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Oh BG, Yoon JY, Ju HJ. RT-RPA Assay Combined with a Lateral Flow Strip to Detect Soybean Mosaic Virus. THE PLANT PATHOLOGY JOURNAL 2024; 40:337-345. [PMID: 39117333 PMCID: PMC11309845 DOI: 10.5423/ppj.oa.02.2024.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/27/2024] [Accepted: 06/13/2024] [Indexed: 08/10/2024]
Abstract
Soybean (Glycine max L.) is one of the most widely planted and used legumes in the world, being used for food, animal feed products, and industrial production. The soybean mosaic virus (SMV) is the most prevalent virus infecting soybean plants. This study developed a diagnostic method for the rapid and sensitive detection of SMV using a reverse transcription-recombinase polymerase amplification (RT-RPA) technique combined with a lateral flow strip (LFS). The RT-RPA and RT-RPA-LFS conditions to detect the SMV were optimized using the selected primer set that amplified part of the VPg protein gene. The optimized reaction temperature for the RT-RPA primer and RT-RPA-LFS primer used in this study was 38℃ for both, and the minimum reaction time was 10 min and 5 min, respectively. The RT-RPA-LFS was as sensitive as RT-PCR to detect SMV with 10 pg/μl of total RNA. The reliability of the developed RT-RPA-LFS assay was evaluated using leaves collected from soybean fields. The RT-RPA-LFS diagnostic method developed in this study will be useful as a diagnostic method that can quickly and precisely detect SMV in the epidemiological investigation of SMV, in the selection process of SMV-resistant varieties, on local farms with limited resources.
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Affiliation(s)
- Bong Geun Oh
- Department of Agricultural Biology, Jeonbuk National University, Jeonju 54896, Korea
| | - Ju-Yeon Yoon
- Department of Plant Protection and Quarantine, Jeonbuk National University, Jeonju 54896, Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, Jeonbuk National University, Jeonju 54896, Korea
- Department of Plant Protection and Quarantine, Jeonbuk National University, Jeonju 54896, Korea
- Plant Medical Research Center, Jeonbuk National University, Jeonju 54896, Korea
- Institute of Agricultural Science and Technology, Jeonbuk National University, Jeonju 54896, Korea
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2
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Ling L, Liang L, Wang H, Lin X, Li C. Real-Time Monitoring on the Chinese Giant Salamander Using RPA-LFD. Int J Mol Sci 2024; 25:4946. [PMID: 38732163 PMCID: PMC11084824 DOI: 10.3390/ijms25094946] [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: 03/09/2024] [Revised: 04/16/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The Chinese giant salamander (Andrias davidianus), listed as an endangered species under "secondary protection" in China, faces significant threats due to ecological deterioration and the expansion of human activity. Extensive field investigations are crucial to ascertain the current status in the wild and to implement effective habitat protection measures to safeguard this species and support its population development. Traditional survey methods often fall short due to the elusive nature of the A. davidianus, presenting challenges that are time-consuming and generally ineffective. To overcome these obstacles, this study developed a real-time monitoring method that uses environmental DNA (eDNA) coupled with recombinase polymerase amplification and lateral flow strip (RPA-LFD). We designed five sets of species-specific primers and probes based on mitochondrial genome sequence alignments of A. davidianus and its close relatives. Our results indicated that four of these primer/probe sets accurately identified A. davidianus, distinguishing it from other tested caudata species using both extracted DNA samples and water samples from a tank housing an individual. This method enables the specific detection of A. davidianus genomic DNA at concentrations as low as 0.1 ng/mL within 50 min, without requiring extensive laboratory equipment. Applied in a field survey across four sites in Huangshan City, Anhui Province, where A. davidianus is known to be distributed, the method successfully detected the species at three of the four sites. The development of these primer/probe sets offers a practical tool for field surveying and monitoring, facilitating efforts in population recovery and resource conservation for A. davidianus.
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Affiliation(s)
- Lanxin Ling
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Linyan Liang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Huifang Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaolong Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Chenhong Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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3
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Martin CD, Bender AT, Sullivan BP, Lillis L, Boyle DS, Posner JD. SARS-CoV-2 recombinase polymerase amplification assay with lateral flow readout and duplexed full process internal control. SENSORS & DIAGNOSTICS 2024; 3:421-430. [PMID: 38495597 PMCID: PMC10939122 DOI: 10.1039/d3sd00246b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024]
Abstract
Nucleic acid amplification tests for the detection of SARS-CoV-2 have been an important testing mechanism for the COVID-19 pandemic. While these traditional nucleic acid diagnostic methods are highly sensitive and selective, they are not suited to home or clinic-based uses. Comparatively, rapid antigen tests are cost-effective and user friendly but lack in sensitivity and specificity. Here we report on the development of a one-pot, duplexed reverse transcriptase recombinase polymerase amplification SARS-CoV-2 assay with MS2 bacteriophage as a full process control. Detection is carried out with either real-time fluorescence or lateral flow readout with an analytical sensitivity of 50 copies per reaction. Unlike previously published assays, the RNA-based MS2 bacteriophage control reports on successful operation of lysis, reverse transcription, and amplification. This SARS-CoV-2 assay features highly sensitive detection, visual readout through an LFA strip, results in less than 25 minutes, minimal instrumentation, and a useful process internal control to rule out false negative test results.
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Affiliation(s)
- Coleman D Martin
- Department of Chemical Engineering, University of Washington Seattle Washington USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
| | | | | | - Jonathan D Posner
- Department of Chemical Engineering, University of Washington Seattle Washington USA
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
- Department of Family Medicine, University of Washington Seattle Washington USA
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4
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Lee HJ, Kim HJ, Cho IS, Jeong RD. Identification of Viruses Infecting Phalaenopsis Orchids Using Nanopore Sequencing and Development of an RT-RPA-CRISPR/Cas12a for Rapid Visual Detection of Nerine Latent Virus. Int J Mol Sci 2024; 25:2666. [PMID: 38473916 DOI: 10.3390/ijms25052666] [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: 01/30/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Phalaenopsis orchids are one of the most popular ornamental plants. More than thirty orchid viruses have been reported, and virus-infected Phalaenopsis orchids significantly lose their commercial value. Therefore, the development of improved viral disease detection methods could be useful for quality control in orchid cultivation. In this study, we first utilized the MinION, a portable sequencing device based on Oxford Nanopore Technologies (ONT) to rapidly detect plant viruses in Phalaenopsis orchids. Nanopore sequencing revealed the presence of three plant viruses in Phalaenopsis orchids: odontoglossum ringspot virus, cymbidium mosaic virus, and nerine latent virus (NeLV). Furthermore, for the first time, we detected NeLV infection in Phalaenopsis orchids using nanopore sequencing and developed the reverse transcription-recombinase polymerase amplification (RT-RPA)-CRISPR/Cas12a method for rapid, instrument-flexible, and accurate diagnosis. The developed RT-RPA-CRISPR/Cas12a technique can confirm NeLV infection in less than 20 min and exhibits no cross-reactivity with other viruses. To determine the sensitivity of RT-RPA-CRISPR/Cas12a for NeLV, we compared it with RT-PCR using serially diluted transcripts and found a detection limit of 10 zg/μL, which is approximately 1000-fold more sensitive. Taken together, the ONT platform offers an efficient strategy for monitoring plant viral pathogens, and the RT-RPA-CRISPR/Cas12a method has great potential as a useful tool for the rapid and sensitive diagnosis of NeLV.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
| | - Hae-Jun Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
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5
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Soliman MA, Azab MS, Hussein HA, Roushdy MM, Abu El-Naga MN. FBPP: software to design PCR primers and probes for nucleic acid base detection of foodborne pathogens. Sci Rep 2024; 14:1229. [PMID: 38216615 PMCID: PMC10786913 DOI: 10.1038/s41598-024-51372-5] [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: 09/12/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024] Open
Abstract
Foodborne pathogens can be found in various foods, and it is important to detect foodborne pathogens to provide a safe food supply and to prevent foodborne diseases. The nucleic acid base detection method is one of the most rapid and widely used methods in the detection of foodborne pathogens; it depends on hybridizing the target nucleic acid sequence to a synthetic oligonucleotide (probes or primers) that is complementary to the target sequence. Designing primers and probes for this method is a preliminary and critical step. However, new bioinformatics tools are needed to automate, specific and improve the design sets to be used in the nucleic acid‒base method. Thus, we developed foodborne pathogen primer probe design (FBPP), an open-source, user-friendly graphical interface Python-based application supported by the SQL database for foodborne pathogen virulence factors, for (i) designing primers/probes for detection purposes, (ii) PCR and gel electrophoresis photo simulation, and (iii) checking the specificity of primers/probes.
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Affiliation(s)
- Mohamed A Soliman
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt.
| | - Mohamed S Azab
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hala A Hussein
- Department of Radiation Microbiology, National Centre for Radiation Research and Technology, Atomic Energy Authority, Nasr City, Cairo, Egypt
| | - Mohamed M Roushdy
- Department of Botany and Microbiology, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed N Abu El-Naga
- Department of Radiation Microbiology, National Centre for Radiation Research and Technology, Atomic Energy Authority, Nasr City, Cairo, Egypt
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6
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Chang MM, Ma A, Novak EN, Barra M, Kundrod KA, Montealegre JR, Scheurer ME, Castle PE, Schmeler K, Richards-Kortum R. A novel tailed primer nucleic acid test for detection of HPV 16, 18 and 45 DNA at the point of care. Sci Rep 2023; 13:20397. [PMID: 37989845 PMCID: PMC10663460 DOI: 10.1038/s41598-023-47582-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023] Open
Abstract
Cervical cancer is a leading cause of death for women in low-resource settings despite being preventable through human papillomavirus (HPV) vaccination, early detection, and treatment of precancerous lesions. The World Health Organization recommends high-risk HPV (hrHPV) as the preferred cervical cancer screening strategy, which is difficult to implement in low-resource settings due to high costs, reliance on centralized laboratory infrastructure, and long sample-to-answer times. To help meet the need for rapid, low-cost, and decentralized cervical cancer screening, we developed tailed primer isothermal amplification and lateral flow detection assays for HPV16, HPV18, and HPV45 DNA. We translated these assays into a self-contained cartridge to achieve multiplexed detection of three hrHPV genotypes in a disposable cartridge. The developed test achieves clinically relevant limits of detection of 50-500 copies per reaction with extracted genomic DNA from HPV-positive cells. Finally, we performed sample-to-answer testing with direct lysates of HPV-negative and HPV-positive cell lines and demonstrated consistent detection of HPV16, HPV18, and HPV45 with 5000-50,000 cells/mL in < 35 min. With additional optimization to improve cartridge reliability, incorporation of additional hrHPV types, and validation with clinical samples, the assay could serve as a point-of-care HPV DNA test that improves access to cervical cancer screening in low-resource settings.
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Affiliation(s)
- Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ariel Ma
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jane Richards Montealegre
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael E Scheurer
- Department of Pediatrics Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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7
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D'Agnese E, Chase D, Andruszkiewicz-Allan E. ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES. J Wildl Dis 2023; 59:545-556. [PMID: 37791744 DOI: 10.7589/jwd-d-22-00128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 06/01/2023] [Indexed: 10/05/2023]
Abstract
Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon (Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum, is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20-40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.
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Affiliation(s)
- Erin D'Agnese
- University of Washington, School of Marine and Environmental Affairs, 3737 Brooklyn Ave. NE, Seattle, Washington 98105, USA
- Wild EcoHealth LLC, Tacoma, Washington 98465, USA
| | - Dorothy Chase
- U.S. Geological Survey, Western Fisheries Research Center, 6505 Northeast 65th St., Seattle, Washington 98115, USA
| | - Elizabeth Andruszkiewicz-Allan
- University of Washington, School of Marine and Environmental Affairs, 3737 Brooklyn Ave. NE, Seattle, Washington 98105, USA
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8
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Kundrod KA, Barra M, Wilkinson A, Smith CA, Natoli ME, Chang MM, Coole JB, Santhanaraj A, Lorenzoni C, Mavume C, Atif H, Montealegre JR, Scheurer ME, Castle PE, Schmeler KM, Richards-Kortum RR. An integrated isothermal nucleic acid amplification test to detect HPV16 and HPV18 DNA in resource-limited settings. Sci Transl Med 2023; 15:eabn4768. [PMID: 37343083 PMCID: PMC10566637 DOI: 10.1126/scitranslmed.abn4768] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
High-risk human papillomavirus (HPV) DNA testing is widely acknowledged as the most sensitive cervical cancer screening method but has limited availability in resource-limited settings, where the burden of cervical cancer is highest. Recently, HPV DNA tests have been developed for use in resource-limited settings, but they remain too costly for widespread use and require instruments that are often limited to centralized laboratories. To help meet the global need for low-cost cervical cancer screening, we developed a prototype, sample-to-answer, point-of-care test for HPV16 and HPV18 DNA. Our test relies on isothermal DNA amplification and lateral flow detection, two technologies that reduce the need for complex instrumentation. We integrated all test components into a low-cost, manufacturable platform, and performance of the integrated test was evaluated with synthetic samples, provider-collected clinical samples in a high-resource setting in the United States, and self-collected clinical samples in a low-resource setting in Mozambique. We demonstrated a clinically relevant limit of detection of 1000 HPV16 or HPV18 DNA copies per test. The test requires six user steps, yields results in 45 min, and can be performed using a benchtop instrument and minicentrifuge by minimally trained personnel. The projected per-test cost is <$5, and the projected instrumentation cost is <$1000. These results show the feasibility of a sample-to-answer, point-of-care HPV DNA test. With the inclusion of other HPV types, this test has the potential to fill a critical gap for decentralized and globally accessible cervical cancer screening.
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Affiliation(s)
- Kathryn A Kundrod
- Department of Bioengineering, Rice University, Houston, TX, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Maria Barra
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Chelsey A Smith
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mary E Natoli
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Megan M Chang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jackson B Coole
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Cesaltina Lorenzoni
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Celda Mavume
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | - Hira Atif
- Ministério da Saúde de Moçambique (MISAU), Hospital Central de Maputo, Hospital Geral de Mavalane, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | | | - Michael E Scheurer
- Department of Pediatrics-Hematology/Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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9
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Togoobat B, Wu N, Wang X, Cao M, Xu Z. Viromic approach reveals differences in the composition, diversity and relative abundance of pumpkin viruses across main growing regions of China. Virology 2023; 585:61-71. [PMID: 37295338 DOI: 10.1016/j.virol.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
China is the leading country for pumpkin production in the world. As other cucurbits, diseases caused by viruses are among the serious threats to pumpkin production, but our knowledge on the virus species infecting pumpkin plants is fragmentary. To understand the occurrence of viral diseases on pumpkin, we determined the geographical distribution characteristics, relative abundance and evolutionary relationship of pumpkin infected viruses by meta-transcriptome sequencing (RNA-seq) and viromic analysis of 159 samples exhibited typical viral symptoms collected across China in this study. Totally, 11 known and 3 new viruses were identified. Interestingly, 3 new viruses identified in this study should be positive-sense single-stranded RNA virus whose hosts are prokaryotes. The viruses identified in different sampling locations exhibit significant variations in term of virus species and relative abundance. Here, the results provide valuable information for understanding the virus species and their diversity in cultivated pumpkin across major growing regions of China.
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Affiliation(s)
- Batchimeg Togoobat
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; Laboratory for Plant Pathology, Institute of Plant Protection, Ulaanbaatar, Mongolia
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China.
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10
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Daddy Gaoh S, Kweon O, Ahn Y. Propidium Monoazide (PMAxx)-Recombinase Polymerase Amplification Exo (RPA Exo) Assay for Rapid Detection of Burkholderia cepacia Complex in Chlorhexidine Gluconate (CHX) and Benzalkonium Chloride (BZK) Solutions. Microorganisms 2023; 11:1401. [PMID: 37374904 DOI: 10.3390/microorganisms11061401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and dead loads of BCC. We have assessed an exo probe-based recombinase polymerase amplification (RPA) with 10 µM propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in various concentrations of antiseptics (i.e., chlorhexidine gluconate (CHX) and benzalkonium chloride (BZK) solutions) after 24 h. The optimized assay conducted using a set of primer-probes targeting gbpT was performed at 40 °C for 20 min and shows a detection limit of 10 pg/µL of genomic DNA from B. cenocepacia J2315, equivalent to 104 colony-forming units (CFU/mL). The specificity of a newly designed primer and probe was 80% (20 negatives out of 25). The readings for total cells (i.e., without PMAxx) from 200 µg/mL CHX using PMAxx-RPA exo assay was 310 relative fluorescence units (RFU), compared to 129 RFU with PMAxx (i.e., live cells). Furthermore, in 50-500 µg/mL BZK-treated cells, a difference in the detection rate was observed between the PMAxx-RPA exo assay in live cells (130.4-459.3 RFU) and total cells (207.82-684.5 RFU). This study shows that the PMAxx-RPA exo assay appears to be a valid tool for the simple, rapid and presumptive detection of live BCC cells in antiseptics, thereby ensuring the quality and safety of pharmaceutical products.
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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
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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11
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Tao J, Liu D, Xiong J, Shan W, Dou L, Zhai W, Wang Y, Shen J, Wen K. MC-PRPA-HLFIA Cascade Detection System for Point-of-Care Testing Pan-Drug-Resistant Genes in Urinary Tract Infection Samples. Int J Mol Sci 2023; 24:ijms24076784. [PMID: 37047757 PMCID: PMC10095522 DOI: 10.3390/ijms24076784] [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: 02/21/2023] [Revised: 03/21/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Recently, urinary tract infection (UTI) triggered by bacteria carrying pan-drug-resistant genes, including carbapenem resistance gene blaNDM and blaKPC, colistin resistance gene mcr-1, and tet(X) for tigecycline resistance, have been reported, posing a serious challenge to the treatment of clinical UTI. Therefore, point-of-care (POC) detection of these genes in UTI samples without the need for pre-culturing is urgently needed. Based on PEG 200-enhanced recombinase polymerase amplification (RPA) and a refined Chelex-100 lysis method with HRP-catalyzed lateral flow immunoassay (LFIA), we developed an MCL-PRPA-HLFIA cascade assay system for detecting these genes in UTI samples. The refined Chelex-100 lysis method extracts target DNA from UTI samples in 20 min without high-speed centrifugation or pre-incubation of urine samples. Following optimization, the cascade detection system achieved an LOD of 102 CFU/mL with satisfactory specificity and could detect these genes in both simulated and actual UTI samples. It takes less than an hour to complete the process without the use of high-speed centrifuges or other specialized equipment, such as PCR amplifiers. The MCL-PRPA-HLFIA cascade assay system provides new ideas for the construction of rapid detection methods for pan-drug-resistant genes in clinical UTI samples and provides the necessary medication guidance for UTI treatment.
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Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Wenchong Shan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100083, China
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12
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Tian J, Chen B, Zhang B, Li T, Liang Z, Guo Y, Jiao H, Liang F, Xiang L, Lin F, Ren R, Liu Q. A New Auto-RPA-Fluorescence Detection Platform for SARS-CoV-2. Lab Med 2023; 54:182-189. [PMID: 36200614 PMCID: PMC9619631 DOI: 10.1093/labmed/lmac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVE The outbreak of COVID-19 caused by SARS-CoV-2 has led to a serious worldwide pandemic. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR)-based methods were recommended for routine detection of SARS-CoV-2 RNA. Because the reaction time and analytical sensitivity of qRT-PCR limits the diagnosis of SARS-CoV-2, development of a quick process of SARS-CoV-2 detection technology with high analytical sensitivity remains urgent. METHODS We combined isothermal amplification and fluorescence detection technology to develop a new auto-recombinase polymerase amplification (RPA)-fluorescence platform that could be used in the diagnosis of SARS-CoV-2. RESULTS By optimization of primers and probes, the RPA platform could detect SARS-CoV-2 nucleotides within 15 min. The limits of detection and specificity of the auto-RPA-fluorescence platform were 5 copies/µL and 100%, respectively. The accuracy of detection of the auto-RPA-fluorescence platform in the 16 positive samples was 100%. CONCLUSION The RPA platform is a potential technology for the diagnosis of SARS-CoV-2 infection.
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Affiliation(s)
- Jing Tian
- Centers for Disease Control and Prevention, People's Liberation Army Southern Theater Command, Guangzhou, China
| | - Biao Chen
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Bin Zhang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tantan Li
- Jining Precision Medical Test Center, Jining No. 1 People's Hospital, Jining, China
| | - Zhiqiang Liang
- Medical Laboratory Department, Jining No. 1 People's Hospital, Jining, China
| | - Yujin Guo
- Institute of Clinical Pharmacy & Pharmacology, Jining No. 1 People's Hospital, Jining, China
| | | | - Fenghong Liang
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
| | - Longquan Xiang
- Department of Pathology, Jining No. 1 People's Hospital, Jining, China
| | - Fanzhong Lin
- Department of Pathology, Jining No. 1 People's Hospital, Jining, China
| | - Ruiwen Ren
- Centers for Disease Control and Prevention, People's Liberation Army Southern Theater Command, Guangzhou, China
| | - Qingbin Liu
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, China
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Roumani F, Barros-Velázquez J, Garrido-Maestu A, Prado M. Real-time PCR, and Recombinase Polymerase Amplification combined with SYBR Green I for naked-eye detection, along with Propidium Monoazide (PMA) for the detection of viable patulin-producing fungi in apples and by-products. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Wang J, Jiang H, Pan L, Gu X, Xiao C, Liu P, Tang Y, Fang J, Li X, Lu C. Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems. Front Bioeng Biotechnol 2023; 11:1020430. [PMID: 36815884 PMCID: PMC9930993 DOI: 10.3389/fbioe.2023.1020430] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.
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Affiliation(s)
- Jingwen Wang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Han Jiang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Leiming Pan
- Zhejiang Hongzheng Testing Co., Ltd., Ningbo, China
| | - Xiuying Gu
- Zhejiang Gongzheng Testing Center Co., Ltd., Hangzhou, China
| | - Chaogeng Xiao
- Institute of Food Science, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Pengpeng Liu
- Key Laboratory of Biosafety detection for Zhejiang Market Regulation, Zhejiang Fangyuan Testing Group LO.T, Hangzhou, China
| | - Yulong Tang
- Hangzhou Tiannie Technology Co., Ltd., Hangzhou, China
| | - Jiehong Fang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoqian Li
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Chenze Lu
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
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Multiplex recombinase polymerase amplification for high-risk and low-risk type HPV detection, as potential local use in single tube. Sci Rep 2023; 13:829. [PMID: 36646782 PMCID: PMC9841928 DOI: 10.1038/s41598-023-28038-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
High rates of new cervical cancer cases and deaths occur in low- and middle-income countries yearly, and one reason was found related to limitation of regular cervical cancer screening in local and low-resource settings. HPV has over 150 types, yet certain 14-20 high-risk and 13-14 low-risk types are common, and, thus, most conventional HPV nucleic acid assays, for examples, Cobas 4800 HPV test (Roche Diagnostics, New Jersey, USA) and REBA HPV-ID (Molecules and Diagnostics, Wonju, Republic of Korea) were developed to cover these types. We thereby utilized bioinformatics combined with recent isothermal amplification technique at 35-42 °C to firstly describe multiplex recombinase polymerase amplification assay that is specific to these common 20 high-risk and 14 low-risk types, and also L1 and E6/E7 genes that target different stages of cervical cancer development. Multiplex primer concentrations and reaction incubation conditions were optimized to allow simultaneous two gene detections at limit of detection of 1000 copies (equivalent to 2.01 fg) for L1 and 100 copies (0.0125 fg) for E6/E7, respectively. The assay was validated against urogenital and other pathogens, normal flora, and human control. In 130 real clinical sample tests, the assay demonstrated 100% specificity, 78% diagnostic accuracy, and 75% sensitivity compared with REBA HPV-ID test, and is much more rapid (15-40 min), less expensive (~ 3-4 USD/reaction) and does not require instrumentation (35-42 °C reaction condition so hand holding or tropical temperature is possible). Hence, the developed novel assay provides alternative screening tool for potential local screening. Furthermore, as this assay uses safe chemical reagents, it is safe for users.
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16
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Tao J, Liu D, Xiong J, Dou L, Zhai W, Zhang R, Wang Y, Shen J, Wen K. Rapid On-Site Detection of Extensively Drug-Resistant Genes in Enterobacteriaceae via Enhanced Recombinase Polymerase Amplification and Lateral Flow Biosensor. Microbiol Spectr 2022; 10:e0334422. [PMID: 36445091 PMCID: PMC9769758 DOI: 10.1128/spectrum.03344-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The widespread emergence of transferable extensively drug-resistant (XDR) genes, including blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance, in Enterobacteriaceae poses a major threat to public health. Thus, rapid on-site detection of these XDR genes is urgently needed. We developed a cascade system with a unitary polyethylene glycol (PEG) 200-enhanced recombinase polymerase amplification (RPA) as the core, combined with a modified Chelex-100 lysis method and a horseradish peroxidase (HRP)-catalyzed lateral flow immunoassay (LFIA) biosensor, to accurately detect these genes in Enterobacteriaceae. The conventional Chelex-100 lysis method was modified to allow in situ extraction of bacterial DNA in 20 min without requiring bulky high-speed centrifuges. Using PEG 200 increased the amplification efficiency of the RPA by 13%, and the HRP-catalyzed LFIA biosensor intensified the colorimetric signal of the test line. Following optimization, the sensitivity of the cascade system was <10 copies/μL with satisfactory specificity, allowing for highly sensitive detection of these XDR genes in Enterobacteriaceae. The complete detection procedure can be completed in less than 1 h without using large-scale instruments. This assay is conducive to rapid on-site visual detection of these XDR genes in Enterobacteriaceae in practical applications, thus providing better technical support for clinical surveillance of these genes and better treatment of XDR pathogens. IMPORTANCE Carbapenem, colistin, and tigecycline are considered the last resorts for treating severe bacterial infections caused by extensively drug-resistant (XDR) pathogens. A major threat to public health is the emergence and prevalence of transferable XDR genes in Enterobacteriaceae, such as blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance. Therefore, it is imperative to develop rapid on-site methods to detect these XDR genes. In this study, we constructed a cascade system for detecting these genes based on PEG 200-enhanced recombinase polymerase amplification combined with a modified Chelex-100 lysis method and HRP-catalyzed lateral flow immunoassay. The current method is capable of detecting the above-mentioned XDR genes in situ with satisfactory specificity and sensitivity, which could provide technical support for the surveillance of these genes and provide medication recommendations for the treatment of relevant clinical infections.
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Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rong Zhang
- Clinical Microbiology Laboratory, 2nd Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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17
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Wang X, Sui X, Ma Y, Li M, Zhang X, Fei D, Ma M. Real-time reverse transcription recombinase polymerase amplification for rapid detection of murine hepatitis virus. Front Microbiol 2022; 13:1067694. [PMID: 36532497 PMCID: PMC9755729 DOI: 10.3389/fmicb.2022.1067694] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 10/29/2023] Open
Abstract
UNLABELLED Murine hepatitis virus (MHV) is a highly infectious murine coronavirus that has a high potential for causing harm to host animals. This study aimed to develop a real-time reverse transcription recombinase polymerase amplification (RT-RPA) method for rapid detection of MHV in laboratory mice. METHODS Specific primers and probes for RT-RPA assay were designed targeting the conserved region in the M gene of the MHV reference strain (accession no. FJ6647223) according to the TwistDx manual instructions. The specificity, sensitivity, and reproducibility of the RT-RPA method were evaluated and compared with those of the standard RT-qPCR method. The clinical applicability of this assay was evaluated using 68 field samples. RESULTS Amplification using the newly developed RT-RPA assay was completed within 20 min at 37°C, while that using the RT-qPCR method required nearly 60 min. The RT-RPA method exhibited an obvious time-saving advantage. Both RT-RPA and RT-PCR methods had the same limit of detection, which was 4.45 × 101 copies/μL. The specificity was indicated by a lack of cross-reaction with MHV, pneumonia virus of mice, Sendai virus, hantavirus, minute virus of mice, and reovirus type III. The MHV detection rate of RT-RPA assays was 13.63% (9/66) and RT-qPCR assays was 15.15% (10/66). Cohen's "kappa" (κ) analysis results exhibited a very good agreement between two methods with the value of κ ≥ 0.750(since κ = 0.939) and p < 0.0005 (since p = 0.000). CONCLUSION The RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of MHV in laboratory mice and has significant potential for application in laboratories.
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Affiliation(s)
- Xiao Wang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Xin Sui
- First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yueyu Ma
- Experimental Animal Center of Jinzhou Medical University, Jinzhou, China
| | - Ming Li
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Xu Zhang
- The Centers for Disease Control and Prevention in Jinzhou, Jinzhou, China
| | - Dongliang Fei
- Experimental Animal Center of Jinzhou Medical University, Jinzhou, China
| | - Mingxiao Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
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18
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Naranitus P, Aiamsa-At P, Sukonta T, Hannanta-Anan P, Chaijarasphong T. Smartphone-compatible, CRISPR-based platforms for sensitive detection of acute hepatopancreatic necrosis disease in shrimp. JOURNAL OF FISH DISEASES 2022; 45:1805-1816. [PMID: 35946585 DOI: 10.1111/jfd.13702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Acute Hepatopancreatic Necrosis Disease (AHPND), caused by bacterial isolates expressing PirAB binary toxins, represents the severest and most economically destructive disease affecting penaeid shrimp. Its rapid disease progression and associated massive mortalities call for vigilant monitoring and early diagnosis, but molecular detection methods that simultaneously satisfy the requirements of sensitivity, specificity, and portability are still scarce. In this work, the CRISPR-Cas12a technology was harnessed for the development of two fluorescent assays compatible with naked-eye visualization. The first assay, AP4-Cas12a, was based on the OIE-recommended AP4 two-tubed nested PCR method and was designed to bypass the time-consuming and potentially hazardous agarose gel electrophoresis step. Using AP4-Cas12a, the detection limit of 10 copies per reaction could be achieved within less than 30 minutes post-PCR. The second assay, RPA-Cas12a, utilized recombinase polymerase amplification (RPA) to rapidly and isothermally amplify the target DNA, followed by amplicon detection by Cas12a, resulting in a protocol that can be completed in less than an hour at a constant temperature of 37°C. The detection limit of RPA-Cas12a is 100 copies of plasmid DNA or 100 fg of bacterial genomic DNA per reaction. Importantly, we validated that both assays are compatible with a previously reported smartphone-based device for facile visualization of fluorescence, thereby providing an affordable option that requires less consumables than lateral flow detection. Using this portable device for readouts, the AP4-Cas12a and RPA-Cas12a methods showed excellent concordance with the AP4-agarose gel electrophoresis approach in the evaluation of clinical samples. Therefore, the developed Cas12a assays have the potential to streamline both in-laboratory and onsite diagnosis of AHPND.
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Affiliation(s)
- Punyaporn Naranitus
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Praphutson Aiamsa-At
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanwarat Sukonta
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimkhuan Hannanta-Anan
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Thawatchai Chaijarasphong
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
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Rattner RJ, Godfrey KE, Hajeri S, Yokomi RK. An Improved Recombinase Polymerase Amplification Coupled with Lateral Flow Assay for Rapid Field Detection of ' Candidatus Liberibacter asiaticus'. PLANT DISEASE 2022; 106:3091-3099. [PMID: 35596249 DOI: 10.1094/pdis-09-21-2098-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Huanglongbing (HLB) is a destructive citrus disease that affects citrus production worldwide. 'Candidatus Liberibacter asiaticus' (CLas), a phloem-limited bacterium, is the associated causal agent of HLB. The current standard for detection of CLas is real-time quantitative polymerase chain reaction (qPCR) using either the CLas 16S rRNA gene or the ribonucleotide reductase (RNR) gene-specific primers/probe. qPCR requires well-equipped laboratories and trained personnel, which is not convenient for rapid field detection of CLas-infected trees. Recombinase polymerase amplification (RPA) assay is a fast, portable alternative to PCR-based diagnostic methods. In this study, an RPA assay was developed to detect CLas in crude citrus extracts utilizing isothermal amplification, without the need for DNA purification. Primers were designed to amplify a region of the CLas RNR gene, and a fluorescent labeled probe allowed for detection of the amplicon in real-time within 8 mins at 39°C. The assay was specific to CLas, and the sensitivity was comparable to qPCR, with a detection limit cycle threshold of 34. Additionally, the RPA assay was combined with a lateral flow device for a point-of-use assay that is field deployable. Both assays were 100% accurate in detecting CLas in fresh citrus crude extracts from leaf midribs and roots from five California strains of CLas tested in the Contained Research Facility in Davis, California. This assay will be important for distinguishing CLas-infected trees in California from those infected by other pathogens that cause similar disease symptoms and can help control HLB spread.
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Affiliation(s)
- Rachel J Rattner
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Kris E Godfrey
- Contained Research Facility, University of California at Davis, Davis, CA 95616
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA 93274
| | - Raymond K Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
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20
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Dorendorf A, Bachmann I, Spiegel M, Abd El Wahed A, Dame G, Hufert F. Rapid detection of human coronavirus NL63 by isothermal reverse transcription recombinase polymerase amplification. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:100115. [PMID: 36248766 PMCID: PMC9546502 DOI: 10.1016/j.jcvp.2022.100115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Background Human coronaviruses are one of the leading causes for respiratory tract infections and for frequent primary care consultation. The human coronavirus NL63 (HCoV..µNL63) is one representative of the seasonal coronaviruses and capable of infecting the upper and lower respiratory tract and causative agent for croup in children. Objectives For fast detection of HCoV-NL63, we developed an isothermal reverse transcription recombinase polymerase amplification (RT-RPA) assay. Study design The analytical sensitivities of the RT-RPA assay were identified for in vitro transcribed ribonucleic acid (RNA) and for genomic viral RNA from cell culture supernatant. Moreover, specificity was tested with nucleic acids from other human coronaviruses and a variety of clinically relevant respiratory viruses. Finally, a clinical nasopharyngeal swab sample with spiked genomic viral HCoV-NL63 RNA was analyzed. Results Our HCoV-NL63 RT-RPA assay is highly specific and has an analytical sensitivity of 13 RNA molecules/reaction for in vitro transcribed RNA. For genomic viral RNA from cell culture supernatant spiked into a clinical nasopharyngeal swab sample the assay...s analytical sensitivity is 170 RNA molecules/reaction. The assay shows amplification of the lowest detectable target copy number after 8 minutes and 7 minutes, respectively. Conclusions We were able to design a sensitive and specific RT-RPA assay for the detection of HCoV-NL63. Additionally, the assay is characterized by short duration, isothermal amplification, and simple instrumentation.
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Affiliation(s)
- Aline Dorendorf
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Martin Spiegel
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany.,Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany
| | - Frank Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Neuruppin, Germany.,Brandenburg University of Technology Cottbus, Senftenberg, Germany.,Faculty of Health Sciences, Joint Faculty of Brandenburg University of Technology Cottbus - Senftenberg, Brandenburg Medical School Theodor Fontane, Neuruppin and University of Potsdam, Potsdam, Germany
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21
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Characterizing the Impact of Primer-Template Mismatches on Recombinase Polymerase Amplification. J Mol Diagn 2022; 24:1207-1216. [PMID: 36116701 DOI: 10.1016/j.jmoldx.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/18/2022] [Accepted: 08/16/2022] [Indexed: 01/13/2023] Open
Abstract
Recombinase polymerase amplification (RPA) is an isothermal amplification assay that has been ubiquitously utilized in the detection of infectious agents. Like any nucleic acid amplification technology, primer-template complementarity is critical to RPA reaction success. Mismatches arising in the primer-template complex are known to impact reaction kinetics, invalidate downstream analysis, such as nucleic acid quantification, and result in false negatives if used in a diagnostic capacity. Although the impact of specific primer-template mismatches has been well characterized for techniques such as PCR, characterization remains limited for RPA. Through our study, we systematically characterize the impact of mismatches on the RPA reaction, when located in the 3'-anchor region of the primer-template complex. Our investigation identified that the nucleotides involved, as well as position of each mismatch, influence the size of the impact, with terminal cytosine-thymine and guanine-adenine mismatches being the most detrimental. The presence of some mismatch combinations, such as a penultimate cytosine-cytosine and a terminal cytosine-adenine mismatch pairing, led to complete RPA reaction inhibition. Through the successful characterization of 315 mismatch combinations, researchers can optimize their RPA assay accordingly and seek to implement RPA technology for rapid, in-field genotyping.
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22
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Mann JG, Pitts RJ. PrimedSherlock: a tool for rapid design of highly specific CRISPR-Cas12 crRNAs. BMC Bioinformatics 2022; 23:428. [PMID: 36241974 PMCID: PMC9569017 DOI: 10.1186/s12859-022-04968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background CRISPR-Cas based diagnostic assays provide a portable solution which bridges the benefits of qRT-PCR and serological assays in terms of portability, specificity and ease of use. CRISPR-Cas assays are rapidly fieldable, specific and have been rigorously validated against a number of targets, including HIV and vector-borne pathogens. Recently, CRISPR-Cas12 and CRISPR-Cas13 diagnostic assays have been granted FDA approval for the detection of SARS-CoV-2. A critical step in utilizing this technology requires the design of highly-specific and efficient CRISPR RNAs (crRNAs) and isothermal primers. This process involves intensive manual curation and stringent parameters for design in order to minimize off-target detection while also preserving detection across divergent strains. As such, a single, streamlined bioinformatics platform for rapidly designing crRNAs for use with the CRISPR-Cas12 platform is needed. Here we offer PrimedSherlock, an automated, computer guided process for selecting highly-specific crRNAs and primers for targets of interest. Results Utilizing PrimedSherlock and publicly available databases, crRNAs were designed against a selection of Flavivirus genomes, including West Nile, Zika and all four serotypes of Dengue. Using outputs from PrimedSherlock in concert with both wildtype A.s Cas12a and Alt-R Cas12a Ultra nucleases, we demonstrated sensitive detection of nucleic acids of each respective arbovirus in in-vitro fluorescence assays. Moreover, primer and crRNA combinations facilitated the detection of their intended targets with minimal off-target background noise. Conclusions PrimedSherlock is a novel crRNA design tool, specific for CRISPR-Cas12 diagnostic platforms. It allows for the rapid identification of highly conserved crRNA targets from user-provided primer pairs or PrimedRPA output files. Initial testing of crRNAs against arboviruses of medical importance demonstrated a robust ability to distinguish multiple strains by exploiting polymorphisms within otherwise highly conserved genomic regions. As a freely-accessible software package, PrimedSherlock could significantly increase the efficiency of CRISPR-Cas12 diagnostics. Conceptually, the portability of detection kits could also be enhanced when coupled with isothermal amplification technologies. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04968-5.
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Affiliation(s)
- James G Mann
- Department of Biology, Baylor University, 101 Bagby Avenue, Waco, TX, 76706, USA
| | - R Jason Pitts
- Department of Biology, Baylor University, 101 Bagby Avenue, Waco, TX, 76706, USA.
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Viromes of 15 Pepper ( Capsicum annuum L.) Cultivars. Int J Mol Sci 2022; 23:ijms231810507. [PMID: 36142418 PMCID: PMC9504177 DOI: 10.3390/ijms231810507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Pepper (Capsicum annuum L.) plants produce berry fruits that are used as spices. Here, we examined the viromes of 15 pepper cultivars through RNA sequencing. We obtained 1,325 virus-associated contigs derived from 8 virus species. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, followed by potato virus Y, bell pepper endornavirus, and hot pepper endornavirus. The proportion of viral reads in each transcriptome ranged from 0.04% to 24.5%. BBWV2 was the dominant virus in seven cultivars, whereas CMV was dominant in five cultivars. All the bell pepper cultivars showed severe viral disease symptoms, whereas the commercially developed hot pepper cultivars were asymptomatic or had mild symptoms. In addition, 111 complete viral segments were obtained from 7 viruses. Based on the obtained viral genomes, the genetic relationship between the identified viruses and quasispecies of BBWV2 and CMV in each pepper plant was determined. Newly designed primers for nine viruses confirmed the results of RNA sequencing. Taken together, this study, for the first time, provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing.
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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25
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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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26
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Kim NK, Lee HJ, Kim SM, Jeong RD. Rapid and Visual Detection of Barley Yellow Dwarf Virus by Reverse Transcription Recombinase Polymerase Amplification with Lateral Flow Strips. THE PLANT PATHOLOGY JOURNAL 2022; 38:159-166. [PMID: 35385920 PMCID: PMC9343894 DOI: 10.5423/ppj.nt.01.2022.0009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Barley yellow dwarf virus (BYDV) has been a major viral pathogen causing significant losses of cereal crops including oats worldwide. It spreads naturally through aphids, and a rapid, specific, and reliable diagnostic method is imperative for disease monitoring and management. Here, we established a rapid and reliable method for isothermal reverse transcription recombinase polymerase amplification (RT-RPA) combined with a lateral flow strips (LFS) assay for the detection of BYDV-infected oat samples based on the conserved sequences of the BYDV coat protein gene. Specific primers and a probe for RT-RPA reacted and optimally incubated at 42 o C for 10 min, and the end-labeled amplification products were visualized on LFS within 10 min. The RT-RPA-LFS assay showed no cross-reactivity with other major cereal viruses, including barley mild mosaic virus, barley yellow mosaic virus, and rice black streaked dwarf virus, indicating high specificity of the assay. The sensitivity of the RT-RPA-LFS assay was similar to that of reverse transcription polymerase chain reaction, and it was successfully validated to detect BYDV in oat samples from six different regions and in individual aphids. These results confirm the out-standing potential of the RT-RPA-LFS assay for rapid detection of BYDV.
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Affiliation(s)
- Na-Kyeong Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Sang-Min Kim
- Crop Foundation Research Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
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27
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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28
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Advances in nucleic acid amplification techniques (NAATs): COVID-19 point-of-care diagnostics as an example. Biosens Bioelectron 2022; 206:114109. [PMID: 35245867 DOI: 10.1016/j.bios.2022.114109] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/24/2022] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Achieving superhigh sensitivity is the ultimate goal for bio-detection in modern analytical science and life science. Among variable signal amplification strategies, nucleic acid amplification technologies are revolutionizing the field of bio-detection, providing greater possibilities in novel diagnosis achieving high efficiency, specificity, and cost-effectiveness. Nucleic acid amplification techniques (NAATs), such as Polymerase Chain Reaction (PCR), Rolling Circle Amplification (RCA), Loop-Mediated Isothermal Amplification (LAMP), Recombinase Polymerase Amplification (RPA), CRISPR-related amplification, and others are dominating methods employed in research and clinical settings. They each provide distinctively unique features that can offer desirable performance in terms of sensitivity, specificity, simplicity, stability, and cost. NAATs are in unmet demand in molecular diagnosis, especially in point-of-care scenario. This review will discuss the principles and recent advancements of each NAAT, respectively, revealing their strengths and challenges in achieving rapid and accurate bio-detection with a focus on point-of-care diagnosis. Furthermore, this review will explore the application of each of the technologies through the contemporary COVID-19 pandemic, analyzing their ability in point-of-care diagnosis of the COVID-19 with high sensitivity to emphasize significance of developing NAATs based methods in battling COVID-19. Finally, advantages and potentials of each NAAT in enhancements of sensitivity and specificity in bio-detection from bench side to the bedside will be discussed, aiming for full exploitation of capability of each NAAT. This review will provide novel aspects in the selection and combination of usages of various NAATs based on their distinctive characteristics and limitations. A possible advancing direction of future accurate POCT is also proposed.
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29
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Santiago-McRae E, Oh SW, Carlo AM, Bar O, Guan E, Zheng D, Grgicak C, Fu J. Rapid Nucleic Acid Reaction Circuits for Point-Of-Care Diseases Diagnosis. Curr Top Med Chem 2022; 22:686-698. [PMID: 35139798 DOI: 10.2174/1570163819666220207114148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
An urgent need exists for a rapid, cost-effective, facile, and reliable nucleic acid assay for mass screening to control and prevent the spread of emerging pandemic diseases. This urgent need is not fully met by current diagnostic tools. In this review, we summarize the current state-of-the-art research in novel nucleic acid amplification and detection that could be applied to point-of-care (POC) diagnosis and mass screening of diseases. The critical technological breakthroughs will be discussed for their advantages and disadvantages. Finally, we will discuss the future challenges of developing nucleic acid-based POC diagnosis.
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Affiliation(s)
| | - Sung Won Oh
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Anthony Monte Carlo
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Omri Bar
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | | | - Doris Zheng
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Catherine Grgicak
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
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30
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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31
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Guo M, Feng P, Zhang L, Feng C, Fu J, Pu X, Liu F. Rapid Detection of Clostridium tetani by Recombinase Polymerase Amplification Using an Exo Probe. J Microbiol Biotechnol 2022; 32:91-98. [PMID: 34818665 PMCID: PMC9628835 DOI: 10.4014/jmb.2109.09022] [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: 09/09/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022]
Abstract
Tetanus is a potentially fatal public health illness resulted from the neurotoxins generated by Clostridium tetani. C. tetani is not easily culturable and culturing the relevant bacteria from infected wounds has rarely been useful in diagnosis; PCR-based assays can only be conducted at highly sophisticated laboratories. Therefore, a real-time recombinase polymerase amplification assay (Exo-RPA) was constructed to identify the fragments of the neurotoxin gene of C. tetani. Primers and the exo probe targeting the conserved region were designed, and the resulting amplicons could be detected in less than 20 min, with a detection limit of 20 copies/reaction. The RPA assay displayed good selectivity, and there were no cross-reactions with other infectious bacteria common in penetrating wounds. Tests of target-spiked serum and pus extract revealed that RPA is robust to interfering factors and has great potential for further development for biological sample analysis. This method has been confirmed to be reliable for discriminating between toxic and nontoxic C. tetani strains. The RPA assay dramatically improves the diagnostic efficacy with simplified device architecture and is a promising alternative to real-time PCR for tetanus detection.
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Affiliation(s)
- Mingjing Guo
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China
| | - Pan Feng
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China
| | - Liqun Zhang
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China
| | - Chunfeng Feng
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China
| | - Jie Fu
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China
| | - Xiaoyun Pu
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China,
X. Pu Phone: +86-23-68755637 E-mail:
| | - Fei Liu
- Department of clinical laboratory, Xinqiao Hospital and The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Main St, Shapingba District, Chongqing 400037, P.R. China,Corresponding authors F. Liu E-mail:
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32
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Tortajada-Genaro LA. Design of Oligonucleotides for Allele-Specific Amplification Based on PCR and Isothermal Techniques. Methods Mol Biol 2022; 2392:35-51. [PMID: 34773613 DOI: 10.1007/978-1-0716-1799-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-nucleotide variations have been associated to various genetic diseases, variations on drug efficiency, and differences in cancer prognostics. The detection of these changes in nucleic acid sequences from patient samples is particularly useful for accurate diagnosis, therapeutics, and disease management. A reliable allele-specific amplification is still an important challenge for molecular-based diagnostic technologies. In the last years, allele-specific primers have been designed for promoting the enrichment of certain variants, based on a higher stability of primer/template duplexes. Also, several methods are based on the addition of a blocking oligonucleotide that prevent the amplification of a specific variant, enabling that other DNA variants can be observed. In this context, genotyping methods based on isothermal amplification techniques are increasing, especially those assays aimed to be deployed at point-of-care applications. The correct selection of target sequences is crucial for reaching the required analytical performances, in terms of reaction time, amplification yield, and selectivity. The present chapter describes the design criteria for the selection of primers and blockers for relevant PCR approaches and novel isothermal strategies. Several successful examples are provided in order to highlight the main design restrictions and the potential to be extended to other applications.
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Affiliation(s)
- Luis Antonio Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Valencia, Spain.
- Departamento de Química, Universitat Politècnica de València, Valencia, Spain.
- Unidad Mixta UPV-La Fe, Nanomedicine and sensors, Valencia, Spain.
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33
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The developed molecular biological identification tools for mycetoma causative agents: An update. Acta Trop 2022; 225:106205. [PMID: 34687643 DOI: 10.1016/j.actatropica.2021.106205] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022]
Abstract
Mycetoma is a chronic granulomatous inflammatory disease that is caused either by bacteria or fungi. Bacterial mycetoma (actinomycetoma) can be caused by various causative agents of the genera Nocardia, Streptomyces and Actinomadura. On the other hand, fungal mycetoma (eumycetoma) is most commonly caused by causative agents belonging to the genera Madurella, Scedosporium and Falciformispora. Early and accurate diagnosis of the causative organisms can guide proper patient management and treatment. To allow rapid and accurate species identification, different molecular techniques were developed over the past decades. These techniques can be protein based (MALDI-TOF MS) as well as DNA based (Sequencing, PCR and isothermal amplification methods). In this review, we provide an overview of the different molecular techniques currently in use and identify knowledge gaps, which need to be addressed before we can implement molecular diagnostics for mycetoma in different clinical settings.
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34
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Zyrina NV, Antipova VN. Nonspecific Synthesis in the Reactions of Isothermal Nucleic Acid Amplification. BIOCHEMISTRY (MOSCOW) 2021; 86:887-897. [PMID: 34284713 DOI: 10.1134/s0006297921070099] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The review focuses on the main factors involved in the formation of nonspecific products in isothermal nucleic acid amplification, such as mispriming, ab initio DNA synthesis, and additional activities of DNA polymerases, and discusses approaches to prevent formation of such nonspecific products in LAMP, RPA, NASBA, RCA, SDA, LSDA, NDA, and EXPAR.
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Affiliation(s)
- Nadezhda V Zyrina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Valeriya N Antipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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35
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Lee HJ, Cho IS, Ju HJ, Jeong RD. Rapid and visual detection of tomato spotted wilt virus using recombinase polymerase amplification combined with lateral flow strips. Mol Cell Probes 2021; 57:101727. [PMID: 33789127 DOI: 10.1016/j.mcp.2021.101727] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 01/18/2023]
Abstract
Tomato spotted wilt virus (TSWV) is economically important in Korea as it causes significant losses to a wide range of important ornamental and vegetable crops. Therefore, a rapid detection method is imperative for TSWV diagnosis. Specific primers and probes were designed based on the conserved sequences of the TSWV coat protein gene. In this study, an isothermal reverse transcription recombinase polymerase amplification (RT-RPA) assay, combined with lateral flow strips (LFS), was established for rapid detection of TSWV in pepper infected leaves. The RT-RPA reaction was performed at an optimal condition of 38 °C for 10 min and an LFS incubation time of approximately 5 min. There was no cross-reactivity with other viruses infecting pepper such as cucumber mosaic virus, pepper mottle virus, pepper mild mottle virus, and broad bean wilt virus 2, thus confirming the specificity of RT-RPA-LFS. The sensitivity of the RT-RPA assay was similar to that of RT-PCR, and RT-RPA-LFS was successfully applied to detect TSWV in the pepper samples collected from the field. Thus, RT-RPA-LFS assay might be a promising candidate for quick diagnosis of TSWV-infected pepper plants.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, South Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju-si, 54896, South Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea.
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36
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Rani A, Ravindran VB, Surapaneni A, Shahsavari E, Haleyur N, Mantri N, Ball AS. Evaluation and comparison of recombinase polymerase amplification coupled with lateral-flow bioassay for Escherichia coli O157:H7 detection using diifeerent genes. Sci Rep 2021; 11:1881. [PMID: 33479307 PMCID: PMC7820579 DOI: 10.1038/s41598-021-81312-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli serotype O157:H7 is a food and waterborne zoonotic pathogen causing gastroenteritis in humans. Rapid and simple detection in water and food is imperative to control its spread. However, traditional microbial detection approaches are time-consuming, expensive and complex to operate at the point-of-care without professional training. We present a rapid, simple, sensitive, specific and portable method for detection of E. coli O157:H7 in drinking water, apple juice and milk. We evaluated the effect of gene selection in detecting E. coli O157:H7 using recombinase polymerase amplification coupled with a lateral flow assay using rfbE, fliC and stx gene targets. As low as 100 ag and 1 fg DNA, 4-5 CFU/mL and 101 CFU/mL of E. coli O157:H7 was detected using the stx and rfbE gene targets respectively with 100% specificity, whilst the detection limit was 10 fg DNA and 102 CFU/mL for the fliC gene target, with 72.8% specificity. The RPA-LFA can be completed within 8 min at temperatures between 37 and 42 °C with reduced handling and simple equipment requirements. The test threshold amplification of the target was achieved in 5-30 min of incubation. In conclusion, RPA-LFA represents a potential rapid and effective alternative to conventional methods for the monitoring of E. coli O157:H7 in food and water.
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Affiliation(s)
- Alka Rani
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia.
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Aravind Surapaneni
- South East Water, Frankston, VIC, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora West, VIC, 3083, Australia
| | | | | | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora West, VIC, 3083, Australia
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37
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Behrmann O, Bachmann I, Hufert F, Dame G. Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification. BIOSPEKTRUM 2020; 26:624-627. [PMID: 33078045 PMCID: PMC7556600 DOI: 10.1007/s12268-020-1458-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractThe COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes.
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Affiliation(s)
- Ole Behrmann
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
- Professur für Sensoren, Institut für Mikrosystemtechnik (IMTEK), Universität, Freiburg, Deutschland
| | - Iris Bachmann
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| | - Frank Hufert
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| | - Gregory Dame
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
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Rapid detection of peach latent mosaic viroid by reverse transcription recombinase polymerase amplification. Mol Cell Probes 2020; 53:101627. [DOI: 10.1016/j.mcp.2020.101627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022]
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Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria. Proc Natl Acad Sci U S A 2020; 117:25722-25731. [PMID: 32958655 PMCID: PMC7568265 DOI: 10.1073/pnas.2010196117] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Detection of submicroscopic malaria in asymptomatic individuals is needed for eradication and remains a diagnostic gap in resource-limited settings. Nonfalciparum clinical diagnostics are a second gap, as these infections have a low parasite density and are commonly undetected. We describe an integrated, 60-min, ultrasensitive and specific CRISPR-based diagnostic for the four major pathogenic Plasmodium species that can fill these gaps. Using the SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform, we designed assays with limits of detection below that recommended by the World Health Organization. These assays have a simplified sample preparation method: the SHERLOCK parasite rapid extraction protocol, which eliminates complicated nucleic acid extraction steps. Our work further translates the SHERLOCK platform into a field-deployable diagnostic. Asymptomatic carriers of Plasmodium parasites hamper malaria control and eradication. Achieving malaria eradication requires ultrasensitive diagnostics for low parasite density infections (<100 parasites per microliter blood) that work in resource-limited settings (RLS). Sensitive point-of-care diagnostics are also lacking for nonfalciparum malaria, which is characterized by lower density infections and may require additional therapy for radical cure. Molecular methods, such as PCR, have high sensitivity and specificity, but remain high-complexity technologies impractical for RLS. Here we describe a CRISPR-based diagnostic for ultrasensitive detection and differentiation of Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae, using the nucleic acid detection platform SHERLOCK (specific high-sensitivity enzymatic reporter unlocking). We present a streamlined, field-applicable, diagnostic comprised of a 10-min SHERLOCK parasite rapid extraction protocol, followed by SHERLOCK for 60 min for Plasmodium species-specific detection via fluorescent or lateral flow strip readout. We optimized one-pot, lyophilized, isothermal assays with a simplified sample preparation method independent of nucleic acid extraction, and showed that these assays are capable of detection below two parasites per microliter blood, a limit of detection suggested by the World Health Organization. Our P. falciparum and P. vivax assays exhibited 100% sensitivity and specificity on clinical samples (5 P. falciparum and 10 P. vivax samples). This work establishes a field-applicable diagnostic for ultrasensitive detection of asymptomatic carriers as well as a rapid point-of-care clinical diagnostic for nonfalciparum malaria species and low parasite density P. falciparum infections.
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Behrmann O, Bachmann I, Spiegel M, Schramm M, Abd El Wahed A, Dobler G, Dame G, Hufert FT. Rapid Detection of SARS-CoV-2 by Low Volume Real-Time Single Tube Reverse Transcription Recombinase Polymerase Amplification Using an Exo Probe with an Internally Linked Quencher (Exo-IQ). Clin Chem 2020; 66:1047-1054. [PMID: 32384153 PMCID: PMC7239256 DOI: 10.1093/clinchem/hvaa116] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/05/2020] [Indexed: 01/22/2023]
Abstract
Background The current outbreak of SARS-CoV-2 has spread to almost every country with more than three million confirmed cases and over two hundred thousand deaths as of April 28, 2020. Rapid first-line testing protocols are needed for outbreak control and surveillance. Methods We used computational and manual design to generate a suitable set of reverse transcription recombinase polymerase amplification (RT-RPA) primer and exonuclease probe, internally quenched (exo-IQ) probe sequences targeting the SARS-CoV-2 N gene. RT-RPA sensitivity was determined by amplification of in vitro transcribed RNA standards. Assay selectivity was demonstrated with a selectivity panel of 32 nucleic acid samples derived from common respiratory viruses. To validate the assay against full-length SARS-CoV-2 RNA, total viral RNA derived from cell culture supernatant and 19 nasopharyngeal swab samples (8 positive and 11 negative for SARS-CoV-2) were screened. All results were compared to established RT-qPCR assays. Results The 95% detection probability of the RT-RPA assay was determined to be 7.74 (95% CI: 2.87 - 27.39) RNA copies per reaction. The assay showed no cross-reactivity to any other screened coronaviruses or respiratory viruses of clinical significance. The developed RT-RPA assay produced 100% diagnostic sensitivity and specificity when compared to RT-qPCR (n=20). Conclusion With a run time of 15 to 20 minutes and first results being available in under 7 minutes for high RNA concentrations, the reported assay constitutes one of the fastest nucleic acid based detection methods for SARS-CoV-2 to date and may provide a simple to use alternative to RT-qPCR for first-line screening at the point of need.
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Affiliation(s)
- Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Martin Spiegel
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Marina Schramm
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, University of Göttingen, Germany.,Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology (IMB), Munich, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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Behrmann O, Hügle M, Eckardt F, Bachmann I, Heller C, Schramm M, Turner C, Hufert FT, Dame G. 3D Printed Monolithic Microreactors for Real-Time Detection of Klebsiella pneumoniae and the Resistance Gene blaNDM-1 by Recombinase Polymerase Amplification. MICROMACHINES 2020; 11:mi11060595. [PMID: 32560308 PMCID: PMC7344889 DOI: 10.3390/mi11060595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 05/07/2023]
Abstract
We investigate the compatibility of three 3D printing materials towards real-time recombinase polymerase amplification (rtRPA). Both the general ability of the rtRPA reaction to occur while in contact with the cured 3D printing materials as well as the residual autofluorescence and fluorescence drift in dependence on post curing of the materials is characterized. We 3D printed monolithic rtRPA microreactors and subjected the devices to different post curing protocols. Residual autofluorescence and drift, as well as rtRPA kinetics, were then measured in a custom-made mobile temperature-controlled fluorescence reader (mTFR). Furthermore, we investigated the effects of storage on the devices over a 30-day period. Finally, we present the single- and duplex rtRPA detection of both the organism-specific Klebsiella haemolysin (khe) gene and the New Delhi metallo-β-lactamase 1 (blaNDM-1) gene from Klebsiella pneumoniae. Results: No combination of 3D printing resin and post curing protocol completely inhibited the rtRPA reaction. The autofluorescence and fluorescence drift measured were found to be highly dependent on printing material and wavelength. Storage had the effect of decreasing the autofluorescence of the investigated materials. Both khe and blaNDM-1 were successfully detected by single- and duplex-rtRPA inside monolithic rtRPA microreactors printed from NextDent Ortho Clear (NXOC). The reaction kinetics were found to be close to those observed for rtRPA performed in a microcentrifuge tube without the need for mixing during amplification. Singleplex assays for both khe and blaNDM-1 achieved a limit of detection of 2.5 × 101 DNA copies while the duplex assay achieved 2.5 × 101 DNA copies for khe and 2.5 × 102 DNA copies for blaNDM-1. Impact: We expand on the state of the art by demonstrating a technology that can manufacture monolithic microfluidic devices that are readily suitable for rtRPA. The devices exhibit very low autofluorescence and fluorescence drift and are compatible with RPA chemistry without the need for any surface pre-treatment such as blocking with, e.g., BSA or PEG.
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Affiliation(s)
- Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
- Laboratory for Sensors, Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Matthias Hügle
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
- Laboratory for Sensors, Department of Microsystems Engineering - IMTEK, University of Freiburg, 79110 Freiburg, Germany
| | - Franz Eckardt
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Cecilia Heller
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Marina Schramm
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Carrie Turner
- National Infections Service, Public Health England, Porton Down SP4 0JG, UK;
| | - Frank T. Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 16816 Neuruppin, Germany; (O.B.); (M.H.); (F.E.); (I.B.); (C.H.); (M.S.); (F.T.H.)
- Correspondence:
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Li J, Ma B, Fang J, Zhi A, Chen E, Xu Y, Yu X, Sun C, Zhang M. Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow Immunoassay for Rapid Detection of Salmonella in Food. Foods 2019; 9:foods9010027. [PMID: 31887998 PMCID: PMC7022641 DOI: 10.3390/foods9010027] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Salmonella can cause serious foodborne diseases. We have developed a lateral flow immunoassay combined with recombinase polymerase amplification (LFD-RPA) for detection of Salmonella in food. The conserved fragment (fimY) was selected as the target gene. Under an optimal condition (37 °C, 10 min), the sensitivity was 12 colony-forming units (CFU)/mL in a pure culture. Testing with 16 non-Salmonella strains as controls revealed that LFD-RPA was specific to the fimY gene of Salmonella. The established assay could detect Salmonella at concentrations as low as 1.29 × 102 CFU/mL in artificially contaminated samples. This detection was at a slightly higher level than that for a pure bacterial culture. Combined with the test strip reader, the LFD-RPA is a feasible method for quantitative detection of Salmonella based on the test line intensity, which was the ratio for the test line and control line of the reflected light. The method could be a potential point-of-care test in limited resource areas and provides a new approach and technical support for the diagnosis of food safety.
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Affiliation(s)
- Jiali Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Biao Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Jiehong Fang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Antong Zhi
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Erjing Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Ying Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Science (SLU), P.O. Box 7080, SE-75007 Uppsala, Sweden;
| | - Mingzhou Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (J.L.); (B.M.); (J.F.); (A.Z.); (E.C.); (Y.X.); (X.Y.)
- Correspondence: ; Tel.: +86-571-86914476
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