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Wang N, Zhang J, Xiao B, Sun X, Chen J, Huang F, Chen A. Amplification-free quantitative detection of genomic DNA using lateral flow strips for milk authentication. Biosens Bioelectron 2024; 252:116140. [PMID: 38394702 DOI: 10.1016/j.bios.2024.116140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
With the globalization and complexity of the food supply chain, the market is becoming increasingly competitive and food fraudulent activities are intensifying. The current state of food detection faced two primary challenges. Firstly, existing testing methods were predominantly laboratory-based, requiring complex procedures and precision instruments. Secondly, there was a lack of accurate and efficient quantitative detection methods. Taking cow's milk as an example, this study introduced a novel method for nucleic acid quantification in dairy products, based on lateral flow strips (LFS). The core idea of this method is to design single-stranded DNA (ssDNA) probes to hybridize with mitochondrial genes, which are abundant, stable, and species-specific in dairy products, as detection targets. Drawing inspiration from the principles of nucleic acid amplification, this research innovatively established a new DNA hybridization method, named LAMP-Like Hybridization (HybLAMP-Like). Leveraging the denaturation and DNA polymerization functions of the bst enzyme, efficient binding of the probe and template strand was achieved. This method eliminated the need for nucleic acid amplification, simplifying the procedure and mitigating aerosol contamination, thereby ensuring the accuracy of the detection results. The method exhibited exceptional sensitivity, capable of detecting extremely low to 12.5 ng in visual inspection and 3.125 ng when using a reader. In terms of practicality, it could achieve visual detection of cow's milk content as low as 1% in adulterated dairy products. When combined with a portable LFS reader, it also enabled precise quantitative analysis of milk adulteration.
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Affiliation(s)
- Nan Wang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Juan Zhang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Xiao
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyun Sun
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaci Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengchun Huang
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ailiang Chen
- Institute of Quality Standard & Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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3
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Ganesh PS, Elugoke SE, Lee SH, Kim SY, Ebenso EE. Smart and emerging point of care electrochemical sensors based on nanomaterials for SARS-CoV-2 virus detection: Towards designing a future rapid diagnostic tool. CHEMOSPHERE 2024; 352:141269. [PMID: 38307334 DOI: 10.1016/j.chemosphere.2024.141269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
In the recent years, researchers from all over the world have become interested in the fabrication of advanced and innovative electrochemical and/or biosensors for respiratory virus detection with the use of nanotechnology. These fabricated sensors demonstrated a number of benefits, including precision, affordability, accessibility, and miniaturization which makes them a promising test method for point-of-care (PoC) screening for SARS-CoV-2 viral infection. In order to comprehend the principles of electrochemical sensing and the role of various types of sensing interfaces, we comprehensively explored the underlying principles of electroanalytical methods and terminologies related to it in this review. In addition, it is addressed how to fabricate electrochemical sensing devices incorporating nanomaterials as graphene, metal/metal oxides, metal organic frameworks (MOFs), MXenes, quantum dots, and polymers. We took an effort to carefully compile current developments, advantages, drawbacks, possible solutions in nanomaterials based electrochemical sensors.
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Affiliation(s)
- Pattan Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Saheed Eluwale Elugoke
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa
| | - Seok-Han Lee
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Eno E Ebenso
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa.
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Li M, Jin X, Jiang Q, Wei H, Deng A, Mao Z, Wang Y, Zeng Z, Wu Y, Liu S, Kim J, Wang X, Liu Y, Liu J, Lv W, Huang L, Liao Q, Huang G, Zhang L. Loop-Mediated Isothermal Amplification (LAMP): Potential Point-of-Care Testing for Vulvovaginal Candidiasis. J Fungi (Basel) 2023; 9:1159. [PMID: 38132760 PMCID: PMC10744362 DOI: 10.3390/jof9121159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The aim of this study is to establish a loop-mediated isothermal amplification (LAMP) method for the rapid detection of vulvovaginal candidiasis (VVC). METHODS We developed and validated a loop-mediated isothermal amplification (LAMP) method for detecting the most common Candida species associated with VVC, including C. albicans, N. glabratus, C. tropicalis, and C. parapsilosis. We evaluated the specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV), and Kappa value of the LAMP method to detect different Candida species, using the conventional culture method and internal transcribed spacer (ITS) sequencing as gold standards and smear Gram staining and real-time Rolymerase Chain Reaction (PCR) as controls. RESULTS A total of 202 cases were enrolled, of which 88 were VVC-positive and 114 were negative. Among the 88 positive patients, the fungal culture and ITS sequencing results showed that 67 cases (76.14%) were associated with C. albicans, 13 (14.77%) with N. glabratus, 5 (5.68%) with C. tropicalis, and 3 (3.41%) with other species. Regarding the overall detection rate, the LAMP method presented sensitivity, specificity, PPV, NPV, and Kappa values of 90.91%, 100%, 100%, 93.4%, and 0.919, respectively. Moreover, the LAMP had a specificity of 100% for C. albicans, N. glabratus, and C. tropicalis, with a sensitivity of 94.03%, 100%, and 80%, respectively. Moreover, the microscopy evaluation had the highest sensitivity, while the real-time PCR was less specific for C. albicans than LAMP. In addition, CHROMagar Candida was inferior to LAMP in detecting non-albicans Candida (NAC) species. CONCLUSIONS Based on the cost-effective, rapid, and inexpensive characteristics of LAMP, coupled with the high sensitivity and specificity of our VVC-associated Candida detection method, we provided a possibility for the point-of-care testing (POCT) of VVC, especially in developing countries and some laboratories with limited resources.
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Affiliation(s)
- Meng Li
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Qingyun Jiang
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Hongbo Wei
- Beijing Institute of Spacecraft System Engineering, China Academy of Space Technology, Beijing 100094, China
| | - Anni Deng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Zeyin Mao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Ying Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Zhen Zeng
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Yifan Wu
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Shuai Liu
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Juhyun Kim
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Xiaoqian Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Ying Liu
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Jun Liu
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Leyang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
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Arabi-Jeshvaghani F, Javadi-Zarnaghi F, Löchel HF, Martin R, Heider D. LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens. Infection 2023; 51:1809-1818. [PMID: 37828369 DOI: 10.1007/s15010-023-02100-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE AND METHODS The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation. RESULTS LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database. CONCLUSION LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.
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Affiliation(s)
- Fatemeh Arabi-Jeshvaghani
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Hannah Franziska Löchel
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Roman Martin
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Dominik Heider
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, University of Marburg, Marburg, Germany
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Luna-Callejas B, Oropeza-Ramos L, Ramón-Gallegos E. Comparative genomic analysis of Mycoplasma related to cell culture for infB gene-based loop-mediated isothermal amplification. World J Microbiol Biotechnol 2023; 39:355. [PMID: 37878143 DOI: 10.1007/s11274-023-03794-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Mycoplasma contamination in cell culture affects the properties of cell lines. Gold standard detection by microbiological culture takes days and requires specialists. The polymerase chain reaction and loop-mediated isothermal amplification (LAMP) are fast molecular options, but LAMP only requires one heating block for DNA amplification. This study presents a comparative genomic analysis of Mycoplasma species to identify common target genes different from the rrsA gene, which encodes 16 S rRNA. The aim is to implement a LAMP assay to detect Mycoplasma species, reducing the time and specialized equipment required for detection. We performed a comparative genomic analysis through Mauve software and the GView server and selected infB and clpB genes as target candidates for designing LAMP primers. We evaluated both genes by multiple sequence alignment (MSA). The infB gene presented the best score MSA assessment with lower odd-log values (5,480,281) than other genes. We selected the infB gene to design LAMP primers specific to Mycoplasma spp. We used these primers to implement LAMP at 63 °C for 30 min, which showed 100% positive amplifications for detecting Mycoplasma spp. In conclusion, we present a methodology utilizing the infB gene-based LAMP assay to detect three of the six most prevalent Mycoplasma species in cell culture.
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Affiliation(s)
- Benjamín Luna-Callejas
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, 04510, Mexico City, México
- Department of Morphology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, Mexico City, México
| | - Laura Oropeza-Ramos
- Facultad de Ingeniería, Universidad Nacional Autónoma de México, 04510, Mexico City, México
| | - Eva Ramón-Gallegos
- Department of Morphology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 07738, Mexico City, México.
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Wright BR, Jelocnik M, Casteriano A, Muir YSS, Legione AR, Vaz PK, Devlin JM, Higgins DP. Development of diagnostic and point of care assays for a gammaherpesvirus infecting koalas. PLoS One 2023; 18:e0286407. [PMID: 37262062 DOI: 10.1371/journal.pone.0286407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/14/2023] [Indexed: 06/03/2023] Open
Abstract
The recent listing of koala populations as endangered across much of their range has highlighted the need for better management interventions. Disease is a key threat to koala populations but currently there is no information across the threatened populations on the distribution or impact of a gammaherpesvirus, phascolarctid gammaherpesvirus 1 (PhaHV-1). PhaHV-1 is known to infect koalas in southern populations which are, at present, not threatened. Current testing for PhaHV-1 involves lengthy laboratory techniques that do not permit quantification of viral load. In order to better understand distribution, prevalence and impacts of PhaHV-1 infections across koala populations, diagnostic and rapid point of care tests are required. We have developed two novel assays, a qPCR assay and an isothermal assay, that will enable researchers, clinicians and wildlife managers to reliably and rapidly test for PhaHV-1 in koalas. The ability to rapidly diagnose and quantify viral load will aid quarantine practices, inform translocation management and guide research into the clinical significance and impacts of PhaHV-1 infection in koalas.
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Affiliation(s)
- Belinda R Wright
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of The Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Andrea Casteriano
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - Yasmine S S Muir
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
| | - Alistair R Legione
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Paola K Vaz
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Joanne M Devlin
- Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Damien P Higgins
- Koala Health Hub, Sydney School of Veterinary Science, University of Sydney, Camperdown, New South Wales, Australia
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8
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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9
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Baláž V, Rivory P, Hayward D, Jaensch S, Malik R, Lee R, Modrý D, Šlapeta J. Angie-LAMP for diagnosis of human eosinophilic meningitis using dog as proxy: A LAMP assay for Angiostrongylus cantonensis DNA in cerebrospinal fluid. PLoS Negl Trop Dis 2023; 17:e0011038. [PMID: 37126515 PMCID: PMC10174499 DOI: 10.1371/journal.pntd.0011038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/11/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Angiostrongylus cantonensis (rat lungworm) is recognised as the leading cause of human eosinophilic meningitis, a serious condition observed when nematode larvae migrate through the CNS. Canine Neural Angiostrongyliasis (CNA) is the analogous disease in dogs. Both humans and dogs are accidental hosts, and a rapid diagnosis is warranted. A highly sensitive PCR based assay is available but often not readily accessible in many jurisdictions. An alternative DNA amplification assay that would further improve accessibility is needed. This study aimed to assess the diagnostic utility of a newly designed LAMP assay to detect DNA of globally distributed and invasive A. cantonensis and Angiostrongylus mackerrasae, the other neurotropic Angiostrongylus species, which is native to Australia. METHODOLOGY/PRINCIPAL FINDINGS Cerebrospinal fluid (CSF) from dogs with a presumptive diagnosis of A. cantonensis infection (2020-2022) were received for confirmatory laboratory testing and processed for DNA isolation and ultrasensitive Angiostrongylus qPCR targeting AcanR3390. A newly designed LAMP assay targeting the same gene target was directly compared to the reference ultrasensitive qPCR in a diagnostic laboratory setting to determine the presence of A. cantonensis DNA to diagnose CNA. The LAMP assay (Angie-LAMP) allowed the sensitive detection of A. cantonensis DNA from archived DNA specimens (Kappa = 0.81, 95%CI 0.69-0.92; n = 93) and rapid single-step lysis of archived CSF samples (Kappa = 0.77, 95%CI 0.59-0.94; n = 52). Only A. cantonensis DNA was detected in canine CSF samples, and co-infection with A. mackerrasae using amplicon deep sequencing (ITS-2 rDNA) was not demonstrated. Both SYD.1 and AC13 haplotypes were detected using sequencing of partial cox1. CONCLUSIONS/SIGNIFICANCE The Angie-LAMP assay is a useful molecular tool for detecting Angiostrongylus DNA in canine CSF and performs comparably to a laboratory Angiostrongylus qPCR. Adaptation of single-step sample lysis improved potential applicability for diagnosis of angiostrongyliasis in a clinical setting for dogs and by extension, to humans.
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Affiliation(s)
- Vojtech Baláž
- Institute of Parasitology, Biology Center of Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Phoebe Rivory
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Douglas Hayward
- Vetnostics, Laverty Pathology - North Ryde Laboratory, Macquarie Park, New South Wales, Australia
| | - Susan Jaensch
- Vetnostics, Laverty Pathology - North Ryde Laboratory, Macquarie Park, New South Wales, Australia
| | - Richard Malik
- Centre for Veterinary Education, Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Rogan Lee
- Parasitology Laboratory, Centre for Infectious Diseases and Microbiology Lab Services, Level 3 ICPMR, Westmead Hospital, Westmead, New South Wales, Australia
- Westmead Clinical School, Faculty of Medicine and Health Sciences, The University of Sydney, Westmead Hospital, Westmead, New South Wales, Australia
| | - David Modrý
- Institute of Parasitology, Biology Center of Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Veterinary Sciences and CINeZ, FAPPZ, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jan Šlapeta
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
- The University of Sydney Institute for Infectious Diseases, Sydney, New South Wales, Australia
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10
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You J, Park H, Lee H, Jang K, Park J, Na S. Sensitive and selective DNA detecting electrochemical sensor via double cleaving CRISPR Cas12a and dual polymerization on hyperbranched rolling circle amplification. Biosens Bioelectron 2023; 224:115078. [PMID: 36641878 DOI: 10.1016/j.bios.2023.115078] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Electrochemical sensors are widely used for nucleic acid detection. However, they exhibit low sensitivity and specificity. To overcome these limitations, DNA amplification method is necessary. In this study, we introduced CRISPR (Clustered regularly interspaced short palindromic repeats) Cas12a-dependent hyperbranched rolling circle amplification (HRCA) into an electrochemical sensor platform. By resolving the existing false-positive issue of HRCA, CRISPR Cas12a determines the real positive amplification that able to enhance its sensitivity for extremely low concentrations of nucleic acids and specificity for single-point mutations. In detail, CRISPR Cas12a, which activates the nucleic acid amplification reaction, was used for both trans and cis cleavage for the first time. Finally, selectively amplified DNA was detected using a screen-printed electrode. Using the change in surface coverage by DNA, the electrochemical sensor detected a decrease in the redox signal. In summary, combining a novel DNA amplification method and electrochemical sensor platform, our proposed method compensates for the shortcomings of existing RCA and hyperbranched RCA, secures a high sensitivity of 10 aM, and overcomes false-positivity problems. Moreover, such creative applications of CRISPR Cas12a may lead to the expansion of its applications to other nucleic acid amplification methods.
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Affiliation(s)
- Juneseok You
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunjun Park
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Hakbeom Lee
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Kuewhan Jang
- School of Mechanical and Automotive Engineering, Hoseo University, Asan, 31499, Republic of Korea
| | - Jinsung Park
- Department of Biomechatronics Engineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Suwon, 16419, Republic of Korea.
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea.
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11
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Tavakoli-Koopaei R, Javadi-Zarnaghi F, Aboutalebian S, Mirhendi H. Malachite Green-Based Detection of SARS-CoV-2 by One-Step Reverse Transcription Loop-Mediated Isothermal Amplification. IRANIAN JOURNAL OF SCIENCE 2023. [PMCID: PMC9898859 DOI: 10.1007/s40995-022-01392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The pandemic of severe acute respiratory syndrome 2 (SARS-CoV-2) revealed the necessity of diagnosis of the infected people to prevent the prevalence infection cycle. Many commercial pathogen diagnosis methods are based on the detection of genomic materials. Isothermal amplification methods such as loop-mediated-isothermal amplification (LAMP) are the method of choice in these cases. Reverse transcription steps are efficiently coupled to LAMP for the detection of pathogens with genomic RNAs such as SARS-CoV-2. Many detection systems for LAMP include fluorescent readout systems. Although such systems result in desirable limits of detection, the need for special instrumentation is the main dispute of such systems to become real point of care assays. In contrast, colorimetric detection methods would reduce costs and improve the applicability of the system. In this study one-step reverse transcription-LAMP reaction was established that enables visual detection of the SARS-CoV-2 genome. Nasopharyngeal RNA samples were first validated by reverse transcription quantitative polymerase chain reaction and then subjected to RT-LAMP. To lower the cost associated with the readout system equipment, malachite green (MG) was used. The color change of MG to blue allowed visual detection of the virus. Firstly, experiments were set up as two-step RT-LAMP reaction to identify the best primer sets. In addition, MG concentration was optimized with the significant colorimetric signal for the positive samples. Next, a one-step colorimetric method was developed for the detection of SARS-CoV-2 based on MG color shift in 2 h.
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Affiliation(s)
- Reyhaneh Tavakoli-Koopaei
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Fatemeh Javadi-Zarnaghi
- grid.411750.60000 0001 0454 365XDepartment of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Shima Aboutalebian
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- grid.411036.10000 0001 1498 685XDepartment of Medical Parasitology and Mycology, School of Medicine, Research Core Facilities Laboratory, Isfahan University of Medical Sciences, Isfahan, Iran
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12
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Das D, Lin CW, Chuang HS. LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection. BIOSENSORS 2022; 12:bios12121068. [PMID: 36551035 PMCID: PMC9775414 DOI: 10.3390/bios12121068] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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13
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Alič Š, Dermastia M, Burger J, Dickinson M, Pietersen G, Pietersen G, Dreo T. Genome-Informed Design of a LAMP Assay for the Specific Detection of the Strain of ' Candidatus Phytoplasma asteris' Phytoplasma Occurring in Grapevines in South Africa. PLANT DISEASE 2022; 106:2927-2939. [PMID: 35380469 DOI: 10.1094/pdis-10-21-2312-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine 'Candidatus Phytoplasma asteris' that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Špela Alič
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Marina Dermastia
- National Institute of Biology, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
| | - Johan Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Matthew Dickinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Gerhard Pietersen
- Department of Microbiology and Plant Pathology, University of Pretoria, Hatfield 0028, South Africa
| | | | - Tanja Dreo
- National Institute of Biology, 1000 Ljubljana, Slovenia
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14
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Ganesh PS, Kim SY. A comparison of conventional and advanced electroanalytical methods to detect SARS-CoV-2 virus: A concise review. CHEMOSPHERE 2022; 307:135645. [PMID: 35817176 PMCID: PMC9270057 DOI: 10.1016/j.chemosphere.2022.135645] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are a serious threat to human wellbeing that can cause pandemic disease. As a result, it is critical to identify virus in a timely, sensitive, and precise manner. The present novel coronavirus-2019 (COVID-19) disease outbreak has increased these concerns. The research of developing various methods for COVID-19 virus identification is one of the most rapidly growing research areas. This review article compares and addresses recent improvements in conventional and advanced electroanalytical approaches for detecting COVID-19 virus. The popular conventional methods such as polymerase chain reaction (PCR), loop mediated isothermal amplification (LAMP), serology test, and computed tomography (CT) scan with artificial intelligence require specialized equipment, hours of processing, and specially trained staff. Many researchers, on the other hand, focused on the invention and expansion of electrochemical and/or bio sensors to detect SARS-CoV-2, demonstrating that they could show a significant role in COVID-19 disease control. We attempted to meticulously summarize recent advancements, compare conventional and electroanalytical approaches, and ultimately discuss future prospective in the field. We hope that this review will be helpful to researchers who are interested in this interdisciplinary field and desire to develop more innovative virus detection methods.
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Affiliation(s)
- Pattan-Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
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15
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Owoicho O, Olwal CO, Tettevi EJ, Atu BO, Durugbo EU. Loop-mediated isothermal amplification for Candida species surveillance in under-resourced setting: a review of evidence. Expert Rev Mol Diagn 2022; 22:643-653. [PMID: 35920288 DOI: 10.1080/14737159.2022.2109963] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Non-albicans Candida species (NACS) have emerged as a major public health burden although they are still underappreciated. Some NACS have intrinsic antifungal resistance, requiring constant surveillance to improve patient care and thwart outbreaks of recalcitrant candida infections. However, effective Candida species surveillance has relied on PCR-based or other high-end techniques that are largely unaffordable in under-resourced countries. Loop-mediated isothermal amplification (LAMP) has emerged as a potentially effective and affordable technique for infectious disease surveillance, especially in under resourced settings. AREAS COVERED We critically reviewed current literature on application of LAMP for Candida species identification in pure fungal isolates, and in clinical and non-clinical samples. EXPERT OPINION LAMP has been studied for Candida species identification, including the NACS. Besides a short turnaround time, LAMP has analytical sensitivity and specificity that are not only higher than culture method but also comparable with conventional and quantitative PCR techniques. However, extensive evaluation of LAMP for Candida species detection using various types of clinical and environmental samples are required before deploying the technique for Candida species surveillance.
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Affiliation(s)
- Oloche Owoicho
- Department of Biological Sciences, Benue State University, P.M.B. 102119, Makurdi, Benue State, Nigeria
| | | | - Edward Jenner Tettevi
- Biomedical and Public Health Research Unit, Water Research Institute, Council for Scientific and Industrial Research, Accra, Ghana
| | - Bernard Ortwer Atu
- Department of Biological Sciences, Benue State University, P.M.B. 102119, Makurdi, Benue State, Nigeria
| | - Ernest Uzodimma Durugbo
- Department of Biological Sciences, Redeemer's University, P.M.B. 230, Ede, Osun State, Nigeria
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16
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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17
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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18
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Xie X, Li B, Fan Y, Duan R, Gao C, Zheng Y, Tian E. Identification of Gyromitra infula: A Rapid and Visual Method Based on Loop-Mediated Isothermal Amplification. Front Microbiol 2022; 13:842178. [PMID: 35250953 PMCID: PMC8894891 DOI: 10.3389/fmicb.2022.842178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Abstract
With mushroom poisoning emerging as one of the most serious food safety problems worldwide, a rapid identification method of poisonous mushrooms is urgently required to investigate the source of poisoning. Gyromitra infula, a kind of poisonous mushroom, contains gyromitrin toxin, which causes epileptogenic neurotoxicity and hemolytic disease. This study aimed to establish a rapid and visual method of G. infula identification based on loop-mediated isothermal amplification (LAMP). A set of specific LAMP primers was designed, and its specificity in G. infula was confirmed against various mushroom species, including its closely related species and other macrofungi. The sensitivity assay showed that the minimum concentration of genomic DNA detected by LAMP was 1 ng/μl. The method’s applicability was conducted by preparing mushroom samples that were boiled and digested in artificial gastric juice. The results showed that the content as low as 1% G. infula can be successfully detected. This method can be completed within 90 min, and the reaction results can be directly observed by the naked eyes. Hence, the identification method of G. infula established based on LAMP in this study is accurate, rapid, sensitive, and low-cost, which is required for clinical treatment or forensic analysis when mushroom poisoning occurs.
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Affiliation(s)
- Xiaomei Xie
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Bu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yuguang Fan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Pharmacy, Hainan Medical University, Haikou, China
| | - Renhe Duan
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chonghua Gao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yuan Zheng
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Enjing Tian
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
- *Correspondence: Enjing Tian,
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19
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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20
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Daddy Gaoh S, Kweon O, Lee YJ, LiPuma JJ, Hussong D, Marasa B, Ahn Y. Loop-Mediated Isothermal Amplification (LAMP) Assay for Detecting Burkholderia cepacia Complex in Non-Sterile Pharmaceutical Products. Pathogens 2021; 10:pathogens10091071. [PMID: 34578104 PMCID: PMC8468478 DOI: 10.3390/pathogens10091071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Simple and rapid detection of Burkholderia cepacia complex (BCC) bacteria, a common cause of pharmaceutical product recalls, is essential for consumer safety. In this study, we developed and evaluated a ribB-based colorimetric loop-mediated isothermal amplification (LAMP) assay for the detection of BCC in (i) nuclease-free water after 361 days, (ii) 10 μg/mL chlorhexidine gluconate (CHX) solutions, and (iii) 50 μg/mL benzalkonium chloride (BZK) solutions after 184 days. The RibB 5 primer specifically detected 20 strains of BCC but not 36 non-BCC strains. The limit of detection of the LAMP assay was 1 pg/μL for Burkholderia cenocepacia strain J2315. Comparison of LAMP with a qPCR assay using 1440 test sets showed higher sensitivity: 60.6% in nuclease-free water and 42.4% in CHX solution with LAMP vs. 51.3% and 31.1%, respectively, with qPCR. These results demonstrate the potential of the ribB-based LAMP assay for the rapid and sensitive detection of BCC in pharmaceutical manufacturing.
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Affiliation(s)
- Soumana Daddy Gaoh
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Yong-Jin Lee
- Department of Natural Sciences, Albany State University, Albany, GA 31707, USA;
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA;
| | | | - Bernard Marasa
- Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
- Correspondence: ; Tel.: +1-870-540-7084
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21
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Field-Deployable Recombinase Polymerase Amplification Assay for Specific, Sensitive and Rapid Detection of the US Select Agent and Toxigenic Bacterium, Rathayibacter toxicus. BIOLOGY 2021; 10:biology10070620. [PMID: 34356474 PMCID: PMC8301136 DOI: 10.3390/biology10070620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/15/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Early, accurate, and rapid detection of R. toxicus is extremely important to improve inspections of imported annual ryegrass hay and seed at ports of entry and enhance in-field detection. RPA is a comparatively new, easy to use, and robust technology that can be performed in the palm of the hand without losing specificity. The RPA assay was more sensitive than endpoint PCR and did not require lab equipment in the field. The developed assay has tremendous applications for in-field plant diagnostics and biosecurity surveillance. Abstract Rathayibacter toxicus is a toxigenic bacterial pathogen of several grass species and is responsible for massive livestock deaths in Australia and South Africa. Due to concern for animal health and livestock industries, it was designated a U.S. Select Agent. A rapid, accurate, and sensitive in-field detection method was designed to assist biosecurity surveillance surveys and to support export certification of annual ryegrass hay and seed. Complete genomes from all known R. toxicus populations were explored, unique diagnostic sequences identified, and target-specific primers and a probe for recombinase polymerase amplification (RPA) and endpoint PCR were designed. The RPA reaction ran at 37 °C and a lateral flow device (LFD) was used to visualize the amplified products. To enhance reliability and accuracy, primers and probes were also designed to detect portions of host ITS regions. RPA assay specificity and sensitivity were compared to endpoint PCR using appropriate inclusivity and exclusivity panels. The RPA assay sensitivity (10 fg) was 10 times more sensitive than endpoint PCR with and without a host DNA background. In comparative tests, the RPA assay was unaffected by plant-derived amplification inhibitors, unlike the LAMP and end-point PCR assays. In-field validation of the RPA assay at multiple sites in South Australia confirmed the efficiency, specificity, and applicability of the RPA assay. The RPA assay will support disease management and evidence-based in-field biosecurity decisions.
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22
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Ptasinska A, Whalley C, Bosworth A, Poxon C, Bryer C, Machin N, Grippon S, Wise EL, Armson B, Howson ELA, Goring A, Snell G, Forster J, Mattocks C, Frampton S, Anderson R, Cleary D, Parker J, Boukas K, Graham N, Cellura D, Garratt E, Skilton R, Sheldon H, Collins A, Ahmad N, Friar S, Burns D, Williams T, Godfrey KM, Deans Z, Douglas A, Hill S, Kidd M, Porter D, Kidd SP, Cortes NJ, Fowler V, Williams T, Richter A, Beggs AD. Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations. Clin Microbiol Infect 2021; 27:1348.e1-1348.e7. [PMID: 33901668 PMCID: PMC8064897 DOI: 10.1016/j.cmi.2021.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023]
Abstract
Objectives Rapid, high throughput diagnostics are a valuable tool, allowing the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations so as to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as quantitative RT-PCR (RT-qPCR), particularly throughout the first months of the coronavirus disease 2019 pandemic. We investigated the use of LamPORE, where loop-mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS-CoV-2 in symptomatic and asymptomatic populations. Methods In an asymptomatic prospective cohort, for 3 weeks in September 2020, health-care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self-swabbed with nasopharyngeal swabs weekly and supplied a saliva specimen daily. These samples were tested for SARS-CoV-2 RNA using the Oxford Nanopore LamPORE system and a reference RT-qPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza-like illness from March 2020 to June 2020 were similarly tested from nasopharyngeal swabs. Results In the asymptomatic cohort a total of 1200 participants supplied 23 427 samples (3966 swab, 19 461 saliva) over a 3-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (decreasing to approximately 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared with the reference RT-qPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%. Conclusions LamPORE is a highly accurate methodology for the detection of SARS-CoV-2 in both symptomatic and asymptomatic population settings and can be used as an alternative to RT-qPCR.
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Affiliation(s)
- Anetta Ptasinska
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Celina Whalley
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Andrew Bosworth
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Charlotte Poxon
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Claire Bryer
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Nicholas Machin
- Public Health England, Manchester University NHS Foundation Trust, Department of Virology, Manchester, UK
| | - Seden Grippon
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK
| | - Emma L Wise
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK; Department of Virology, University of Surrey, Guildford, UK
| | - Bryony Armson
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK; School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Emma L A Howson
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK; The Pirbright Institute, Woking, UK
| | - Alice Goring
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK
| | | | | | | | | | | | | | - Joe Parker
- University of Southampton, Southampton, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, NIHR Southampton Biomedical Research Centre, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Zandra Deans
- NHS England, NHS Improvement, NHS Test and Trace, London, UK; GenQA, NHS Lothian, Edinburgh, UK
| | - Angela Douglas
- NHS England, NHS Improvement, NHS Test and Trace, London, UK
| | - Sue Hill
- NHS England, NHS Improvement, NHS Test and Trace, London, UK
| | - Michael Kidd
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK; Public Health West Midlands Laboratory, Birmingham, UK
| | - Deborah Porter
- NHS England, NHS Improvement, NHS Test and Trace, London, UK
| | - Stephen P Kidd
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK
| | - Nicholas J Cortes
- Department of Microbiology, Basingstoke & North Hants Hospital, Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | | | - Tony Williams
- University of Southampton, Southampton, UK; University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Alex Richter
- Institute of Immunology & Immunotherapy, University of Birmingham, UK
| | - Andrew D Beggs
- Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
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23
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Wang N, Zhao Z, Gao J, Tian E, Yu W, Li H, Zhang J, Xie R, Zhao X, Chen A. Rapid and Visual Identification of Chlorophyllum molybdites With Loop-Mediated Isothermal Amplification Method. Front Microbiol 2021; 12:638315. [PMID: 33815325 PMCID: PMC8013719 DOI: 10.3389/fmicb.2021.638315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/10/2021] [Indexed: 11/14/2022] Open
Abstract
Chlorophyllum molybdites is a kind of common poisonous mushroom in China that is widely distributed in different areas. Food poisoning caused by accidentally eating C. molybdites has become more frequent in recent years. In 2019, there were 55 food poisoning incidents caused by eating this mushroom in China. Mushroom poisoning continues to be a common health issue of global concern. When mushroom poisoning occurs, an effective, simple, and rapid detection method is required for accurate clinical treatment or forensic analysis. For the first time, we established a loop-mediated isothermal amplification (LAMP) assay for the visual detection of C. molybdites. A set of specific LAMP primers was designed, and the specificity was confirmed against 43 different mushroom species. The LAMP method could detect as low as 1 pg of genomic DNA. Boiled mushrooms and artificial gastric-digested mushroom samples were prepared to test the applicability of the method, and the results showed that as low as 1% C. molybdites in boiled and digested samples could be successfully detected. The LAMP method can also be completed within 45 min, and the reaction results could be directly observed based on a color change under daylight by the naked eye. Therefore, the LAMP assay established in this study provides an accurate, sensitive, rapid, and low-cost method for the detection of C. molybdites.
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Affiliation(s)
- Nan Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyong Zhao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jie Gao
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Enjing Tian
- Institute of Mycology, Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Jilin, China
| | - Wenjie Yu
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruibin Xie
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyan Zhao
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ailiang Chen
- Institute of Quality Standard and Testing Technology for Agro-Products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing, China
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24
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Climent E, Gotor R, Tobias C, Bell J, Martin-Sanchez PM, Rurack K. Dip Sticks Embedding Molecular Beacon-Functionalized Core-Mesoporous Shell Particles for the Rapid On-Site Detection of Microbiological Fuel Contamination. ACS Sens 2021; 6:27-34. [PMID: 33356175 DOI: 10.1021/acssensors.0c01178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microbial contamination of fuels by fungi and bacteria presents risks of corrosion and fuel system fouling. In this work, a rapid test for the determination of microbial genomic DNA from aqueous fuel extracts is presented. It combines test strips coated with polystyrene core/mesoporous silica shell particles, to the surface of which modified fluorescent molecular beacons are covalently grafted, with a smartphone detection system. In the hairpin loop, the beacons incorporate a target sequence highly conserved in all bacteria, corresponding to a fragment of the 16S ribosomal RNA gene, which is also present to a significant extent in the 18S rRNA gene of fungi, allowing for broadband microbial detection. In the developed assay, the presence of genomic DNA extracts from bacteria and fungi down to ca. 20-50 μg L-1 induced a distinct fluorescence response. The optical read-out was adapted for on-site monitoring by combining a 3D-printed case with a conventional smartphone, taking advantage of the sensitivity of contemporary complementary metal oxide semiconductor (CMOS) detectors. Such an embedded assembly allowed to detect microbial genomic DNA in aqueous extracts down to ca. 0.2-0.7 mg L-1 and presents an important step toward the on-site uncovering of fuel contamination in a rapid and simple fashion.
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Affiliation(s)
- Estela Climent
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Raúl Gotor
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Charlie Tobias
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Jérémy Bell
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Pedro M. Martin-Sanchez
- Department 4 Materials & Environment, Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205 Berlin, Germany
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, P.O.
Box 1066 Blindern, 0316 Oslo, Norway
| | - Knut Rurack
- Department 1 Analytical Chemistry, Reference Materials, Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany
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25
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Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, Kevadiya BD, S. Thakor A. Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Coronaviruses in the Context of COVID-19 Pandemic. BIOLOGY 2020; 9:E182. [PMID: 32707972 PMCID: PMC7464797 DOI: 10.3390/biology9080182] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
The rampant spread of COVID-19 and the worldwide prevalence of infected cases demand a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. The most common molecular tests approved by regulatory bodies across the world for COVID-19 diagnosis are based on Polymerase Chain Reaction (PCR). While PCR-based tests are highly sensitive, specific, and remarkably reliable, they have many limitations ranging from the requirement of sophisticated laboratories, need of skilled personnel, use of complex protocol, long wait times for results, and an overall high cost per test. These limitations have inspired researchers to search for alternative diagnostic methods that are fast, economical, and executable in low-resource laboratory settings. The discovery of Loop-mediated isothermal Amplification (LAMP) has provided a reliable substitute platform for the accurate detection of low copy number nucleic acids in the diagnosis of several viral diseases, including epidemics like Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). At present, a cocktail of LAMP assay reagents along with reverse transcriptase enzyme (Reverse Transcription LAMP, RT-LAMP) can be a robust solution for the rapid and cost-effective diagnosis for COVID-19, particularly in developing, and low-income countries. In summary, the development of RT-LAMP based diagnostic tools in a paper/strip format or the integration of this method into a microfluidic platform such as a Lab-on-a-chip may revolutionize the concept of PoCT for COVID-19 diagnosis. This review discusses the principle, technology and past research underpinning the success for using this method for diagnosing MERS and SARS, in addition to ongoing research, and the prominent prospect of RT-LAMP in the context of COVID-19 diagnosis.
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Affiliation(s)
- Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Suvarthi Das
- Department of Medicine, Stanford University Medical Center, Palo Alto, CA 94304, USA;
| | - Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Yasuyoshi Mori
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Tsugunori Notomi
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Bhavesh D. Kevadiya
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
| | - Avnesh S. Thakor
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
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