resistive heater panel for temperature control, and solenoid valves for controlling the movement of on-chip reagent solutions. The proposed device is portable and features a touchscreen for user control and result display. We evaluated the performance of the platform using 11 clinical respiratory virus samples, including 5 SARS-CoV-2 samples, 2 influenza A samples, and 4 influenza B samples. All tested clinical samples were accurately identified with high specificity and fidelity, demonstrating the ability to simultaneously detect multiple respiratory viruses. The combination of the integrated microfluidic chip with the POC device offers a simple, cost-effective, and scalable solution for rapid molecular diagnosis of respiratory viruses in resource-limited settings.
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Affiliation(s)
- Huynh Quoc Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
| | - Van Dan Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
| | - Vu Minh Phan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
| | - Tae Seok Seo
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin, 17104, South Korea.
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Wu S, Duan H, Zhang Y, Wang S, Zheng L, Cai G, Lin J, Yue X. A Salmonella Microfluidic Chip Combining Non-Contact Eddy Heater and 3D Fan-Shaped Mixer with Recombinase Aided Amplification. Biosensors 2022; 12:bios12090726. [PMID: 36140111 PMCID: PMC9496460 DOI: 10.3390/bios12090726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Foodborne pathogenic bacteria have become a worldwide threat to human health, and rapid and sensitive bacterial detection methods are urgently needed. In this study, a facile microfluidic chip was developed and combined with recombinase-aided amplification (RAA) for rapid and sensitive detection of Salmonella typhimurium using a non-contact eddy heater for dynamic lysis of bacterial cells and a 3D-printed fan-shaped active mixer for continuous-flow mixing. First, the bacterial sample was injected into the chip to flow through the spiral channel coiling around an iron rod under an alternating electromagnetic field, resulting in the dynamic lysis of bacterial cells by this non-contact eddy heater to release their nucleic acids. After cooling to ~75 °C, these nucleic acids were continuous-flow mixed with magnetic silica beads using the fan-shaped mixer and captured in the separation chamber using a magnet. Finally, the captured nucleic acids were eluted by the eluent from the beads to flow into the detection chamber, followed by RAA detection of nucleic acids to determine the bacterial amount. Under the optimal conditions, this microfluidic chip was able to quantitatively detect Salmonella typhimurium from 1.1 × 102 to 1.1 × 105 CFU/mL in 40 min with a detection limit of 89 CFU/mL and might be prospective to offer a simple, low-cost, fast and specific bacterial detection technique for ensuring food safety.
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Affiliation(s)
- Shangyi Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Hong Duan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Yingchao Zhang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Lingyan Zheng
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China
| | - Gaozhe Cai
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
- Correspondence: (J.L.); (X.Y.)
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (J.L.); (X.Y.)
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Entesari M, Zamani M, Heidarizadeh M, Moradi R, Khakdan F, Rafiei F. An Insight Into Detection Pathways/Biosensors of Highly Infectious Coronaviruses. Mol Biotechnol 2022; 64:339-354. [PMID: 34655396 PMCID: PMC8520350 DOI: 10.1007/s12033-021-00417-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/07/2021] [Indexed: 01/12/2023]
Abstract
The outbreak of COVID-19 pandemic and its consequences have inflicted a substantial damage on the world. In this study, it was attempted to review the recent coronaviruses appeared among the human being and their epidemic/pandemic spread throughout the world. Currently, there is an inevitable need for the establishment of a quick and easily available biosensor for tracing COVID-19 in all countries. It has been known that the incubation time of COVID-19 lasts about 14 days and 25% of the infected individuals are asymptomatic. To improve the ability to determine SARS-CoV-2 precisely and reduce the risk of eliciting false-negative results produced by mutating nature of coronaviruses, many researchers have established a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay using mismatch-tolerant molecular beacons as multiplex real-time RT-PCR to distinguish between pathogenic and non-pathogenic strains of coronaviruses. The possible mechanisms and pathways for the detection of coronaviruses by biosensors have been reviewed in this study.
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Affiliation(s)
- Mehrnaz Entesari
- Department of Genetic Engineering and Molecular Genetics, Zanjan University, Zanjan, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Heidarizadeh
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Rasoul Moradi
- Department of Chemical Engineering, School of Engineering & Applied Science, Khazar University, Baku, Azerbaijan
| | | | - Fariba Rafiei
- Department of Agronomy & Plant Breeding, Collage of Agriculture & Natural Resources, University of Tehran, Karaj, Iran
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5
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Li JS, Hao YZ, Hou ML, Zhang X, Zhang XG, Cao YX, Li JM, Ma J, Zhou ZX. Development of a Recombinase-aided Amplification Combined With Lateral Flow Dipstick Assay for the Rapid Detection of the African Swine Fever Virus. Biomed Environ Sci 2022; 35:133-140. [PMID: 35197178 DOI: 10.3967/bes2022.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/15/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To establish a sensitive, simple and rapid detection method for African swine fever virus (ASFV) B646L gene. METHODS A recombinase-aided amplification-lateral flow dipstick (RAA-LFD) assay was developed in this study. Recombinase-aided amplification (RAA) is used to amplify template DNA, and lateral flow dipstick (LFD) is used to interpret the results after the amplification is completed. The lower limits of detection and specificity of the RAA assay were verified using recombinant plasmid and pathogenic nucleic acid. In addition, 30 clinical samples were tested to evaluate the performance of the RAA assay. RESULTS The RAA-LFD assay was completed within 15 min at 37 °C, including 10 min for nucleic acid amplification and 5 minutes for LFD reading results. The detection limit of this assay was found to be 200 copies per reaction. And there was no cross-reactivity with other swine viruses. CONCLUSION A highly sensitive, specific, and simple RAA-LFD method was developed for the rapid detection of the ASFV.
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Affiliation(s)
- Jiang Shuai Li
- Faculty of environment and life, Beijing University of Technology, Beijing 100024, China
| | - Yan Zhe Hao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Mei Ling Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xuan Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiao Guang Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yu Xi Cao
- National Institute of Viral Disease Control and Prevention, Beijing 100052, China
| | - Jin Ming Li
- China Animal Health and Epidemiology Center, Qingdao 266032, Shandong, China
| | - Jing Ma
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zhi Xiang Zhou
- Faculty of environment and life, Beijing University of Technology, Beijing 100024, China
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6
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Zhang X, Yin Y, Du S, Kong L, Yang Z, Chang Y, Chai Y, Yuan R. Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier. Adv Sci (Weinh) 2022; 9:e2104084. [PMID: 34913619 PMCID: PMC8811820 DOI: 10.1002/advs.202104084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/08/2021] [Indexed: 05/09/2023]
Abstract
Herein, a programmable dual-catalyst hairpin assembly (DCHA) for realizing the synchronous recycle of two catalysts is developed, displaying high reaction rate and outstanding conversion efficiency beyond traditional nucleic acid signal amplifications (NASA). Once catalyst I interacts with the catalyst II, the DCHA can be triggered to realize the simultaneous recycle of catalysts I and II to keep the highly concentrated intermediate product duplex I-II instead of the steadily decreased one in typical NASA, which can accomplish in about only 16 min and achieves the outstanding conversion efficiency up to 4.54 × 108 , easily conquering the main predicaments of NASA: time-consuming and low-efficiency. As a proof of the concept, the proposed DCHA as a high-speed and hyper-efficiency DNA signal magnifier is successfully applied in the rapid and ultrasensitive detection of miRNA-21 in cancer cell lysates, which exploits the new generation of universal strategy for the applications in biosensing assay, clinic diagnose, and DNA nanobiotechnology.
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Affiliation(s)
- Xiao‐Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Yang Yin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Shu‐Min Du
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Ling‐Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Zhe‐Han Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Yuan‐Yuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Ya‐Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)Ministry of EducationCollege of Chemistry and Chemical EngineeringSouthwest UniversityChongqing400715P. R. China
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Chakraborty S, Connor S, Velagic M. Development of a simple, rapid, and sensitive diagnostic assay for enterotoxigenic E. coli and Shigella spp applicable to endemic countries. PLoS Negl Trop Dis 2022; 16:e0010180. [PMID: 35089927 PMCID: PMC8827434 DOI: 10.1371/journal.pntd.0010180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/09/2022] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Enterotoxigenic E. coli (ETEC) and Shigella spp (Shigella) are complex pathogens. The diagnostic assays currently used to detect these pathogens are elaborate or complicated, which make them difficult to apply in resource poor settings where these diseases are endemic. The culture methods used to detect Shigella are not sensitive, and the methods used to detect ETEC are only available in a few research labs. To address this gap, we developed a rapid and simple diagnostic assay–"Rapid LAMP based Diagnostic Test (RLDT)." The six minutes sample preparation method directly from the fecal samples with lyophilized reaction strips and using established Loop-mediated Isothermal Amplification (LAMP) platform, ETEC [heat labile toxin (LT) and heat stable toxins (STh, and STp) genes] and Shigella (ipaH gene) detection was made simple, rapid (<50 minutes), and inexpensive. This assay is cold chain and electricity free. Moreover, RLDT requires minimal equipment. To avoid any end user’s bias, a battery-operated, handheld reader was used to read the RLDT results. The results can be read as positive/negative or as real time amplification depending on the end user’s need. The performance specifications of the RLDT assay, including analytical sensitivity and specificity, were evaluated using fecal samples spiked with ETEC and Shigella strains. The limit of detection was ~105 CFU/gm of stool for LT, STh, and STp and ~104 CFU/gm of stool for the ipaH gene, which corresponds to about 23 CFU and 1 CFU respectively for ETEC and Shigella per 25uL reaction within 40 minutes. The RLDT assay from stool collection to result is simple, and rapid and at the same time sufficiently sensitive. RLDT has the potential to be applied in resource poor endemic settings for the rapid diagnosis of ETEC and Shigella. Enterotoxigenic E. coli and Shigella are the leading causes of moderate to severe diarrhea in the low-and middle-income countries (LMICs). A critical constraint to determine the ETEC and Shigella disease burden at the country or sub-national level, is the complex diagnostic methods currently required for detecting these pathogens. These methods are neither sufficiently sensitive nor standardized and are not feasible in the resource poor settings where these infections occur most commonly. We developed a simple and rapid diagnostic assay called "Rapid Loop-mediated isothermal amplification based Diagnostic Test (RLDT)" for the detection of these pathogens in low-resource settings. Using RLDT, ETEC and Shigella were detected directly from the stool, in less than 1 hour with minimal hands-on time. The assay does not require maintaining a cold chain and is electricity-free. Being rapid, simple, and sensitive, RLDT can be scaled up and is appropriate to apply in the LMICs where ETEC and Shigella diarrhea are endemic.
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Affiliation(s)
- Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Sean Connor
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Mirza Velagic
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Trinh KTL, Lee NY. Fabrication of Wearable PDMS Device for Rapid Detection of Nucleic Acids via Recombinase Polymerase Amplification Operated by Human Body Heat. Biosensors (Basel) 2022; 12:bios12020072. [PMID: 35200333 PMCID: PMC8869297 DOI: 10.3390/bios12020072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 05/28/2023]
Abstract
Pathogen detection by nucleic acid amplification proved its significance during the current coronavirus disease 2019 (COVID-19) pandemic. The emergence of recombinase polymerase amplification (RPA) has enabled nucleic acid amplification in limited-resource conditions owing to the low operating temperatures around the human body. In this study, we fabricated a wearable RPA microdevice using poly(dimethylsiloxane) (PDMS), which can form soft-but tight-contact with human skin without external support during the body-heat-based reaction process. In particular, the curing agent ratio of PDMS was tuned to improve the flexibility and adhesion of the device for better contact with human skin, as well as to temporally bond the microdevice without requiring further surface modification steps. For PDMS characterization, water contact angle measurements and tests for flexibility, stretchability, bond strength, comfortability, and bendability were conducted to confirm the surface properties of the different mixing ratios of PDMS. By using human body heat, the wearable RPA microdevices were successfully applied to amplify 210 bp from Escherichia coli O157:H7 (E. coli O157:H7) and 203 bp from the DNA plasmid SARS-CoV-2 within 23 min. The limit of detection (LOD) was approximately 500 pg/reaction for genomic DNA template (E. coli O157:H7), and 600 fg/reaction for plasmid DNA template (SARS-CoV-2), based on gel electrophoresis. The wearable RPA microdevice could have a high impact on DNA amplification in instrument-free and resource-limited settings.
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Affiliation(s)
- Kieu The Loan Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Korea;
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Korea
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Lin EE, Razzaque UA, Burrows SA, Smoukov SK. End-to-end system for rapid and sensitive early-detection of SARS-CoV-2 for resource-poor and field-test environments using a $51 lab-in-a-backpack. PLoS One 2022; 17:e0259886. [PMID: 35081119 PMCID: PMC8791454 DOI: 10.1371/journal.pone.0259886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/28/2021] [Indexed: 11/19/2022] Open
Abstract
COVID-19 has exposed stark inequalities between resource-rich and resource-poor countries. International UN- and WHO-led efforts, such as COVAX, have provided SARS-CoV-2 vaccines but half of African countries have less than 2% vaccinated in their population, and only 15 have reached 10% by October 2021, further disadvantaging local economic recovery. Key for this implementation and preventing further mutation and spread is the frequency of voluntary [asymptomatic] testing. It is limited by expensive PCR and LAMP tests, uncomfortable probes deep in the throat or nose, and the availability of hardware to administer in remote locations. There is an urgent need for an inexpensive "end-to-end" system to deliver sensitive and reliable, non-invasive tests in resource-poor and field-test conditions. We introduce a non-invasive saliva-based LAMP colorimetric test kit and a $51 lab-in-a-backpack system that detects as few as 4 viral RNA copies per μL. It consists of eight chemicals, a thermometer, a thermos bottle, two micropipettes and a 1000-4000 rcf electronically operated centrifuge made from recycled computer hard drives (CentriDrive). The centrifuge includes a 3D-printed rotor and a 12 V rechargeable Li-ion battery, and its 12 V standard also allows wiring directly to automobile batteries, to enable field-use of this and other tests in low infrastructure settings. The test takes 90 minutes to process 6 samples and has reagent costs of $3.5 per sample. The non-invasive nature of saliva testing would allow higher penetration of testing and wider adoption of the test across cultures and settings (including refugee camps and disaster zones). The attached graphical procedure would make the test suitable for self-testing at home, performing it in the field, or in mobile testing centers by minimally trained staff.
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Affiliation(s)
- E. Emily Lin
- School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
| | - Umar A. Razzaque
- School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
| | - Stephen A. Burrows
- School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
| | - Stoyan K. Smoukov
- School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
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10
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Chaouch M. Loop-mediated isothermal amplification (LAMP): An effective molecular point-of-care technique for the rapid diagnosis of coronavirus SARS-CoV-2. Rev Med Virol 2021; 31:e2215. [PMID: 33476080 PMCID: PMC7995099 DOI: 10.1002/rmv.2215] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022]
Abstract
The novel coronavirus disease-2019 (Covid-19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost-effective methodology. The advent of the loop-mediated isothermal amplification (LAMP) assay provided an innovative tool for establishing a rapid diagnostic technique based on the molecular amplification of pathogen RNA or DNA. In this review, we explore the applications, diagnostic effectiveness of LAMP test for molecular diagnosis and surveillance of severe acute respiratory syndrome coronavirus 2. Our results show that LAMP can be considered as an effective point-of-care test for the diagnosis of Covid-19 in endemic areas, especially for low- and middle-income countries.
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Affiliation(s)
- Melek Chaouch
- Laboratory of Medical ParasitologyBiotechnology and Biomolecules LR 11 IPT 06Institut Pasteur de TunisTunisTunisia
- Laboratory of BioinformaticsBiomathematics and Biostatistics LR 16 IPT 09Institut Pasteur de TunisTunisTunisia
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11
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Alvarez MM, Bravo-González S, González-González E, Trujillo-de Santiago G. Portable and Label-Free Quantitative Loop-Mediated Isothermal Amplification (LF-qLamp) for Reliable COVID-19 Diagnostics in Three Minutes of Reaction Time: Arduino-Based Detection System Assisted by a pH Microelectrode. Biosensors 2021; 11:bios11100386. [PMID: 34677342 PMCID: PMC8533988 DOI: 10.3390/bios11100386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been recently studied as an alternative method for cost-effective diagnostics in the context of the current COVID-19 pandemic. Recent reports document that LAMP-based diagnostic methods have a comparable sensitivity and specificity to that of RT-qPCR. We report the use of a portable Arduino-based LAMP-based amplification system assisted by pH microelectrodes for the accurate and reliable diagnosis of SARS-CoV-2 during the first 3 min of the amplification reaction. We show that this simple system enables a straightforward discrimination between samples containing or not containing artificial SARS-CoV-2 genetic material in the range of 10 to 10,000 copies per 50 µL of reaction mix. We also spiked saliva samples with SARS-CoV-2 synthetic material and corroborated that the LAMP reaction can be successfully monitored in real time using microelectrodes in saliva samples as well. These results may have profound implications for the design of real-time and portable quantitative systems for the reliable detection of viral pathogens including SARS-CoV-2.
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Affiliation(s)
- Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Correspondence: (M.M.A.); (G.T.-d.S.)
| | - Sergio Bravo-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Ingeniería Mecatrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, Mexico
- Correspondence: (M.M.A.); (G.T.-d.S.)
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12
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Pascual-Garrigos A, Maruthamuthu MK, Ault A, Davidson J, Rudakov G, Pillai D, Koziol J, Schoonmaker JP, Johnson T, Verma MS. On-farm colorimetric detection of Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni in crude bovine nasal samples. Vet Res 2021; 52:126. [PMID: 34600578 PMCID: PMC8487530 DOI: 10.1186/s13567-021-00997-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
This work modifies a loop-mediated isothermal amplification (LAMP) assay to detect the bovine respiratory disease (BRD) bacterial pathogens Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni in a colorimetric format on a farm. BRD causes a significant health and economic burden worldwide that partially stems from the challenges involved in determining the pathogens causing the disease. Methods such as polymerase chain reaction (PCR) have the potential to identify the causative pathogens but require lab equipment and extensive sample processing making the process lengthy and expensive. To combat this limitation, LAMP allows accurate pathogen detection in unprocessed samples by the naked eye allowing for potentially faster and more precise diagnostics on the farm. The assay developed here offers 66.7-100% analytical sensitivity, and 100% analytical specificity (using contrived samples) while providing 60-100% concordance with PCR results when tested on five steers in a feedlot. The use of a consumer-grade water bath enabled on-farm execution by collecting a nasal swab from cattle and provided a colorimetric result within 60 min. Such an assay holds the potential to provide rapid pen-side diagnostics to cattle producers and veterinarians.
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Affiliation(s)
- Ana Pascual-Garrigos
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN 47907 USA
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47906 USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN 47907 USA
| | - Murali Kannan Maruthamuthu
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN 47907 USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN 47907 USA
| | - Aaron Ault
- School of Electrical and Computer Engineering, Purdue University, 465 Northwestern Avenue, West Lafayette, IN 47907 USA
| | - Josiah
Levi
Davidson
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN 47907 USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN 47907 USA
| | - Grigorii Rudakov
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN 47907 USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN 47907 USA
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907 USA
| | - Deepti Pillai
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, IN 47907 USA
| | - Jennifer Koziol
- School of Veterinary Medicine, Texas Tech University,
7671 Evans Drive
,
Amarillo
, TX 79106 USA
| | - Jon P. Schoonmaker
- Department of Animal Sciences, Purdue University, 270 S Russell Street, West Lafayette, IN 47907 USA
| | - Timothy Johnson
- Department of Animal Sciences, Purdue University, 270 S Russell Street, West Lafayette, IN 47907 USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN 47907 USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN 47907 USA
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907 USA
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13
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Rezaei M, Razavi Bazaz S, Morshedi Rad D, Shimoni O, Jin D, Rawlinson W, Ebrahimi Warkiani M. A Portable RT-LAMP/CRISPR Machine for Rapid COVID-19 Screening. Biosensors (Basel) 2021; 11:bios11100369. [PMID: 34677325 PMCID: PMC8534004 DOI: 10.3390/bios11100369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/19/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic has changed people’s lives and has brought society to a sudden standstill, with lockdowns and social distancing as the preferred preventative measures. To lift these measurements and reduce society’s burden, developing an easy-to-use, rapid, and portable system to detect SARS-CoV-2 is mandatory. To this end, we developed a portable and semi-automated device for SARS-CoV-2 detection based on reverse transcription loop-mediated isothermal amplification followed by a CRISPR/Cas12a reaction. The device contains a heater element mounted on a printed circuit board, a cooler fan, a proportional integral derivative controller to control the temperature, and designated areas for 0.2 mL Eppendorf® PCR tubes. Our system has a limit of detection of 35 copies of the virus per microliter, which is significant and has the capability of being used in crisis centers, mobile laboratories, remote locations, or airports to diagnose individuals infected with SARS-CoV-2. We believe the current methodology that we have implemented in this article is beneficial for the early screening of infectious diseases, in which fast screening with high accuracy is necessary.
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Affiliation(s)
- Meysam Rezaei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
- Genea, Sydney, NSW 2000, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
| | - Dorsa Morshedi Rad
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
| | - Olga Shimoni
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - William Rawlinson
- Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia;
- School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (D.M.R.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (O.S.); (D.J.)
- Genea, Sydney, NSW 2000, Australia
- Correspondence:
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14
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Pascual-Garrigos A, Maruthamuthu MK, Ault A, Davidson JL, Rudakov G, Pillai D, Koziol J, Schoonmaker JP, Johnson T, Verma MS. On-farm colorimetric detection of Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni in crude bovine nasal samples. Vet Res 2021; 52:126. [PMID: 34600578 DOI: 10.1021/acsagscitech.0c00072] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/03/2021] [Indexed: 05/28/2023] Open
Abstract
This work modifies a loop-mediated isothermal amplification (LAMP) assay to detect the bovine respiratory disease (BRD) bacterial pathogens Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni in a colorimetric format on a farm. BRD causes a significant health and economic burden worldwide that partially stems from the challenges involved in determining the pathogens causing the disease. Methods such as polymerase chain reaction (PCR) have the potential to identify the causative pathogens but require lab equipment and extensive sample processing making the process lengthy and expensive. To combat this limitation, LAMP allows accurate pathogen detection in unprocessed samples by the naked eye allowing for potentially faster and more precise diagnostics on the farm. The assay developed here offers 66.7-100% analytical sensitivity, and 100% analytical specificity (using contrived samples) while providing 60-100% concordance with PCR results when tested on five steers in a feedlot. The use of a consumer-grade water bath enabled on-farm execution by collecting a nasal swab from cattle and provided a colorimetric result within 60 min. Such an assay holds the potential to provide rapid pen-side diagnostics to cattle producers and veterinarians.
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Affiliation(s)
- Ana Pascual-Garrigos
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47906, USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN, 47907, USA
| | - Murali Kannan Maruthamuthu
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN, 47907, USA
| | - Aaron Ault
- School of Electrical and Computer Engineering, Purdue University, 465 Northwestern Avenue, West Lafayette, IN, 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN, 47907, USA
| | - Grigorii Rudakov
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN, 47907, USA
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN, 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN, 47907, USA
| | - Deepti Pillai
- Department of Comparative Pathobiology, Purdue University, 625 Harrison Street, West Lafayette, IN, 47907, USA
| | - Jennifer Koziol
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Drive , Amarillo , TX, 79106, USA
| | - Jon P Schoonmaker
- Department of Animal Sciences, Purdue University, 270 S Russell Street, West Lafayette, IN, 47907, USA
| | - Timothy Johnson
- Department of Animal Sciences, Purdue University, 270 S Russell Street, West Lafayette, IN, 47907, USA
| | - Mohit S Verma
- Department of Agricultural and Biological Engineering, Purdue University, 225 S University Street, West Lafayette, IN, 47907, USA.
- Birck Nanotechnology Center, Purdue University, 1205 W State St, West Lafayette, IN, 47907, USA.
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN, 47907, USA.
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15
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Toppings NB, Mohon AN, Lee Y, Kumar H, Lee D, Kapoor R, Singh G, Oberding L, Abdullah O, Kim K, Berenger BM, Pillai DR. A rapid near-patient detection system for SARS-CoV-2 using saliva. Sci Rep 2021; 11:13378. [PMID: 34183720 PMCID: PMC8238998 DOI: 10.1038/s41598-021-92677-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
The highly infectious nature of SARS-CoV-2 necessitates the use of widespread testing to control the spread of the virus. Presently, the standard molecular testing method (reverse transcriptase-polymerase chain reaction, RT-PCR) is restricted to the laboratory, time-consuming, and costly. This increases the turnaround time for getting test results. This study sought to develop a rapid, near-patient saliva-based test for COVID-19 (Saliva-Dry LAMP) with similar accuracy to that of standard RT-PCR tests. A lyophilized dual-target reverse transcription-loop-mediated isothermal amplification (RT-LAMP) test with fluorometric detection by the naked eye was developed. The assay relies on dry reagents that are room temperature stable. A device containing a centrifuge, heat block, and blue LED light system was manufactured to reduce the cost of performing the assay. This test has a limit of detection of 1 copy/µL and achieved a positive percent agreement of 100% [95% CI 88.43% to 100.0%] and a negative percent agreement of 96.7% [95% CI 82.78-99.92%] relative to a reference standard test. Saliva-Dry LAMP can be completed in 105 min. Precision, cross-reactivity, and interfering substances analysis met international regulatory standards. The combination of ease of sample collection, dry reagents, visual detection, low capital equipment cost, and excellent analytical sensitivity make Saliva-Dry LAMP particularly useful for resource-limited settings.
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Affiliation(s)
- Noah B Toppings
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Abu Naser Mohon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Yoonjung Lee
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada
| | - Hitendra Kumar
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada
- School of Engineering, University of British Columbia, Kelowna, BC, Canada
| | - Daniel Lee
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada
| | - Ratik Kapoor
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada
| | - Gurmukh Singh
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada
| | - Lisa Oberding
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Omar Abdullah
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Keekyoung Kim
- Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, AB, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Byron M Berenger
- Clinical Section of Microbiology, Alberta Precision Laboratories, Calgary, AB, Canada
- Department Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Dylan R Pillai
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
- Clinical Section of Microbiology, Alberta Precision Laboratories, Calgary, AB, Canada.
- Department Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
- Clinical Section of Infectious Diseases, Department of Medicine, University of Calgary, Calgary, AB, Canada.
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16
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Zhang M, Liu J, Shen Z, Liu Y, Song Y, Liang Y, Li Z, Nie L, Fang Y, Zhao Y. A newly developed paper embedded microchip based on LAMP for rapid multiple detections of foodborne pathogens. BMC Microbiol 2021; 21:197. [PMID: 34182947 PMCID: PMC8240391 DOI: 10.1186/s12866-021-02223-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/30/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Microfluidic chip detection technology is considered a potent tool for many bioanalytic applications. Rapid detection of foodborne pathogens in the early stages is imperative to prevent the outbreak of foodborne diseases, known as a severe threat to human health. Conventional bacterial culture methods for detecting foodborne pathogens are time-consuming, laborious, and lacking in pathogen diagnosis. To overcome this problem, we have created an embedded paper-based microchip based on isothermal loop amplification (LAMP), which can rapidly and sensitively detect foodborne pathogens. RESULTS We embed paper impregnated with LAMP reagent and specific primers in multiple reaction chambers of the microchip. The solution containing the target pathogen was injected into the center chamber and uniformly distributed into the reaction chamber by centrifugal force. The purified DNA of Escherichia coli O157:H7, Salmonella spp., Staphylococcus aureus, and Vibrio parahaemolyticus has been successfully amplified and directly detected on the microchip. The E. coli O157:H7 DNA was identified as low as 0.0134 ng μL- 1. Besides, the potential of this microchip in point-of-care testing was further tested by combining the on-chip sample purification module and using milk spiked with Salmonella spp.. The pyrolyzed milk sample was filtered through a polydopamine-coated paper embedded in the inside of the sample chamber. It was transported to the reaction chamber by centrifugal force for LAMP amplification. Then direct chip detection was performed in the reaction chamber embedded with calcein-soaked paper. The detection limit of Salmonella spp. in the sample measured by the microchip was approximately 12 CFU mL- 1. CONCLUSION The paper embedded LAMP microchip offers inexpensive, user-friendly, and highly selective pathogen detection capabilities. It is expected to have great potential as a quick, efficient, and cost-effective solution for future foodborne pathogen detection.
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Affiliation(s)
- Mimi Zhang
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China.
| | - Jinfeng Liu
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Zhiqiang Shen
- Tianjin Institute of Health and Environmental Medicine, A Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, 300050, China.
| | - Yongxin Liu
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Yang Song
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Yu Liang
- Tianjin Institute of Health and Environmental Medicine, A Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, 300050, China
| | - Zhende Li
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Lingmei Nie
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Yanjun Fang
- Tianjin Institute of Health and Environmental Medicine, A Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, 300050, China
| | - Youquan Zhao
- College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China.
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17
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Phan LMT, Tieu MV, Pham TT, Cho S. Clinical Utility of Biosensing Platforms for Confirmation of SARS-CoV-2 Infection. Biosensors (Basel) 2021; 11:bios11060167. [PMID: 34073756 PMCID: PMC8225209 DOI: 10.3390/bios11060167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/30/2022]
Abstract
Despite collaborative efforts from all countries, coronavirus disease 2019 (COVID-19) pandemic has been continuing to spread globally, forcing the world into social distancing period, making a special challenge for public healthcare system. Before vaccine widely available, the best approach to manage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is to achieve highest diagnostic accuracy by improving biosensor efficacy. For SARS-CoV-2 diagnostics, intensive attempts have been made by many scientists to ameliorate the drawback of current biosensors of SARS-CoV-2 in clinical diagnosis to offer benefits related to platform proposal, systematic analytical methods, system combination, and miniaturization. This review assesses ongoing research efforts aimed at developing integrated diagnostic tools to detect RNA viruses and their biomarkers for clinical diagnostics of SARS-CoV-2 infection and further highlights promising technology for SARS-CoV-2 specific diagnosis. The comparisons of SARS-CoV-2 biomarkers as well as their applicable biosensors in the field of clinical diagnosis were summarized to give scientists an advantage to develop superior diagnostic platforms. Furthermore, this review describes the prospects for this rapidly growing field of diagnostic research, raising further interest in analytical technology and strategic plan for future pandemics.
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Affiliation(s)
- Le Minh Tu Phan
- Department of Electronic Engineering, Gachon University, Seongnam-si 13120, Korea;
- School of Medicine and Pharmacy, The University of Danang, Danang 550000, Vietnam;
| | - My-Van Tieu
- TST Trading Service Technology Co., Ltd., Hochiminh City 723000, Vietnam;
| | - Thi-Thu Pham
- School of Medicine and Pharmacy, The University of Danang, Danang 550000, Vietnam;
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam-si 13120, Korea;
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Korea
- Correspondence:
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18
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Figueredo F, Stolowicz F, Vojnov A, Coltro WKT, Larocca L, Carrillo C, Cortón E. Towards a versatile and economic Chagas Disease point-of-care testing system, by integrating loop-mediated isothermal amplification and contactless/label-free conductivity detection. PLoS Negl Trop Dis 2021; 15:e0009406. [PMID: 33989282 PMCID: PMC8153438 DOI: 10.1371/journal.pntd.0009406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/26/2021] [Accepted: 04/25/2021] [Indexed: 01/17/2023] Open
Abstract
Rapid diagnosis by using small, simple, and portable devices could represent one of the best strategies to limit the damage and contain the spread of viral, bacterial or protozoa diseases, principally when they can be transmitted by air and are highly contagious, as some respiratory viruses are. The presence of antibodies in blood or serum samples is not the best option for deciding when a person must be quarantined to stop transmission of disease, given that cured patients have antibodies, so the best diagnosis methods rely on the use of nucleic acid amplification procedures. Here we present a very simple device and detection principle, based on paper discs coupled to contactless conductivity (C4D) sensors, can provide fast and easy diagnostics that are needed when an epidemic outbreak develops. The paper device presented here solves one of the main drawbacks that nucleic acid amplification tests have when they are performed outside of central laboratories. As the device is sealed before amplification and integrally disposed in this way, amplimers release cannot occur, allowing repetitive testing in the physician’s practice, ambulances, or other places that are not prepared to avoid cross-contamination of new samples. The use of very low volume samples allows efficient reagent use and the development of low cost, simple, and disposable point-of-care diagnostic systems. In 2005, the World Health Organization (WHO) recognized Chagas Disease as a neglected tropical disease. Meanwhile the serological tests, recommended by WHO, can be performed for chronic disease diagnosis, the nucleic acid amplification tests must be performed for the detection of the acute phase of the disease. Although the existing laboratory diagnosis tests for Chagas Disease are sensitive and highly reproducible, they cannot be performed in rural, low infrastructure environments, where this disease prevails. In this sense, the use of simple and portable analytical devices may be able to offer an affordable solution to this problem, allowing fast sampling, diagnosis and treatment prescription in one simple and fast intervention, as the performed by short term medical missions. In this study we show for the first time a diagnosis test comprising low cost materials and employing a contactless and label-free conductivity detection system that is used to read the result of a nucleic acid amplification reaction. The test showed high sensitivity for Chagas Disease diagnosis showing the potential to be used in rural and low income places.
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Affiliation(s)
- Federico Figueredo
- Biological Chemistry Department, Science School and IQUIBICEN (FCEN–UBA-CONICET), Argentine
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Fabiana Stolowicz
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Adrián Vojnov
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Wendell K. T. Coltro
- Chemistry Institute, Federal University of Goiás, Campus Samambaia, Goiânia, Brazil
- National Institute of Science and Technology in Bioanalytics, Campinas, Brazil
| | - Luciana Larocca
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Carolina Carrillo
- Science and Technology Institute Cesar Milstein (ICT–Milstein–CONICET), Argentine
| | - Eduardo Cortón
- Biological Chemistry Department, Science School and IQUIBICEN (FCEN–UBA-CONICET), Argentine
- * E-mail:
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Ayfan AKS, Macdonald J, Harris PNA, Heney C, Paterson DL, Trembizki E, Wang CYT, Whiley DM, Zowawi HM, Irwin AD. Rapid detection of NDM and VIM carbapenemase encoding genes by recombinase polymerase amplification and lateral flow-based detection. Eur J Clin Microbiol Infect Dis 2021; 40:2447-2453. [PMID: 33974185 DOI: 10.1007/s10096-021-04267-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/29/2021] [Indexed: 12/26/2022]
Abstract
Carbapenemase-producing organisms (CPOs) pose a serious clinical threat and rapid detection tools are essential to aid in patient management. We developed rapid and simple molecular tests to detect blaNDM-type and blaVIM-type carbapenemase genes using recombinase polymerase amplification (RPA) combined with a lateral flow detection. The tests could provide results in approximately 15 min when using DNA extracts, with limits of detection of 9.2 copies/μl for the blaNDM-type assay and 7.5 copies/μl for blaVIM-type assay, and successfully detected all isolates harbouring the carbapenemase encoding genes in a panel of 57 isolates. These RPA tests may be suitable for use in low-resource settings to tailor rapid implementation of infection control precautions and antibiotic stewardship.
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Affiliation(s)
- Abdulrahman K S Ayfan
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Faculty of Science, Biochemistry Department, King Abdul-Aziz University (KAU), Jeddah, Saudi Arabia
| | - Joanne Macdonald
- School of Science and Engineering, Genecology Research Centre, University of Sunshine Coast (USC), Sunshine Coast, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - Claire Heney
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Ella Trembizki
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Claire Y T Wang
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - Hosam M Zowawi
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- College of Medicine, King Saud bin Abdul-Aziz University for Health Science (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
| | - Adam D Irwin
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia.
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20
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Day AS, Ulep TH, Safavinia B, Hertenstein T, Budiman E, Dieckhaus L, Yoon JY. Emulsion-based isothermal nucleic acid amplification for rapid SARS-CoV-2 detection via angle-dependent light scatter analysis. Biosens Bioelectron 2021; 179:113099. [PMID: 33640656 PMCID: PMC7892303 DOI: 10.1016/j.bios.2021.113099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 pandemic, an ongoing global health crisis, has revealed the need for new technologies that integrate the sensitivity and specificity of RT-PCR tests with a faster time-to-detection. Here, an emulsion loop-mediated isothermal amplification (eLAMP) platform was developed to allow for the compartmentalization of LAMP reactions, leading to faster changes in emulsion characteristics, and thus lowering time-to-detection. Within these droplets, ongoing LAMP reactions lead to adsorption of amplicons to the water-oil interface, causing a decrease in interfacial tension, resulting in smaller emulsion diameters. Changes in emulsion diameter allow for the monitoring of the reaction by use of angle-dependent light scatter (based off Mie scatter theory). Mie scatter simulations confirmed that light scatter intensity is diameter-dependent and smaller colloids have lower intensity values compared to larger colloids. Via spectrophotometers and fiber optic cables placed at 30° and 60°, light scatter intensity was monitored. Scatter intensities collected at 5 min, 30° could statistically differentiate 10, 103, and 105 copies/μL initial concentrations compared to NTC. Similarly, 5 min scatter intensities collected at 60° could statistically differentiate 105 copies/μL initial concentrations in comparison to NTC. The use of both angles during the eLAMP assay allows for distinction between high and low initial target concentrations. The efficacy of a smartphone-based platform was also tested and had a similar limit of detection and assay time of less than 10 min. Furthermore, fluorescence-labeled primers were used to validate target nucleic acid amplification. Compared to existing LAMP assays for SARS-CoV-2 detection, these times-to-detections are very rapid.
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Affiliation(s)
- Alexander S Day
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States
| | - Tiffany-Heather Ulep
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States
| | - Babak Safavinia
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States
| | - Tyler Hertenstein
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States
| | - Elizabeth Budiman
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States
| | - Laurel Dieckhaus
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, United States.
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21
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Lai MY, Ooi CH, Lau YL. Validation of SYBR green I based closed-tube loop-mediated isothermal amplification (LAMP) assay for diagnosis of knowlesi malaria. Malar J 2021; 20:166. [PMID: 33766038 PMCID: PMC7995794 DOI: 10.1186/s12936-021-03707-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/17/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND As an alternative to PCR methods, LAMP is increasingly being used in the field of molecular diagnostics. Under isothermal conditions at 65 °C, the entire procedure takes approximately 30 min to complete. In this study, we establish a sensitive and visualized LAMP method in a closed-tube system for the detection of Plasmodium knowlesi. METHODS A total of 71 malaria microscopy positive blood samples collected in blood spots were obtained from the Sarawak State Health Department. Using 18s rRNA as the target gene, nested PCR and SYBR green I LAMP assay were performed following the DNA extraction. The colour changes of LAMP end products were observed by naked eyes. RESULTS LAMP assay demonstrated a detection limit of 10 copies/µL in comparison with 100 copies/µL nested PCR. Of 71 P. knowlesi blood samples collected, LAMP detected 69 microscopy-positive samples. LAMP exhibited higher sensitivity than nested PCR assay. The SYBR green I LAMP assay was 97.1% sensitive (95% CI 90.2-99.7%) and 100% specific (95% CI 83.2-100%). Without opening the cap, incorporation of SYBR green I into the inner cap of the tube enabled the direct visualization of results upon completion of amplification. The positives instantaneously turned green while the negatives remained orange. CONCLUSIONS These results indicate that SYBR green I LAMP assay is a convenient diagnosis tool for the detection of P. knowlesi in remote settings.
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Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Choo Huck Ooi
- Sarawak State Health Department, Jalan Diplomatik, Off Jalan Bako, Kuching, Sarawak, 93050, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia.
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22
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Müller K, Daßen S, Holowachuk S, Zwirglmaier K, Stehr J, Buersgens F, Ullerich L, Stoecker K. Pulse-Controlled Amplification-A new powerful tool for on-site diagnostics under resource limited conditions. PLoS Negl Trop Dis 2021; 15:e0009114. [PMID: 33513140 PMCID: PMC7875409 DOI: 10.1371/journal.pntd.0009114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/10/2021] [Accepted: 01/07/2021] [Indexed: 01/09/2023] Open
Abstract
Background Molecular diagnostics has become essential in the identification of many infectious and neglected diseases, and the detection of nucleic acids often serves as the gold standard technique for most infectious agents. However, established techniques like polymerase chain reaction (PCR) are time-consuming laboratory-bound techniques while rapid tests such as Lateral Flow Immunochromatographic tests often lack the required sensitivity and/or specificity. Methods/Principle findings Here we present an affordable, highly mobile alternative method for the rapid identification of infectious agents using pulse-controlled amplification (PCA). PCA is a next generation nucleic acid amplification technology that uses rapid energy pulses to heat microcyclers (micro-scale metal heating elements embedded directly in the amplification reaction) for a few microseconds, thus only heating a small fraction of the reaction volume. The heated microcyclers cool off nearly instantaneously, resulting in ultra-fast heating and cooling cycles during which classic amplification of a target sequence takes place. This reduces the overall amplification time by a factor of up to 10, enabling a sample-to-result workflow in just 15 minutes, while running on a small and portable prototype device. In this proof of principle study, we designed a PCA-assay for the detection of Yersinia pestis to demonstrate the efficacy of this technology. The observed detection limits were 434 copies per reaction (purified DNA) and 35 cells per reaction (crude sample) respectively of Yersinia pestis. Conclusions/Significance PCA offers fast and decentralized molecular diagnostics and is applicable whenever rapid, on-site detection of infectious agents is needed, even under resource limited conditions. It combines the sensitivity and specificity of PCR with the rapidness and simplicity of hitherto existing rapid tests. Rapid and reliable on-site diagnostics are an essential part of infectious disease outbreak response and the fight against neglected tropical diseases. In this respect, molecular diagnostics represents the current gold standard. However, the vast majority of current molecular diagnostic methods (such as Polymerase Chain Reaction) are lab-bound techniques, require expensive and heavy instrumentation and are time consuming to perform. Moreover, in resource limited countries with little or no infrastructure, samples often have to be transported over long distances to the few reference laboratories capable of such diagnostics. This significantly slows down the entire diagnostic process, thus considerably delaying important decisions necessary to contain outbreaks and to initiate medical countermeasures. Until now, there are only few rapid on-site diagnostic tests for a limited number of infectious agents available and they often lack sensitivity and/or specificity. Here we present a new technology–pulse-controlled amplification–which enables rapid (<20minutes) and portable, yet sensitive and specific on-site molecular diagnostics based on nucleic acid amplification. The device we developed is lightweight, battery operated and we demonstrate that our tests can be performed under resource limited conditions and without nucleic acid extraction, even when wearing full personal protective equipment. Thus, molecular diagnostics can be carried out on-site in a non-laboratory environment without the need for nucleic acid extraction. We envision that this new technology has the potential to become a gold standard method in nucleic acid detection for front-line and in-field applications.
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Affiliation(s)
| | | | - Scott Holowachuk
- Defence Research and Development Canada Suffield Centre, Department of National Defence, Suffield, Canada
| | | | | | | | | | - Kilian Stoecker
- Bundeswehr Institute of Microbiology, Munich, Germany
- * E-mail:
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23
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Choi Y, Song Y, Kim YT, Lee SJ, Lee KG, Im SG. Multifunctional Printable Micropattern Array for Digital Nucleic Acid Assay for Microbial Pathogen Detection. ACS Appl Mater Interfaces 2021; 13:3098-3108. [PMID: 33423455 DOI: 10.1021/acsami.0c16862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The digital nucleic acid assay is a precise, sensitive, and reproducible method for determining the presence of individual target molecules separated in designated partitions; thus, this technique can be used for the nucleic acid detection. Here, we propose a multifunctional micropattern array capable of isolating individual target molecules into partitions and simultaneous on-site cell lysis to achieve a direct DNA extraction and digitized quantification thereof. The multifunctional micropattern array is fabricated by the deposition of a copolymer film, poly(2-dimethylaminomethyl styrene-co-hydroxyethyl methacrylate) (pDH), directly on a microfluidic chip surface via the photoinitiated chemical vapor deposition process, followed by hydrophobic microcontact printing (μCP) to define each partition for the nucleic acid isolation. The pDH layer is a positively charged surface, which is desirable for the bacterial lysis and DNA capture, while showing exceptional water stability for more than 24 h. The hydrophobic μCP-treated pDH surface is stable under aqueous conditions at a high temperature (70 °C) for 1 h and enables the rapid and reliable formation of thousands of sessile microdroplets for the compartmentalization of an aqueous sample solution without involving bulky and costly microfluidic devices. By assembling the multifunctional micropattern array into the microfluidic chip, the isothermal amplification in each partition can detect DNA templates over a concentration range of 0.01-2 ng/μL. The untreated bacterial cells can also be directly compartmentalized via the microdroplet formation, followed by the on-site cell lysis and DNA capture on the compartmentalized pDH surface. For Escherichia coli O157:H7, Salmonella enteritidis, and Staphylococcus aureus cells, cell numbers ranging from 1.4 × 104 to 1.4 × 107 can be distinguished by using the multifunctional micropattern array, regardless of the cell type. The multifunctional micropattern array developed in this study provides a novel multifunctional compartmentalization method for rapid, simple, and accurate digital nucleic acid assays.
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Affiliation(s)
- Yunho Choi
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Younseong Song
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology, Korea Polytechnic University, 237 Sangidaehak-ro, Siheung-si, Gyeonggi-do 15073, Republic of Korea
| | - Seok Jae Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung G Lee
- National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sung Gap Im
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KAIST Institute for NanoCentury, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Pikula M, Ali MM, Filipe C, Hoare T. Single-Step Printable Hydrogel Microarray Integrating Long-Chain DNA for the Discriminative and Size-Specific Sensing of Nucleic Acids. ACS Appl Mater Interfaces 2021; 13:2360-2370. [PMID: 33411496 DOI: 10.1021/acsami.0c21061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A simple approach to fabricating hydrogel-based DNA microarrays is reported by physically entrapping the rolling circle amplification (RCA) product inside printable in situ gelling hydrazone cross-linked poly(oligoethylene glycol methacrylate) hydrogels. The hydrogel-printed RCA microarray facilitates improved RCA immobilization (>65% even after vigorous washing) and resistance to denaturation relative to RCA-only printed microarrays in addition to size-discriminative sensing of DNA probes (herein, 27 or fewer nucleotides) depending on the internal porosity of the hydrogel. Furthermore, the high number of sequence repeats in the concatemeric RCA product enables high-sensitivity detection of complementary DNA probes without the need for signal amplification, with signal/noise ratios of 10 or more achieved over a short 30 min assay time followed by minimal washing. The inherent antifouling properties of the hydrogel enable discriminative hybridization in complex biological samples, particularly for short (∼10 nt) oligonucleotides whose hybridization in other assays tends to be transient and of low affinity. The scalable manufacturability and efficient performance of these hydrogel-printed RCA microarrays thus offer potential for rapid, parallel, and inexpensive sensing of short DNA/RNA biomarkers and ligands, a critical current challenge in diagnostic and affinity screening assays.
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Affiliation(s)
- Milana Pikula
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - M Monsur Ali
- Biointerfaces Institute, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Carlos Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Todd Hoare
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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25
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Wang R, Qian C, Pang Y, Li M, Yang Y, Ma H, Zhao M, Qian F, Yu H, Liu Z, Ni T, Zheng Y, Wang Y. opvCRISPR: One-pot visual RT-LAMP-CRISPR platform for SARS-cov-2 detection. Biosens Bioelectron 2021; 172:112766. [PMID: 33126177 PMCID: PMC7586109 DOI: 10.1016/j.bios.2020.112766] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/23/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022]
Abstract
The 2019 novel coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected all aspects of human life. Rapid, accurate, sensitive and user friendly detection method is urgently needed to facilitate early intervention and control the spread of SARS-CoV-2. Here, we propose a one-pot visual SARS-CoV-2 detection system named "opvCRISPR" by integrating reverse transcription loop-mediated isothermal amplification (RT-LAMP) and Cas12a cleavage in a single reaction system. We demonstrate that the collateral activity against single-stranded DNA (ssDNA) reporters of activated Cas12a triggered by RT-LAMP amplicon increases detection sensitivity and makes detection results observable with naked eye. The opvCRISPR enables detection at nearly single molecule level in 45 min. We validate this method with 50 SARS-CoV-2 potentially infected clinical samples. The opvCRISPR diagnostic results provide 100% agreement with the Centers for Disease Control and Prevention (CDC)-approved quantitative RT-PCR assay. The opvCRISPR holds great potential for SARS-CoV-2 detection in next-generation point-of-care molecular diagnostics.
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Affiliation(s)
- Rui Wang
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, PR China
| | - Chunyan Qian
- The First People's Hospital of Yuhang District, Hangzhou, 311100, PR China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Yanan Pang
- Changhai Hospital, Second Military Medical University, Shanghai, 200433, PR China
| | - Miaomiao Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Yu Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Haijing Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Manying Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Hang Yu
- Shanghai RNAcure BioPharma Co., Ltd, 200438, PR China
| | - Zhenping Liu
- The First People's Hospital of Yuhang District, Hangzhou, 311100, PR China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, PR China.
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, PR China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, PR China; School of Life Sciences, Co-innovation Center of Neuroregeneration, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, 226001, China.
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26
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Garneret P, Coz E, Martin E, Manuguerra JC, Brient-Litzler E, Enouf V, González Obando DF, Olivo-Marin JC, Monti F, van der Werf S, Vanhomwegen J, Tabeling P. Performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification. PLoS One 2021; 16:e0243712. [PMID: 33428641 PMCID: PMC7799764 DOI: 10.1371/journal.pone.0243712] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/27/2020] [Indexed: 11/23/2022] Open
Abstract
To respond to the urgent need for COVID-19 testing, countries perform nucleic acid amplification tests (NAAT) for the detection of SARS-CoV-2 in centralized laboratories. Real-time RT-PCR (Reverse transcription-Polymerase Chain Reaction), used to amplify and detect the viral RNA., is considered, as the current gold standard for diagnostics. It is an efficient process, but the complex engineering required for automated RNA extraction and temperature cycling makes it incompatible for use in point of care settings [1]. In the present work, by harnessing progress made in the past two decades in isothermal amplification and paper microfluidics, we created a portable test, in which SARS-CoV-2 RNA is extracted, amplified isothermally by RT-LAMP (Loop-mediated Isothermal Amplification), and detected using intercalating dyes or fluorescent probes. Depending on the viral load in the tested samples, the detection takes between twenty minutes and one hour. Using a set of 16 pools of naso-pharyngal swab eluates, we estimated a limit of detection comparable to real-time RT-PCR (i.e. 1 genome copies per microliter of clinical sample) and no cross-reaction with eight major respiratory viruses currently circulating in Europe. We designed and fabricated an easy-to-use portable device called "COVIDISC" to carry out the test at the point of care. The low cost of the materials along with the absence of complex equipment will expedite the widespread dissemination of this device. What is proposed here is a new efficient tool to help managing the pandemics.
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27
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Prasannakumar MK, Parivallal PB, Pramesh D, Mahesh HB, Raj E. LAMP-based foldable microdevice platform for the rapid detection of Magnaporthe oryzae and Sarocladium oryzae in rice seed. Sci Rep 2021; 11:178. [PMID: 33420312 PMCID: PMC7794292 DOI: 10.1038/s41598-020-80644-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/24/2020] [Indexed: 11/11/2022] Open
Abstract
Rice blast (caused by Magnaporthe oryzae) and sheath rot diseases (caused by Sarocladium oryzae) are the most predominant seed-borne pathogens of rice. The detection of both pathogens in rice seed is essential to avoid production losses. In the present study, a microdevice platform was designed, which works on the principles of loop-mediated isothermal amplification (LAMP) to detect M. oryzae and S. oryzae in rice seeds. Initially, a LAMP, polymerase chain reaction (PCR), quantitative PCR (qPCR), and helicase dependent amplification (HDA) assays were developed with primers, specifically targeting M. oryzae and S. oryzae genome. The LAMP assay was highly efficient and could detect the presence of M. oryzae and S. oryzae genome at a concentration down to 100 fg within 20 min at 60 °C. Further, the sensitivity of the LAMP, HDA, PCR, and qPCR assays were compared wherein; the LAMP assay was highly sensitive up to 100 fg of template DNA. Using the optimized LAMP assay conditions, a portable foldable microdevice platform was developed to detect M. oryzae and S. oryzae in rice seeds. The foldable microdevice assay was similar to that of conventional LAMP assay with respect to its sensitivity (up to 100 fg), rapidity (30 min), and specificity. This platform could serve as a prototype for developing on-field diagnostic kits to be used at the point of care centers for the rapid diagnosis of M. oryzae and S. oryzae in rice seeds. This is the first study to report a LAMP-based foldable microdevice platform to detect any plant pathogens.
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Affiliation(s)
- M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India.
| | - P Buela Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India.
| | - H B Mahesh
- Department of Genetics and Plant Breeding, College of Agriculture, V.C. Farm, Mandya, India
| | - Edwin Raj
- Plant Pathology Division, ICAR - National Research Center for Banana, Thayanur, India
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28
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Chen Y, Shi Y, Chen Y, Yang Z, Wu H, Zhou Z, Li J, Ping J, He L, Shen H, Chen Z, Wu J, Yu Y, Zhang Y, Chen H. Contamination-free visual detection of SARS-CoV-2 with CRISPR/Cas12a: A promising method in the point-of-care detection. Biosens Bioelectron 2020; 169:112642. [PMID: 32979593 PMCID: PMC7502227 DOI: 10.1016/j.bios.2020.112642] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/21/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
The outbreaks of the infectious disease COVID-19 caused by SARS-CoV-2 seriously threatened the life of humans. A rapid, reliable and specific detection method was urgently needed. Herein, we reported a contamination-free visual detection method for SARS-CoV-2 with LAMP and CRISPR/Cas12a technology. CRISPR/Cas12a reagents were pre-added on the inner wall of the tube lid. After LAMP reaction, CRISPR/Cas12a reagents were flowed into the tube and mixed with amplicon solution by hand shaking, which can effectively avoid possible amplicon formed aerosol contamination caused by re-opening the lid after amplification. CRISPR/Cas12a can highly specific recognize target sequence and discriminately cleave single strand DNA probes (5'-6FAM 3'-BHQ1). With smart phone and portable 3D printing instrument, the produced fluorescence can be seen by naked eyes without any dedicated instruments, which is promising in the point-of-care detection. The whole amplification and detection process could be completed within 40 min with high sensitivity of 20 copies RNA of SARS-CoV-2. This reaction had high specificity and could avoid cross-reactivity with other common viruses such as influenza virus. For 7 positive and 3 negative respiratory swab samples provided by Zhejiang Provincial Center for Disease Control and Prevention, our detection results had 100% positive agreement and 100% negative agreement, which demonstrated the accuracy and application prospect of this method.
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Ya Shi
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Yin Chen
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Zhangnv Yang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Jue Li
- NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Biological Inspection Department, Zhejiang Institute for Food and Drug Control, Hangzhou, 310052, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Luping He
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Hong Shen
- NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Biological Inspection Department, Zhejiang Institute for Food and Drug Control, Hangzhou, 310052, China
| | | | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310016, China.
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Huan Chen
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China.
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Paul R, Ostermann E, Wei Q. Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases. Biosens Bioelectron 2020; 169:112592. [PMID: 32942143 PMCID: PMC7476893 DOI: 10.1016/j.bios.2020.112592] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022]
Abstract
Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.
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Affiliation(s)
- Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emily Ostermann
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA; Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, 27695, USA.
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Edgü G, Freund LJ, Hartje S, Tacke E, Hofferbert HR, Twyman RM, Noll GA, Muth J, Prüfer D. Fast, Precise, and Reliable Multiplex Detection of Potato Viruses by Loop-Mediated Isothermal Amplification. Int J Mol Sci 2020; 21:ijms21228741. [PMID: 33228234 PMCID: PMC7699554 DOI: 10.3390/ijms21228741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/04/2022] Open
Abstract
Potato is an important staple food crop in both developed and developing countries. However, potato plants are susceptible to several economically important viruses that reduce yields by up to 50% and affect tuber quality. One of the major threats is corky ringspot, which is a tuber necrosis caused by tobacco rattle virus (TRV). The appearance of corky ringspot symptoms on tubers prior to commercialization results in ≈ 45% of the tubers being downgraded in quality and value, while ≈ 55% are declared unsaleable. To improve current disease management practices, we have developed simple diagnostic methods for the reliable detection of TRV without RNA purification, involving minimalized sample handling (mini), subsequent improved colorimetric loop-mediated isothermal amplification (LAMP), and final verification by lateral-flow dipstick (LFD) analysis. Having optimized the mini-LAMP-LFD approach for the sensitive and specific detection of TRV, we confirmed the reliability and robustness of this approach by the simultaneous detection of TRV and other harmful viruses in duplex LAMP reactions. Therefore, our new approach offers breeders, producers, and farmers an inexpensive and efficient new platform for disease management in potato breeding and cultivation.
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Affiliation(s)
- Güven Edgü
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Lena Julie Freund
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Eckhard Tacke
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Hans-Reinhard Hofferbert
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Richard M. Twyman
- Twyman Research Management Ltd., P.O. Box 493, Scarborough YO11 9FJ, UK;
| | - Gundula A. Noll
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
| | - Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
- Correspondence: ; Tel.: +49-251-8322302
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Abstract
The complexity of current nucleic acid isolation methods limits their use outside of the modern laboratory environment. Here, we describe a fast and affordable method to purify nucleic acids from animal, plant, viral and microbial samples using a cellulose-based dipstick. Nucleic acids can be purified by dipping in-house-made dipsticks into just three solutions: the extract (to bind the nucleic acids), a wash buffer (to remove impurities) and the amplification reaction (to elute the nucleic acids). The speed and simplicity of this method make it ideally suited for molecular applications, both within and outside the laboratory, including limited-resource settings such as remote field sites and teaching institutions. Detailed instructions for how to easily manufacture large numbers of dipsticks in house are provided. Using the instructions, readers can create more than 200 dipsticks in <30 min and perform dipstick-based nucleic acid purifications in 30 s.
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Affiliation(s)
- Michael G Mason
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia.
| | - José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia.
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32
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Kamber T, Koekemoer LL, Mathis A. Loop-mediated isothermal amplification (LAMP) assays for Anopheles funestus group and Anopheles gambiae complex species. Med Vet Entomol 2020; 34:295-301. [PMID: 32154608 DOI: 10.1111/mve.12437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
Species of the genus Anopheles vary with regard to their vector capacity for Plasmodium spp., the causative agent of malaria, and their accurate identification is often required. Loop-mediated isothermal amplification (LAMP) is a rapid, simple and low-cost method for specific DNA amplification. Primers for LAMP assays specific for the Anopheles funestus group and Anopheles gambiae complex species as well as for the species Anopheles arabiensis, An. funestus, An. gambiae s.s/Anopheles coluzzii (major vectors) and Anopheles rivulorum (minor vector) were designed targeting specific genome or rDNA internal transcribed spacer regions. Reaction conditions (buffer composition, primer concentrations, incubation time) were evaluated and the specificities of the assays confirmed with DNA from non-target Anopheles species. DNA release from the mosquitoes is achieved simply by heating them for 5 min in water. An aliquot of the DNA solutions is transferred to the reaction tube using disposable inoculation loops. The outcome of the LAMP amplifications after 1 h incubation at 65 °C can easily be visualized by a colour change visible to the naked eye. The assays are operable under field conditions requiring only basic equipment (portable heat block programmable at 65 and 80 °C, cooler for master mixes).
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Affiliation(s)
- T Kamber
- Institute of Parasitology, National Centre for Vector Entomology, Zürich, Switzerland
| | - L L Koekemoer
- Wits Research Institute for Malaria, SAMRC Collaborating Centre for Multidisciplinary Research on Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Johannesburg, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - A Mathis
- Institute of Parasitology, National Centre for Vector Entomology, Zürich, Switzerland
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Esbin MN, Whitney ON, Chong S, Maurer A, Darzacq X, Tjian R. Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA 2020; 26:771-783. [PMID: 32358057 PMCID: PMC7297120 DOI: 10.1261/rna.076232.120] [Citation(s) in RCA: 334] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The current COVID-19 pandemic presents a serious public health crisis, and a better understanding of the scope and spread of the virus would be aided by more widespread testing. Nucleic-acid-based tests currently offer the most sensitive and early detection of COVID-19. However, the "gold standard" test pioneered by the U.S. Centers for Disease Control and Prevention takes several hours to complete and requires extensive human labor, materials such as RNA extraction kits that could become in short supply, and relatively scarce qPCR machines. It is clear that a huge effort needs to be made to scale up current COVID-19 testing by orders of magnitude. There is thus a pressing need to evaluate alternative protocols, reagents, and approaches to allow nucleic-acid testing to continue in the face of these potential shortages. There has been a tremendous explosion in the number of papers written within the first weeks of the pandemic evaluating potential advances, comparable reagents, and alternatives to the "gold-standard" CDC RT-PCR test. Here we present a collection of these recent advances in COVID-19 nucleic acid testing, including both peer-reviewed and preprint articles. Due to the rapid developments during this crisis, we have included as many publications as possible, but many of the cited sources have not yet been peer-reviewed, so we urge researchers to further validate results in their own laboratories. We hope that this review can urgently consolidate and disseminate information to aid researchers in designing and implementing optimized COVID-19 testing protocols to increase the availability, accuracy, and speed of widespread COVID-19 testing.
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Affiliation(s)
- Meagan N Esbin
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Shasha Chong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Anna Maurer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
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Lamb LE, Bartolone SN, Ward E, Chancellor MB. Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification. PLoS One 2020; 15:e0234682. [PMID: 32530929 PMCID: PMC7292379 DOI: 10.1371/journal.pone.0234682] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/01/2020] [Indexed: 01/12/2023] Open
Abstract
Novel Corona virus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or 2019-nCoV), and the subsequent disease caused by the virus (coronavirus disease 2019 or COVID-19), is an emerging global health concern that requires a rapid diagnostic test. Quantitative reverse transcription PCR (qRT-PCR) is currently the standard for SARS-CoV-2 detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper field based testing at point-of-risk. The objective of this study was to develop a rapid screening diagnostic test that could be completed in 30-45 minutes. Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. RNA isolated from nasopharyngeal swabs collected from actual COVID-19 patients was also tested. The samples were tested using RT-LAMP as well as by conventional qRT-PCR. Specificity of the RT-LAMP was evaluated by also testing against other related coronaviruses. RT-LAMP specifically detected SARS-CoV-2 in both simulated patient samples and clinical specimens. This test was performed in 30-45 minutes. This approach could be used for monitoring of exposed individuals or potentially aid with screening efforts in the field and potential ports of entry.
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Affiliation(s)
- Laura E. Lamb
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
- Oakland University William Beaumont School of Medicine, Rochester Hills, Michigan, United States of America
| | - Sarah N. Bartolone
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
| | - Elijah Ward
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
| | - Michael B. Chancellor
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
- Oakland University William Beaumont School of Medicine, Rochester Hills, Michigan, United States of America
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Cacho-Soblechero M, Malpartida-Cardenas K, Cicatiello C, Rodriguez-Manzano J, Georgiou P. A Dual-Sensing Thermo-Chemical ISFET Array for DNA-Based Diagnostics. IEEE Trans Biomed Circuits Syst 2020; 14:477-489. [PMID: 32149696 DOI: 10.1109/tbcas.2020.2978000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper presents a 32 × 32 ISFET array with in-pixel dual-sensing and programmability targeted for on-chip DNA amplification detection. The pixel architecture provides thermal and chemical sensing by encoding temperature and ion activity in a single output PWM, modulating its frequency and its duty cycle respectively. Each pixel is composed of an ISFET-based differential linear OTA and a 2-stage sawtooth oscillator. The operating point and characteristic response of the pixel can be programmed, enabling trapped charge compensation and enhancing the versatility and adaptability of the architecture. Fabricated in 0.18 μm standard CMOS process, the system demonstrates a quadratic thermal response and a highly linear pH sensitivity, with a trapped charge compensation scheme able to calibrate 99.5% of the pixels in the target range, achieving a homogeneous response across the array. Furthermore, the sensing scheme is robust against process variations and can operate under various supply conditions. Finally, the architecture suitability for on-chip DNA amplification detection is proven by performing Loop-mediated Isothermal Amplification (LAMP) of phage lambda DNA, obtaining a time-to-positive of 7.71 minutes with results comparable to commercial qPCR instruments. This architecture represents the first in-pixel dual thermo-chemical sensing in ISFET arrays for Lab-on-a-Chip diagnostics.
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36
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Wu H, Qian C, Wu C, Wang Z, Wang D, Ye Z, Ping J, Wu J, Ji F. End-point dual specific detection of nucleic acids using CRISPR/Cas12a based portable biosensor. Biosens Bioelectron 2020; 157:112153. [PMID: 32250930 DOI: 10.1016/j.bios.2020.112153] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/27/2020] [Accepted: 03/12/2020] [Indexed: 12/26/2022]
Abstract
A CRISPR/Cas12a based portable biosensor (Cas12a-PB) was developed to simultaneously visually detect CaMV35S promoter and Lectin gene from genetically modified (GM) soybean powders (Roundup Ready@). The Cas12a-PB, mainly made of polymethylmethacrylate (PMMA) and PMMA tape, has a connection structure, three channels and three detection chambers. The CRISPR/Cas12a detection reagents were preloaded in detection chambers and the reaction tube was connected to the connection structure by screw threads. After amplification, the amplicons were gone into three detection chambers by swinging the Cas12a-PB to conduct dual detection. Positive samples would produce green fluorescence while negative samples were black under the irradiation of 490 nm LED light. In this study, the Cas12a-PB successively combined with ordinary PCR, rapid PCR and loop-mediated isothermal amplification (LAMP) to achieve dual detection, which made detection process more convenient and portable. As low as 0.1% transgenic ingredients in soybean powders could be detected and the specificity of Cas12a-PB was confirmed with GM maize powders (MON810, GA21), GM soybean powders (DP305423), non-GM peanut and rice as targets. In the end, an amplification chamber combining with Cas12a-PB on a PMMA chip was further designed to eliminate the use of reaction tube and mineral oil, which made operation simpler. The established Cas12a-PB would provide a new reliable solution for multiple targets detection in clinic diagnostics, food safety, etc.
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Affiliation(s)
- Hui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zhen Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Dacheng Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zunzhong Ye
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
| | - Feng Ji
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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Kalofonou M, Malpartida-Cardenas K, Alexandrou G, Rodriguez-Manzano J, Yu LS, Miscourides N, Allsopp R, Gleason KLT, Goddard K, Fernandez-Garcia D, Page K, Georgiou P, Ali S, Coombes RC, Shaw J, Toumazou C. A novel hotspot specific isothermal amplification method for detection of the common PIK3CA p.H1047R breast cancer mutation. Sci Rep 2020; 10:4553. [PMID: 32165708 PMCID: PMC7067842 DOI: 10.1038/s41598-020-60852-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/13/2020] [Indexed: 01/07/2023] Open
Abstract
Breast cancer (BC) is a common cancer in women worldwide. Despite advances in treatment, up to 30% of women eventually relapse and die of metastatic breast cancer. Liquid biopsy analysis of circulating cell-free DNA fragments in the patients' blood can monitor clonality and evolving mutations as a surrogate for tumour biopsy. Next generation sequencing platforms and digital droplet PCR can be used to profile circulating tumour DNA from liquid biopsies; however, they are expensive and time consuming for clinical use. Here, we report a novel strategy with proof-of-concept data that supports the usage of loop-mediated isothermal amplification (LAMP) to detect PIK3CA c.3140 A > G (H1047R), a prevalent BC missense mutation that is attributed to BC tumour growth. Allele-specific primers were designed and optimized to detect the p.H1047R variant following the USS-sbLAMP method. The assay was developed with synthetic DNA templates and validated with DNA from two breast cancer cell-lines and two patient tumour tissue samples through a qPCR instrument and finally piloted on an ISFET enabled microchip. This work sets a foundation for BC mutational profiling on a Lab-on-Chip device, to help the early detection of patient relapse and to monitor efficacy of systemic therapies for personalised cancer patient management.
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Affiliation(s)
- Melpomeni Kalofonou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England.
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
| | - George Alexandrou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
| | - Ling-Shan Yu
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
| | - Nicholas Miscourides
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
| | - Rebecca Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, LE2 7LX, England
| | - Kelly L T Gleason
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, England
| | - Katie Goddard
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, England
| | - Daniel Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, LE2 7LX, England
| | - Karen Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, LE2 7LX, England
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
| | - Simak Ali
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, England
| | - R Charles Coombes
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, England
| | - Jacqueline Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, LE2 7LX, England
| | - Christofer Toumazou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London, SW7 2AZ, England
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38
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Waliullah S, Ling KS, Cieniewicz EJ, Oliver JE, Ji P, Ali ME. Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cucurbit Leaf Crumple Virus. Int J Mol Sci 2020; 21:ijms21051756. [PMID: 32143404 PMCID: PMC7084362 DOI: 10.3390/ijms21051756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/16/2022] Open
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed for simple, rapid and efficient detection of Cucurbit leaf crumple virus (CuLCrV), one of the most important begomoviruses that infects cucurbits worldwide. A set of six specific primers targeting a total 240 nt sequence regions in the DNA A of CuLCrV were designed and synthesized for detection of CuLCrV from infected leaf tissues using real-time LAMP amplification with the Genie® III system, which was further confirmed by gel electrophoresis and SYBR™ Green I DNA staining for visual observation. The optimum reaction temperature and time were determined, and no cross-reactivity was seen with other begomoviruses. The LAMP assay could amplify CuLCrV from a mixed virus assay. The sensitivity assay demonstrated that the LAMP reaction was more sensitive than conventional PCR, but less sensitive than qPCR. However, it was simpler and faster than the other assays evaluated. The LAMP assay also amplified CuLCrV-infected symptomatic and asymptomatic samples more efficiently than PCR. Successful LAMP amplification was observed in mixed virus-infected field samples. This simple, rapid, and sensitive method has the capacity to detect CuLCrV in samples collected in the field and is therefore suitable for early detection of the disease to reduce the risk of epidemics.
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Affiliation(s)
- Sumyya Waliullah
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
| | - Kai-Shu Ling
- U. S. Vegetable Laboratory, USDA-ARS, Charleston, SC 29414, USA;
| | | | - Jonathan E. Oliver
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
| | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.W.); (J.E.O.); (P.J.)
- Correspondence:
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39
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Dixon RB, Bonaparte J, Greenwood CJ, Davis M, Dasgupta A. Analytical Performance Evaluation of Aptima Herpes Simplex Virus 1 and 2 Assay Using Hologic Panther Instrument. Ann Clin Lab Sci 2020; 50:278-281. [PMID: 32366570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are responsible for a variety of human diseases. Therefore, rapid detection of these viruses in clinical laboratory is important. Recently Aptima Herpes Simplex 1 and 2 assay has been approved by the FDA. We evaluated analytical performance of this assay by comparing results obtained by analysis of cultures. MATERIALS AND METHODS Aptima Herpes Simplex assay is a nucleic acid amplification test that can be fully automated using the Hologic Panther instrument. This is a qualitative test providing either positive or negative result. We analyzed 115 specimens collected from anogenital locations using the new Aptima Herpes Simplex assay and our current tissue culture method. RESULTS We observed good correlation between results obtained by using Aptima assay and the tissue culture method in 101 specimens but 14 specimens showed discordant results. Further testing in a reference laboratory using PCR (polymerase chain reaction) showed results in agreement with the Aptima assay but not the tissue culture method. The cause of discordance was misidentification of HSV-2 as HSV-1 by the tissue culture method. CONCLUSIONS Aptima Herpes simplex assay on the Hologic Panther instrument is suitable for rapid detection of herpes simplex virus in clinical laboratory.
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Affiliation(s)
- R Brent Dixon
- Public Health Laboratory, South Carolina Department of Health and Environmental Control, Columbia, SC, USA
| | - Jonathan Bonaparte
- Public Health Laboratory, South Carolina Department of Health and Environmental Control, Columbia, SC, USA
| | - Christy J Greenwood
- Public Health Laboratory, South Carolina Department of Health and Environmental Control, Columbia, SC, USA
| | - Megan Davis
- Public Health Laboratory, South Carolina Department of Health and Environmental Control, Columbia, SC, USA
| | - Amitava Dasgupta
- Department of Pathology and Laboratory Medicine, University of Texas McGovern Medical School at Houston, Houston, TX, USA
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Mei M, Chen R, Gao X, Cao Y, Weng W, Duan Y, Tan X, Liu Z. Establishment and application of a 10-plex liquid bead array for the simultaneous rapid detection of animal species. J Sci Food Agric 2020; 100:325-334. [PMID: 31584699 DOI: 10.1002/jsfa.10042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/07/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Meat fraud and adulteration incidents occur frequently in almost all regions of the globe, especially with the increase in the world's population. To ensure the authenticity of meat products, we developed a 10-plex xMAP assay to simultaneously detect ten animal materials: bovine, caprine, poultry, swine, donkey, deer, horse, dog, fox and mink. RESULTS This method was investigated by analyzing DNA extracts from raw muscle, muscle mixtures, meat products and animal feeds. Our results indicated that the species of interest can be identified, differentiated and detected down to 1 g kg-1 in binary mixtures or 0.01-0.001 ng of genomic DNA from specific species. Testing of 125 commercial samples showed a 97.4% coincidence rate with the method used in routine testing in our lab. CONCLUSION These results indicated that the method established in this study could detect ten animal materials simultaneously within 3 h, which provides a new, useful tool for animal ingredient analysis in meat products and animal feeds. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Mingzhu Mei
- Technical Center, Guangzhou Customs District People's Republic of China, Guangzhou, China
| | - Ru Chen
- Technical Center, Guangzhou Customs District People's Republic of China, Guangzhou, China
| | - Xiaobo Gao
- Department of Genetics, National Research Institute for Family Planning, Beijing, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Wenchuan Weng
- Technical Center, Guangzhou Customs District People's Republic of China, Guangzhou, China
| | - Yanyu Duan
- Technical Center, Guangzhou Customs District People's Republic of China, Guangzhou, China
| | - Xin Tan
- State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, China
| | - Zhiling Liu
- Technical Center, Guangzhou Customs District People's Republic of China, Guangzhou, China
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Cha D, Kim D, Choi W, Park S, Han H. Point-of-care diagnostic (POCD) method for detecting Bursaphelenchus xylophilus in pinewood using recombinase polymerase amplification (RPA) with the portable optical isothermal device (POID). PLoS One 2020; 15:e0227476. [PMID: 31935232 PMCID: PMC6959569 DOI: 10.1371/journal.pone.0227476] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/19/2019] [Indexed: 12/02/2022] Open
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, is a causative agent of pine wilt disease (PWD). To date, although several molecular diagnostic methods have been developed, rapid on-site diagnostic tools for detecting PWN in pinewood are limited. In this study, a point of care diagnostic (POCD) method for detecting PWN in pinewood using recombinase polymerase amplification (RPA) assay was developed. This method comprises quick gDNA extraction buffer (DAP buffer) for the direct extraction of gDNA of PWN from pinewood and a battery-mounted portable optical isothermal device (POID) for the detection of PWD in the field. The RPA assay can distinguish between the PWN and its conspecies which exist in pinewood and can complete diagnostic procedures within 25 min in the field. Moreover, the RPA assay can detect PWN in old wood samples in both natural and stored conditions. The POCD-RPA assay to detect PWN will be useful for epidemiological investigations in the field as well as for quarantine processes in the wood trade.
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Affiliation(s)
- Deokjea Cha
- Division of Forest Insect Pests & Diseases, National Institute of Forest Science, Dongdaemun, Seoul, Korea
| | - Dongsoo Kim
- Division of Forest Insect Pests & Diseases, National Institute of Forest Science, Dongdaemun, Seoul, Korea
| | - Wonil Choi
- Division of Forest Ecology & Climate Change, National Institute of Forest Science, Dongdaemun, Seoul, Korea
| | | | - Hyerim Han
- Division of Forest Insect Pests & Diseases, National Institute of Forest Science, Dongdaemun, Seoul, Korea
- * E-mail:
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Hao L, Wang W, Shen X, Wang S, Li Q, An F, Wu S. A Fluorescent DNA Hydrogel Aptasensor Based on the Self-Assembly of Rolling Circle Amplification Products for Sensitive Detection of Ochratoxin A. J Agric Food Chem 2020; 68:369-375. [PMID: 31829586 DOI: 10.1021/acs.jafc.9b06021] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A sensitive fluorescent DNA hydrogel aptasensor based on the self-assembly of rolling circle amplification (RCA) products was developed for ochratoxin A (OTA) detection in beer. A competitive binding mode of aptamer, complementary sequence, and target was integrated into the DNA hydrogel for OTA detection. The OTA aptamer first combined with the primer to form the hybridized product. Then, in the presence of OTA, the aptamer combined with OTA, which released the primer. The released primer hybridized with the padlock probe to form a circular template, and the RCA reaction was initiated by adding ligase, polymerase, and dNTPs. The fluorescent DNA hydrogel was obtained by adding Cy3-dUTP together with dNTPs, and the fluorescence (FL) intensity of the DNA hydrogel was positively correlated with OTA concentration. Under the optimal experimental conditions, the linear range of the relationship varied from 0.05 ng/mL to 100 ng/mL with a detection limit for OTA of 0.01 ng/mL. The fluorescent DNA hydrogel aptasensor showed good specificity and stability in beer samples. Therefore, the fabricated DNA hydrogel aptasensor shows considerable potential applications in detecting OTA for food safety.
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Affiliation(s)
- Liling Hao
- School of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Wei Wang
- School of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Xueqing Shen
- School of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Shuliu Wang
- School of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | | | - Faliang An
- School of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
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Lamb LE, Bartolone SN, Ward E, Chancellor MB. Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification. PLoS One 2020; 15:e0234682. [PMID: 32530929 DOI: 10.1101/2020.02.19.20025155] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/01/2020] [Indexed: 05/18/2023] Open
Abstract
Novel Corona virus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or 2019-nCoV), and the subsequent disease caused by the virus (coronavirus disease 2019 or COVID-19), is an emerging global health concern that requires a rapid diagnostic test. Quantitative reverse transcription PCR (qRT-PCR) is currently the standard for SARS-CoV-2 detection; however, Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) may allow for faster and cheaper field based testing at point-of-risk. The objective of this study was to develop a rapid screening diagnostic test that could be completed in 30-45 minutes. Simulated patient samples were generated by spiking serum, urine, saliva, oropharyngeal swabs, and nasopharyngeal swabs with a portion of the SARS-CoV-2 nucleic sequence. RNA isolated from nasopharyngeal swabs collected from actual COVID-19 patients was also tested. The samples were tested using RT-LAMP as well as by conventional qRT-PCR. Specificity of the RT-LAMP was evaluated by also testing against other related coronaviruses. RT-LAMP specifically detected SARS-CoV-2 in both simulated patient samples and clinical specimens. This test was performed in 30-45 minutes. This approach could be used for monitoring of exposed individuals or potentially aid with screening efforts in the field and potential ports of entry.
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Affiliation(s)
- Laura E Lamb
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
- Oakland University William Beaumont School of Medicine, Rochester Hills, Michigan, United States of America
| | - Sarah N Bartolone
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
| | - Elijah Ward
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
| | - Michael B Chancellor
- Department of Urology, Beaumont Health System, Royal Oak, Michigan, United States of America
- Oakland University William Beaumont School of Medicine, Rochester Hills, Michigan, United States of America
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Stellrecht KA, Cimino JL, Wilson LI, Maceira VP, Butt SA. Panther Fusion® Respiratory Virus Assays for the detection of influenza and other respiratory viruses. J Clin Virol 2019; 121:104204. [PMID: 31743836 PMCID: PMC7172166 DOI: 10.1016/j.jcv.2019.104204] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 09/30/2019] [Accepted: 10/21/2019] [Indexed: 12/16/2022]
Abstract
Panther Fusion RV Assays evaluated using 275 consecutive NP specimens previously used to analyze 5 PCR, as well as 225 archived specimens. Fusion’s overall sensitivity was 100% despite multiple freeze/thaws of these samples, which were previously used in multiple studies. Limit of detection with a variety of FluA isolates ranged from 2.69–2.96 log copies/ml and demonstrated superior as compared to six other commercial tests.
Background Nucleic acid amplification tests (NAATs), such as PCR, are preferred for respiratory virus testing, due to superior diagnostic accuracy and faster turnaround time. Panther Fusion® Respiratory Assays (Fusion), which includes FluA/B/RSV (FFABR), Paraflu and AdV/hMPV/RV, offers a modular approach to syndromic testing on a fully automated platform while improving gene targets and expanding the test menu. Objectives and study design We evaluated Fusion using 275 consecutive nasopharyngeal specimens previously used in an analysis of five PCRs, as well as 225 archived specimens. Results Of the combined 500 specimens, 134 were positive for influenza A (FluA), 54 for FluB, 65 for RSV, 64 for parainfluenza (PIV), 24 for adenovirus (AdV), 21 for humanmetapneumovirus (hMPV), and 40 for rhinovirus (RV) with Fusion. Of the positive samples Fusion correlated with historical results for all but one, despite multiple freeze-thaws cycles of this collection. Fusion was positive for an additional 33 samples, including 11 FluAs, 7 RSVs, 3 PIV3s, 3 AdV, 6 hMPV and 3 RVs. These samples were retested with corresponding Prodesse (Pro) assays using quadruple sample volume. This resolver test confirmed Fusion results for an additional 4 FluAs, 4 RSVs, 1 PIV3 and 3 AdVs. The sensitivity and specificity ranges of Fusion were 99–100% and 98–100%. Limit of detection (LOD) analyses were performed on a variety of Flu isolates. The LODs ranged from 2.69 to 2.99 log copies/ml and demonstrated superior LOD as compared to previously published data for some assays or to concurrent analyses with two new commercial tests.
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Affiliation(s)
- Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, United States; Department of Immunology and Microbial Diseases, Albany Medical College, Albany, New York, United States; Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, New York, United States.
| | - Jesse L Cimino
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, New York, United States
| | - Lisa I Wilson
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, New York, United States
| | - Vincente P Maceira
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, New York, United States
| | - Shafiq A Butt
- Department of Pathology and Laboratory Medicine, Albany Medical Center Hospital, Albany, New York, United States
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Phillips EA, Moehling TJ, Ejendal KFK, Hoilett OS, Byers KM, Basing LA, Jankowski LA, Bennett JB, Lin LK, Stanciu LA, Linnes JC. Microfluidic rapid and autonomous analytical device (microRAAD) to detect HIV from whole blood samples. Lab Chip 2019; 19:3375-3386. [PMID: 31539001 PMCID: PMC7384476 DOI: 10.1039/c9lc00506d] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While identifying acute HIV infection is critical to providing prompt treatment to HIV-positive individuals and preventing transmission, existing laboratory-based testing methods are too complex to perform at the point of care. Specifically, molecular techniques can detect HIV RNA within 8-10 days of transmission but require laboratory infrastructure for cold-chain reagent storage and extensive sample preparation performed by trained personnel. Here, we demonstrate our point-of-care microfluidic rapid and autonomous analysis device (microRAAD) that automatically detects HIV RNA from whole blood. Inside microRAAD, we incorporate vitrified amplification reagents, thermally-actuated valves for fluidic control, and a temperature control circuit for low-power heating. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized using a lateral flow immunoassay (LFIA), resulting in an assay limit of detection of 100 HIV-1 RNA copies when performed as a standard tube reaction. Even after three weeks of room-temperature reagent storage, microRAAD automatically isolates the virus from whole blood, amplifies HIV-1 RNA, and transports amplification products to the internal LFIA, detecting as few as 3 × 105 HIV-1 viral particles, or 2.3 × 107 virus copies per mL of whole blood, within 90 minutes. This integrated microRAAD is a low-cost and portable platform to enable automated detection of HIV and other pathogens at the point of care.
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Affiliation(s)
- Elizabeth A Phillips
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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Punati RD, Mallepaddi PC, Poonati R, Maity SN, Sohal JS, Polavarapu KKB, Polavarapu R. Development and evaluation of LAMP-coupled lateral flow device for the detection of MAP in livestock at point of care resource-limited areas. Braz J Microbiol 2019; 50:1105-1114. [PMID: 31541428 DOI: 10.1007/s42770-019-00116-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022] Open
Abstract
The Mycobacterium avium subspecies paratuberculosis (MAP) causes paratuberculosis (Johne's disease), a systemic and chronic inflammation of intestine that affects bovine, small ruminants like goat and sheep. The disease has a greater economic importance in cattle and in small ruminants. But its effective control is impeded due to lack of rapid and accurate diagnostics. The present study is aimed at developing a LAMP-coupled lateral flow device (LFD) for rapid detection of paratuberculosis in livestock animal species such as cattle and in small ruminants at resource-limited areas. LAMP primers with biotin and FITC end tags were designed for IS900 gene specific for MAP. To determine sensitivity of LAMP assay, 10-fold serial dilutions were made from 10 ng/μl MAP stock DNA and were compared with PCR. The detection limits of LAMP-coupled LFD were defined and reactions were repeated for reproducibility. The specificity was evaluated using other infectious bacteria such as M. bovis, M. tuberculosis, Brucella abortus, Leptospira interrogan, Yersinia enterocolitica, Salmonella typhimurium, Listeria monocytogens, and Staphylococcus aureus. A total of 95 samples turned positive for LAMP-coupled LFD out of 389 fecal samples. All the cultural-positive and PCR-positive samples showed positive in LAMP-coupled LFD. Nine samples with negative cultures turned positive in LAMP assay. The overall sensitivity and specificity of the LAMP-coupled LFD assays were 100% and 97.02% respectively in comparison with the culture as the gold standard method. The sensitivity detection limit of developed assay was 10 fg/μl and specificity was 100%. This assay successfully detected MAP not only by using bacterial DNA but also in clinical fecal samples. The clear band formation at control and test positions was observed on LAMP-coupled LFD. The developed assay is a simple, rapid, easy to perform, and is very useful in early diagnosis of Mycobacterium avium subsp. paratuberculosis at point of care resource-limited areas.
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Affiliation(s)
- Rudrama Devi Punati
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
- Department of Veterinary Microbiology, Genomix Molecular Diagnostics Pvt. Ltd, 5-36/207, Prashanthnagar, Kukatpally, Hyderabad, Telangana, 500 072, India
- Department of Veterinary Microbiology, GenomixCARL Pvt. Ltd., Pulivendula, Kadapa, Andhra Pradesh, 516 390, India
| | - Prudhvi Chand Mallepaddi
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
- Department of Veterinary Microbiology, Genomix Molecular Diagnostics Pvt. Ltd, 5-36/207, Prashanthnagar, Kukatpally, Hyderabad, Telangana, 500 072, India
- Department of Veterinary Microbiology, GenomixCARL Pvt. Ltd., Pulivendula, Kadapa, Andhra Pradesh, 516 390, India
| | - Revathi Poonati
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
- Department of Veterinary Microbiology, Genomix Molecular Diagnostics Pvt. Ltd, 5-36/207, Prashanthnagar, Kukatpally, Hyderabad, Telangana, 500 072, India
- Department of Veterinary Microbiology, GenomixCARL Pvt. Ltd., Pulivendula, Kadapa, Andhra Pradesh, 516 390, India
| | - Soumendra Nath Maity
- Department of Veterinary Microbiology, Genomix Molecular Diagnostics Pvt. Ltd, 5-36/207, Prashanthnagar, Kukatpally, Hyderabad, Telangana, 500 072, India
- Department of Veterinary Microbiology, GenomixCARL Pvt. Ltd., Pulivendula, Kadapa, Andhra Pradesh, 516 390, India
| | - Jagdip Singh Sohal
- AMITY Center for Mycobacterial Division, AMITY University, Jaipur, Rajasthan, 302 001, India
| | - Kavi Kishor B Polavarapu
- Department of Veterinary Microbiology, Genomix Molecular Diagnostics Pvt. Ltd, 5-36/207, Prashanthnagar, Kukatpally, Hyderabad, Telangana, 500 072, India.
- Department of Veterinary Microbiology, GenomixCARL Pvt. Ltd., Pulivendula, Kadapa, Andhra Pradesh, 516 390, India.
| | - Rathnagiri Polavarapu
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
- Department of Veterinary Microbiology, Genomix Molecular Diagnostics Pvt. Ltd, 5-36/207, Prashanthnagar, Kukatpally, Hyderabad, Telangana, 500 072, India
- Department of Veterinary Microbiology, GenomixCARL Pvt. Ltd., Pulivendula, Kadapa, Andhra Pradesh, 516 390, India
- Genomix Biotech Inc, 2620 Braithwood Road, Atlanta, GA, 30345, USA
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Abstract
Recent advances in transcriptomic analysis at single-cell resolution reveal cell-to-cell heterogeneity in a biological sample with unprecedented resolution. Partitioning single cells in individual micro-droplets and harvesting each cell's mRNA molecules for next-generation sequencing has proven to be an effective method for profiling transcriptomes from a large number of cells at high throughput. However, the assays to recover the full transcriptomes are time-consuming in sample preparation and require expensive reagents and sequencing cost. Many biomedical applications, such as pathogen detection, prefer highly sensitive, reliable and low-cost detection of selected genes. Here, we present a droplet-based microfluidic platform that permits seamless on-chip droplet sorting and merging, which enables completing multi-step reaction assays within a short time. By sequentially adding lysis buffers and reactant mixtures to micro-droplet reactors, we developed a novel workflow of single-cell reverse transcription loop-mediated-isothermal amplification (scRT-LAMP) to quantify specific mRNA expression levels in different cell types within one hour. Including single cell encapsulation, sorting, lysing, reactant addition, and quantitative mRNA detection, the fully on-chip workflow provides a rapid, robust, and high-throughput experimental approach for a wide variety of biomedical studies.
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Affiliation(s)
- Meng Ting Chung
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48105, USA. and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48105, USA.
| | - Katsuo Kurabayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48105, USA. and Department of Electrical Engineering and Computer Sci., University of Michigan, Ann Arbor, MI 48105, USA
| | - Dawen Cai
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48105, USA. and Biophysics, College of LS&A, University of Michigan, Ann Arbor, MI 48105, USA
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Ulep TH, Day AS, Sosnowski K, Shumaker A, Yoon JY. Interfacial Effect-Based Quantification of Droplet Isothermal Nucleic Acid Amplification for Bacterial Infection. Sci Rep 2019; 9:9629. [PMID: 31270374 PMCID: PMC6610113 DOI: 10.1038/s41598-019-46028-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/17/2019] [Indexed: 02/08/2023] Open
Abstract
Bacterial infection is a widespread problem in humans that can potentially lead to hospitalization and morbidity. The largest obstacle for physicians/clinicians is the time delay in accurately identifying infectious bacteria, especially their sub-species, in order to adequately treat and diagnose such infected patients. Loop-mediated amplification (LAMP) is a nucleic acid amplification method that has been widely used in diagnostic applications due to its simplicity of constant temperature, use of up to 4 to 6 primers (rendering it highly specific), and capability of amplifying low copies of target sequences. Use of interfacial effect-based monitoring is expected to dramatically shorten the time-to-results of nucleic acid amplification techniques. In this work, we developed a LAMP-based point-of-care platform for detection of bacterial infection, utilizing smartphone measurement of contact angle from oil-immersed droplet LAMP reactions. Whole bacteria (Escherichia coli O157:H7) were assayed in buffer as well as 5% diluted human whole blood. Monitoring of droplet LAMP reactions was demonstrated in a three-compartment, isothermal proportional-integrated-derived (PID)-controlled chip. Smartphone-captured images of droplet LAMP reactions, and their contact angles, were evaluated. Contact angle decreased substantially upon target amplification in both buffer and whole blood samples. In comparison, no-target control (NTC) droplets remained stable throughout the 30 min isothermal reactions. These results were explained by the pre-adsorption of plasma proteins to an oil-water interface (lowering contact angle), followed by time-dependent amplicon formation and their preferential adsorption to the plasma protein-occupied oil-water interface. Time-to-results was as fast as 5 min, allowing physicians to quickly make their decision for infected patients. The developed assay demonstrated quantification of bacteria concentration, with a limit-of-detection at 102 CFU/μL for buffer samples, and binary target or no-target identification with a limit-of-detection at 10 CFU/μL for 5% diluted whole blood samples.
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Affiliation(s)
- Tiffany-Heather Ulep
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona, 85721, United States
| | - Alexander S Day
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona, 85721, United States
| | - Katelyn Sosnowski
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona, 85721, United States
| | - Alexa Shumaker
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona, 85721, United States
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona, 85721, United States.
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Liu Y, Jeraldo P, Jang JS, Eckloff B, Jen J, Walther-Antonio M. Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity. Anal Chem 2019; 91:8036-8044. [PMID: 31188565 PMCID: PMC8422856 DOI: 10.1021/acs.analchem.8b04773] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Single cell RNA sequencing is a technology that provides the capability of analyzing the transcriptome of a single cell from a population. So far, single cell RNA sequencing has been focused mostly on human cells due to the larger starting amount of RNA template for subsequent amplification. One of the major challenges of applying single cell RNA sequencing to microbial cells is to amplify the femtograms of the RNA template to obtain sufficient material for downstream sequencing with minimal contamination. To achieve this goal, efforts have been focused on multiround RNA amplification, but would introduce additional contamination and bias. In this work, we for the first time coupled a microfluidic platform with multiple displacement amplification technology to perform single cell whole transcriptome amplification and sequencing of Porphyromonas somerae, a microbe of interest in endometrial cancer, as a proof-of-concept demonstration of using single cell RNA sequencing tool to unveil gene expression heterogeneity in single microbial cells. Our results show that the bacterial single-cell gene expression regulation is distinct across different cells, supporting widespread heterogeneity.
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Affiliation(s)
- Yuguang Liu
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, Minnesota, United States
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Patricio Jeraldo
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, Minnesota, United States
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Bruce Eckloff
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Jin Jen
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
| | - Marina Walther-Antonio
- Department of Surgery, Division of Surgical Research, Mayo Clinic, Rochester, Minnesota, United States
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota, United States
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Trinh TND, Lee NY. A foldable isothermal amplification microdevice for fuchsin-based colorimetric detection of multiple foodborne pathogens. Lab Chip 2019; 19:1397-1405. [PMID: 30847458 DOI: 10.1039/c8lc01389f] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In this study, we have developed a foldable microdevice fully integrating DNA purification, amplification, and detection processes for detecting multiple foodborne pathogens. Specifically, the loop-mediated isothermal amplification (LAMP) technique was combined with a fuchsin-based direct DNA colorimetric detection method. The microdevice was composed of three parts: a sample zone, reaction zone, and detection zone. A sealing film attached to the sample, reaction, and detection zones served as a bottom layer to make the microdevice foldable. The detection zone was made up of paper strips attached to the sticky side of the sealing film, and fuchsin-stained lines were drawn on the paper strips. The microdevice can be folded to directly transfer the DNA template solution from the sample chambers to the reaction chambers. In this manner, fluid manipulation was readily realized and the use of a bulky instrument such as a pump or rotator was completely dispensed with. After the LAMP reaction, the detection zone was folded so that the fuchsin-stained lines were completely soaked into the reaction chambers. Genomic DNAs of Salmonella spp. and Escherichia coli O157:H7 were first successfully purified from thermally-lysed milk using polydopamine-coated paper, amplified by LAMP, and directly identified by the naked eye using fuchsin within 65 min. Using this microdevice, approximately 102 CFU per mL of Salmonella spp. was detected. These results indicate the significant potential of this microdevice for the sample-in-answer-out genetic analysis of multiple foodborne pathogens in resource-limited environments.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
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