1
|
Wu Q, Liu X, Wang J, Xu S, Zeng F, Chen L, Zhang G, Wang H. An isothermal nucleic acid amplification-based enzymatic recombinase amplification method for dual detection of porcine epidemic diarrhea virus and porcine rotavirus A. Virology 2024; 594:110062. [PMID: 38522136 DOI: 10.1016/j.virol.2024.110062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/06/2024] [Accepted: 03/14/2024] [Indexed: 03/26/2024]
Abstract
Viral diarrhea is the predominant digestive tract sickness in piglings, resulting in substantial profit losses in the porcine industry. Porcine rotavirus A (PoRVA) and porcine epidemic diarrhea virus (PEDV) are the main causes of grave gastroenteritis and massive dysentery, especially in piglets. PoRVA and PEDV have high transmissibility, exhibit similar clinical symptoms, and frequently co-occur. Therefore, to avoid financial losses, a quick, highly efficient, objective diagnostic test for the prevention and detection of these diseases is required. Enzymatic recombinase amplification (ERA) is a novel technology based on isothermal nucleic acid amplification. It demonstrates high sensitivity and excellent specificity, with a short processing time and easy operability, compared with other in vitro nucleic acid amplification technologies. In this study, a dual ERA method to detect and distinguish between PEDV and PoRVA nucleic acids was established. The method shows high sensitivity, as the detection limits were 101 copies/μL for both viruses. To test the usefulness of this method in clinical settings, we tested 64 swine clinical samples. Our results were 100% matched with those acquired using a commercially available kit. Therefore, we have successfully developed a dual diagnostic ERA nucleic acids method for detecting and distinguishing between PEDV and PoRVA.
Collapse
Affiliation(s)
- Qianwen Wu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Xing Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Jingyu Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Sijia Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Fanliang Zeng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China
| | - Ling Chen
- Ganzhou Quannan County Agriculture and Rural Bureau, Ganzhou, 341800, China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510462, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China; National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
2
|
Qi S, Dong X, Hamed EM, Jiang H, Cao W, Yau Li SF, Wang Z. Ratiometric Fluorescence Aptasensor of Allergen Protein Based on Multivalent Aptamer-Encoded DNA Flowers as Fluorescence Resonance Energy Transfer Platform. Anal Chem 2024; 96:6947-6957. [PMID: 38656889 DOI: 10.1021/acs.analchem.3c05894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Life-threatening allergic reactions to food allergens, particularly peanut protein Ara h1, are a growing public health concern affecting millions of people worldwide. Thus, accurate and rapid detection is necessary for allergen labeling and dietary guidance and ultimately preventing allergic incidents. Herein, we present a novel ratiometric fluorescence aptasensor based on multivalent aptamer-encoded DNA flowers (Mul-DNFs) for the high-stability and sensitive detection of allergen Ara h1. The flower-shaped Mul-DNFs were spontaneously packaged using ultralong polymeric DNA amplicons driven by a rolling circle amplification reaction, which contains a large number of Ara h1 specific recognition units and has excellent binding properties. Furthermore, dual-color fluorescence-labeled Mul-DNFs probes were developed by hybridizing them with Cy3- and Cy5-labeled complementary DNA (cDNA) to serve as a ratiometric fluorescence aptasensor platform based on fluorescence resonance energy transfer. Benefiting from the combined merits of the extraordinary synergistic multivalent binding ability of Mul-DNFs, the excellent specificity of the aptamer, and the sensitivity of the ratiometric sensor to avoid exogenous interference. The developed ratiometric aptasensor showed excellent linearity (0.05-2000 ng mL-1) with a limit of detection of 0.02 ng mL-1. Additionally, the developed ratiometric fluorescence aptasensor was utilized for quantifying the presence of Ara h1 in milk, infant milk powder, cookies, bread, and chocolate with recoveries of 95.7-106.3%. The proposed ratiometric aptasensor is expected to be a prospective universal aptasensor platform for the rapid, sensitive, and accurate determination of food and environmental hazards.
Collapse
Affiliation(s)
- Shuo Qi
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Xiaoze Dong
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Eslam M Hamed
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Department of Chemistry, Faculty of Science, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Hongtao Jiang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Wenbo Cao
- Technology Innovation Center of Special Food for State Market Regulation, Wuxi Food Safety Inspection and Test Center, Wuxi 214100, China
| | - Sam Fong Yau Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Wang Y, Zheng T, Li X, Wu P. Integrating Recombinase Polymerase Amplification and Photosensitization Colorimetric Detection in One Tube for Fast Screening of C. sakazakii in Formula Milk Powder. Anal Chem 2024; 96:5727-5733. [PMID: 38546834 DOI: 10.1021/acs.analchem.4c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Cronobacter sakazakii (C. sakazakii) is a widely existing opportunistic pathogen and thus threatens people with low immunity, especially infants. To prevent the outbreak, a rapid and accurate on-site testing method is required. The current standard culture-based method is time-consuming (3-4 days), while the nucleic acid amplification (PCR)-based detection is mostly carried out in central laboratories. Herein, isothermal recombinase polymerase amplification (RPA) coupled with a photosensitization colorimetric assay (PCA) was adopted for the on-site detection of C. sakazakii in powdered infant formulas (PIFs). The lowest visual detection concentration of C. sakazakii is 800 cfu/mL and 2 cfu/g after 8 h bacteria pre-enrichment. Furthermore, to avoid typical cap opening-resulted aerosol pollution, the PCA reagents were lyophilized onto the cap of the RPA tube (containing lyophilized RPA reagents). After amplification, the tube was subjected to simple shaking to mix the PCA reagents with the amplification products for light-driven color development. Such a one-tube assay offered a lowest concentration of 1000 copies of genomic DNA of C. sakazakii within 1 h. After 8 h of bacterial enrichment, the lowest detecting concentration could be pushed down to 5 cfu/g bacteria in PIF. To facilitate on-site monitoring, a portable, battery-powered PCA device was designed to mount the typical RPA 8-tube strip, and a color analysis cellphone APP was further employed for facile readout.
Collapse
Affiliation(s)
- Yanying Wang
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Ting Zheng
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xianming Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Wu
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Liao C, Pan L, Tan M, Zhou Z, Long S, Yi X, Li X, Wei G, Liang L. A dual RPA-LFD assay for the simultaneous detection of Salmonella typhimurium and Salmonella enteritidis. Front Bioeng Biotechnol 2024; 12:1379939. [PMID: 38524195 PMCID: PMC10958489 DOI: 10.3389/fbioe.2024.1379939] [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: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction: Salmonella was one of the most common bacteria that caused foodborne illness, with S. typhimurium (Salmonella typhimurium) and S. enteritidis (Salmonella enteritidis) infections accounting for more than 75% of human salmonella infections. Methods: In this study, we developed a method of dual recombinase polymerase amplification (RPA) combined with a lateral flow dipstick for the rapid detection of S. typhimurium and S. enteritidis in clinical specimens (stool). Results: The entire reaction process, including amplification and result reading, could be completed within 65 min. The detection limits of S. typhimurium and S. enteritidis in pure culture samples were 5.23 × 101 CFU/mL and 3.59 × 101 CFU/mL, respectively. The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were 8.30 × 101 CFU/mL and 2.70 × 102 CFU/mL, respectively. In addition, the method had no cross-reaction with other pathogenic microorganisms. The results in clinical samples were fully consistent with those obtained using Bacterial Analysis Manual, with sensitivity and specificity were 100% (8/8) and 100% (17/17) for S. typhimurium and 100% (4/4) and 100% (21/21) for S. enteritidis, respectively. Discussion: The detection limits of S. typhimurium and S. enteritidis in artificially contaminated samples were higher than those in pure culture samples, which might be attributed to the inherent complex composition of artificially contaminated samples. In addition, the detection limits of S. typhimurium and S. enteritidis in the same sample were also different, which might be attributed to different amplification efficiency of two target genes in the same reaction system. Conclusion: This assay had potential application outdoors, as it could be performed within 1 h at 38°C without a complex instrument, and the results could be observed with the naked eye. In conclusion, the dual RPA-LFD assay established in this study had practical significance for the rapid detection of S. typhimurium and S. enteritidis in the future.
Collapse
Affiliation(s)
- Chuan Liao
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Lele Pan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Meiying Tan
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Zihan Zhou
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Shaoping Long
- Department of Clinical Laboratory, Baise People’s Hospital, Baise, China
| | - Xueli Yi
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| | - Xuebin Li
- Department of Neurology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Guijiang Wei
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
- Modern Industrial College of Biomedicine and Great Health, Youjiang Medical University for Nationalities, Baise, China
| | - Lina Liang
- Center for Medical Laboratory Science, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
- Baise Key Laboratory for Research and Development on Clinical Molecular Diagnosis for High-Incidence Diseases, Baise, China
- Key Laboratory of Research on Clinical Molecular Diagnosis for High Incidence Diseases in Western Guangxi, Baise, China
| |
Collapse
|
7
|
Zhao F, Hu Y, Fan Z, Huang B, Wei L, Xie Y, Huang Y, Mei S, Wang L, Wang L, Ai B, Fang J, Liang C, Xu F, Tan W, Guo F. Rapid and sensitive one-tube detection of mpox virus using RPA-coupled CRISPR-Cas12 assay. CELL REPORTS METHODS 2023; 3:100620. [PMID: 37848032 PMCID: PMC10626268 DOI: 10.1016/j.crmeth.2023.100620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/19/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023]
Abstract
Mpox is caused by a zoonotic virus belonging to the Orthopoxvirus genus and the Poxviridae family. In this study, we develop a recombinase polymerase amplification (RPA)-coupled CRISPR-Cas12a detection assay for the mpox virus. We design and test a series of CRISPR-derived RNAs(crRNAs) targeting the conserved D6R and E9L genes for orthopoxvirus and the unique N3R and N4R genes for mpox viruses. D6R crRNA-1 exhibits the most robust activity in detecting orthopoxviruses, and N4R crRNA-2 is able to distinguish the mpox virus from other orthopoxviruses. The Cas12a/crRNA assay alone presents a detection limit of 108 copies of viral DNA, whereas coupling RPA increases the detection limit to 1-10 copies. The one-tube RPA-Cas12a assay can, therefore, detect viral DNA as low as 1 copy within 30 min and holds the promise of providing point-of-care detection for mpox viral infection.
Collapse
Affiliation(s)
- Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Baoying Huang
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P.R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Yu Xie
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China
| | - Liming Wang
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Lingwa Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Bin Ai
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, P.R. China
| | - Jugao Fang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Chen Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China.
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P.R. China.
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R. China.
| |
Collapse
|
8
|
Deng W, Feng S, Stejskal V, Opit G, Li Z. An advanced approach for rapid visual identification of Liposcelis bostrychophila (Psocoptera: Liposcelididae) based on CRISPR/Cas12a combined with RPA. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:1911-1921. [PMID: 37463293 DOI: 10.1093/jee/toad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelididae) is a booklouse pest that is a threat to commodity storage security worldwide. Accurate and sensitive methods of L. bostrychophila on-site identification are essential prerequisites for its effective management. Evidence suggests that L. bostrychophila contains 3 intraspecific biotypes that are morphologically indistinguishable but can be discriminated at the level of mitochondrial genome organization and sequences. The traditional molecular identification methods, such as DNA barcoding and PCR-RFLP, are instrumentally demanding and time-consuming, limiting the application of the identification in the field. Therefore, this study developed a new CRISPR/Cas12a-based visual nucleic acid system based on the mitochondrial gene coding for NADH dehydrogenase subunit 2 (nad2), combined with recombinase polymerase amplification (RPA) to accurately identify L. bostrychophila from 4 other common stored-product booklice, and also differentiate 3 biotypes of this species at the same time. The entire identification process could be completed at 37 °C within 20 min with high sensitivity. The system could stably detect at least 1 ng/μl of DNA template. The green fluorescence signal produced by the trans-cleaving of the single-stranded DNA reporter could be observed by the naked eye under blue light. Additionally, the suggested system combined with the crude DNA extraction method to extract DNA rapidly, enabled identification of all developmental stages of L. bostrychophila. With crude DNA, this novel diagnostic system successfully identified an unknown booklouse by holding the reaction tubes in the hand, thus can be considered as an accurate, rapid, highly sensitive, and instrument-flexible method for on-site visual identification of L. bostrychophila.
Collapse
Affiliation(s)
- Wenxin Deng
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan, China
| | - Shiqian Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Vaclav Stejskal
- Crop Research Institute, Drnovská 507, 161 06 Prague 6, Czech Republic
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 165 00 Prague, Czech Republic
| | - George Opit
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, Hainan, China
| |
Collapse
|
9
|
Rich M, Noh E, Wang H, Greene J, Gilligan T, Reay-Jones FPF, Turnbull M, Zink F. Field-based recombinase polymerase amplification and lab-based qPCR assays for detection of Helicoverpa armigera. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:973-982. [PMID: 37023722 DOI: 10.1093/jee/toad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/08/2023] [Accepted: 03/06/2023] [Indexed: 06/14/2023]
Abstract
Helicoverpa armigera (Hübner) is a major crop pest native to Europe, Asia, Australia, and Africa which has recently invaded South America and has caused billions of dollars in agricultural losses. Because of challenges in differentiating between H. armigera and Helicoverpa zea (Boddie), a closely related species native to North and South America, genetic tests have previously been developed to detect H. armigera DNA in pooled samples of moth legs. In this study, a field-based recombinase polymerase amplification (RPA) assay using a lateral flow strip and a qPCR melt curve assay were developed for specific detection of H. armigera DNA in pooled moth samples. In addition, a crude DNA extraction protocol for whole moths was developed to allow rapid preparation of DNA samples. The RPA field test was able to detect ≥ 10 pg of purified H. armigera DNA and the crude DNA of one H. armigera sample in a background of 999 H. zea equivalents. The qPCR assay was able to detect ≥ 100 fg of purified H. armigera DNA and the crude DNA of one H. armigera sample in a background of up to 99,999 H. zea equivalents. Both RPA and qPCR assays detected H. armigera in the crude DNA extracted in the field from a pool of one H. armigera moth and 999 H. zea moths. These newly developed molecular assays to detect H. armigera will contribute to large-scale surveillance programs of H. armigera.
Collapse
Affiliation(s)
- Mitchell Rich
- Department of Plant and Environmental Sciences, Edisto Research and Education Center, Clemson University, Blackville, SC, USA
| | - Enoch Noh
- Department of Plant and Environmental Sciences, Edisto Research and Education Center, Clemson University, Blackville, SC, USA
| | - Hehe Wang
- Department of Plant and Environmental Sciences, Edisto Research and Education Center, Clemson University, Blackville, SC, USA
| | - Jeremy Greene
- Department of Plant and Environmental Sciences, Edisto Research and Education Center, Clemson University, Blackville, SC, USA
| | - Todd Gilligan
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO, USA
| | - Francis P F Reay-Jones
- Department of Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC, USA
| | - Matt Turnbull
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Frida Zink
- USDA-APHIS-PPQ-Science & Technology, Identification Technology Program, Fort Collins, CO, USA
| |
Collapse
|
10
|
Li WM, Ren XD, Jiang YZ, Su N, Li BW, Sun XG, Li RX, Lu WP, Deng SL, Li J, Li MX, Huang Q. Rapid detection of EGFR mutation in CTCs based on a double spiral microfluidic chip and the real-time RPA method. Anal Bioanal Chem 2023:10.1007/s00216-023-04743-2. [PMID: 37254002 DOI: 10.1007/s00216-023-04743-2] [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: 02/18/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023]
Abstract
Circulating tumor cells (CTCs) are cells shed from primary or metastatic tumors and spread into the peripheral bloodstream. Mutation detection in CTCs can reveal vital genetic information about the tumors and can be used for "liquid biopsy" to indicate cancer treatment and targeted medication. However, current methods to measure the mutations in CTCs are based on PCR or DNA sequencing which are cumbersome and time-consuming and require sophisticated equipment. These largely limited their applications especially in areas with poor healthcare infrastructure. Here we report a simple, convenient, and rapid method for mutation detection in CTCs, including an example of a deletion at exon 19 (Del19) of the epidermal growth factor receptor (EGFR). CTCs in the peripheral blood of NSCLC patients were first sorted by a double spiral microfluidic chip with high sorting efficiency and purity. The sorted cells were then lysed by proteinase K, and the E19del mutation was detected via real-time recombinase polymerase amplification (RPA). Combining the advantages of microfluidic sorting and real-time RPA, an accurate mutation determination was realized within 2 h without professional operation or complex data interpretation. The method detected as few as 3 cells and 1% target variants under a strongly interfering background, thus, indicating its great potential in the non-invasive diagnosis of E19del mutation for NSCLC patients. The method can be further extended by redesigning the primers and probes to detect other deletion mutations, insertion mutations, and fusion genes. It is expected to be a universal molecular diagnostic tool for real-time assessment of relevant mutations and precise adjustments in the care of oncology patients.
Collapse
Affiliation(s)
- Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Yu-Zhu Jiang
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Bo-Wen Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Shao-Li Deng
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Meng-Xia Li
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China.
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China.
| |
Collapse
|
11
|
Mao G, Luo X, Ye S, Wang X, He J, Kong J, Dai J, Yin W, Ma Y. Fluorescence and Colorimetric Analysis of African Swine Fever Virus Based on the RPA-Assisted CRISPR/Cas12a Strategy. Anal Chem 2023; 95:8063-8069. [PMID: 37167072 DOI: 10.1021/acs.analchem.3c01033] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It is well-established that different detection modes are necessary for corresponding applications, which can effectively reduce matrix interference and improve the detection accuracy. Here, we reported a magnetic separation method based on recombinase polymerase amplification (RPA)-assisted clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a for dual-mode analysis of African swine fever virus (ASFV) genes, including colorimetry and fluorescence. The ASFV gene was selected as the initial RPA template to generate the amplicon. The RPA amplicon was then recognized by CRISPR-associated RNA (crRNA), activating the trans-cleavage activity of Cas12a and leading to the nonspecific cleavage of ssDNA as well as a significant release of alkaline phosphatase (ALP) in the ALP-ssDNA modified magnetic bead. The released ALP can catalyze para-nitrophenyl phosphate to generate para-nitrophenol, resulting in substantial changes in absorbance and fluorescence, both of which can be used for detection with the naked eye. This strategy allows the sensitive detection of ASFV DNA, with a 20 copies/mL detection limit; no cross-reactivity with other viruses was observed. A good linear relationship was obtained in serum. In addition, this sensor displayed 100% specificity and sensitivity for clinical sample analysis. This method integrates the high sensitivity of fluorescence with easy readout of colorimetry and enables a simple, low-cost, and highly sensitive dual-mode detection of viral nucleic acid, thereby providing a broad prospect for the practical application in the diagnosis of virus infection.
Collapse
Affiliation(s)
- Guobin Mao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xing Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Silu Ye
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
12
|
Pu X, Wu W, Yang D, Zhang Q, Fan X, Du Y, Zu L, Xu Y, Sun C, Zhao K. Rapid, visual and highly sensitive sexing of bovine embryos by recombinase polymerase amplification with CFI staining. Heliyon 2023; 9:e14116. [PMID: 36923860 PMCID: PMC10009442 DOI: 10.1016/j.heliyon.2023.e14116] [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: 07/05/2022] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
Early bovine embryo sexing both increases the number of offspring of the desired sex, and reduces the subsequent costs of processing unwanted offspring of the opposite sex. The need for cattle of different sexes varies from industry to industry, and a range of tools have been set up to meet this need, but most are energy- and time-consuming, hence it is important to establish a fast and convenient method for bovine embryo determination. Herein, we established a recombinase polymerase amplification (RPA) method combined with CFI dye (RPA-CFI) for sexing of bovine embryos. The assay is highly sensitive, specific, rapid and simple; it can be carried out in only 5 min at 37 °C in a metal bath, and results are visualised using a fluorescent colorimeter. Highly specific male-female common and male-specific primers were designed based on the 1399 bp repeating unit of bovine 1.715 satellite DNA and the male-specific S4 repeating sequence, respectively. The limit of detection (LOD) of RPA-CFI with male-female common primers was 1 pg/μL, and the LOD with male-specific primers was 2 pg/μL. RPA-CFI could determine the sex of bovine embryos from only two cells. This is the first report using RPA-CFI for sex determination of bovine embryos. The assay could be applied to other economically important animals to improve efficiency in livestock industries. Additionally, the assay could relieve pressure on food demand due to human population growth, and contribute to economic development of global stockbreeding.
Collapse
Affiliation(s)
- Xinyi Pu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenjing Wu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Dan Yang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qi Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaorui Fan
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yanan Du
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Liujing Zu
- Shanghai Bio-full Biotech Co., Ltd., Shanghai 201106, China
| | - Yan Xu
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chuanwen Sun
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kai Zhao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| |
Collapse
|
13
|
Chen X, Zhao L, Wang J, Wang H, Qiu Y, Dong Z, Zhang C, Liu M, Wang X, Bai X. Rapid visual detection of anisakid nematodes using recombinase polymerase amplification and SYBR Green I. Front Microbiol 2022; 13:1026129. [PMID: 36532447 PMCID: PMC9756439 DOI: 10.3389/fmicb.2022.1026129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2023] Open
Abstract
Anisakidosis is a food-borne parasitic disease (FBPD) caused by the third-stage larvae of the family Anisakidae. Therefore, it is important to develop a simple, rapid and equipment-free detection method for anisakids in fish samples or seafood since current methods are time-consuming and require complex instruments. In this study, a recombinase polymerase amplification (RPA)-based method was established for the first time to detect anisakids by targeting the internal transcribed spacer (ITS) regions. The detection results were visualized by including SYBR Green I (SG) in the method. The sensitivity of RPA-SG assay was 102 copies per reaction of recombinant plasmid (within 20 min at 37°C), similar to quantitative real-time PCR (qPCR). The assay had high specificity for detecting anisakids against other related parasites and host fish. In addition, the assay was further used to detect fresh marine fish contaminated with anisakids and it showed high precision. These results indicate that the novel RPA-SG assay suitable for visual detection of anisakids in the field and food safety control.
Collapse
Affiliation(s)
- Xiuqin Chen
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Science, Fuzhou, China
| | - Lianjing Zhao
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiahui Wang
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Haolu Wang
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yangyuan Qiu
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zijian Dong
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Chunling Zhang
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Mingyuan Liu
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Xuelin Wang
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xue Bai
- State Key Laboratory of Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
14
|
Rapid, Sensitive and Simultaneous Detection of Two Wheat RNA Viruses Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA). LIFE (BASEL, SWITZERLAND) 2022; 12:life12121952. [PMID: 36556317 PMCID: PMC9788578 DOI: 10.3390/life12121952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/09/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
In China, wheat yellow mosaic disease is mostly caused by wheat yellow mosaic virus (WYMV) and Chinese wheat mosaic virus (CWMV). If wheat is co-infected with these two viruses, it can cause severe yellow mosaic symptoms and yield losses. Early detection of viruses is crucial for preventing disease in the field. In this study, we optimized a sensitive, specific reverse transcription recombinase polymerase amplification (RT-RPA) detection method for two viruses, WYMV and CWMV. Two sets of primers were designed based on the capsid protein (CP)-encoding genes of the two viruses, and the reaction conditions were determined. The RT-RPA method, which amplified the target amplicon by a handheld reaction mixture for 20 min, was more sensitive than PCR-CP in the detection of WYMV. Finally, the RT-RPA method was performed on 110 randomly selected field samples, demonstrating its applicability to samples from different regions and specificity for co-infected samples. This study not only describes an improved method for detecting WYMV and CWMV using RT-RPA but also demonstrates the potential of this method, which could be applied under field conditions.
Collapse
|
15
|
Lin Z, Lu J, Wu S, Lin X, Zheng L, Lou Y, Xiao X. A novel detection method for the pathogenic Aeromonas hydrophila expressing aerA gene and/or hlyA gene based on dualplex RAA and CRISPR/Cas12a. Front Microbiol 2022; 13:973996. [PMID: 36274718 PMCID: PMC9585296 DOI: 10.3389/fmicb.2022.973996] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/13/2022] [Indexed: 11/20/2022] Open
Abstract
Aeromonas hydrophila is an emerging waterborne and foodborne pathogen with pathogenicity to humans and warm water fishes, which severely threatens human health, food safety and aquaculture. A novel method for the rapid, accurate, and sensitive detection of pathogenic A. hydrophila is still needed to reduce the impact on human health and aquaculture. In this work, we developed a rapid, accurate, sensitive, and visual detection method (dRAA-CRISPR/Cas12a), without elaborate instruments, integrating the dualplex recombinase-assisted amplification (dRAA) assay and CRISPR/Cas12a system to detect pathogenic A. hydrophila expressing aerA and/or hlyA virulence genes. The dRAA-CRISPR/Cas12a method has high sensitivity, which can rapidly detect (about 45 min) A. hydrophila with the limit of detection in 2 copies of genomic DNA per reaction, and has high specificity for three pathogenic A. hydrophila strains (aerA+hlyA−, aerA−hlyA+, and aerA+hlyA+). Moreover, dRAA-CRISPR/Cas12a method shows satisfactory practicability in the analysis of the spiked human blood and stool and fish samples. These results demonstrate that our developed pathogenic A. hydrophila detection method, dRAA-CRISPR/Cas12a, is a promising potential method for the early diagnosis of human A. hydrophila infection and on-site detection of A. hydrophila in food and aquaculture.
Collapse
|
16
|
Tamer C, Benkaroun J, Kurucay HN, Albayrak H, Weidmann M. Development of a recombinase polymerase amplification assay for viral haemorrhagic septicemia virus. JOURNAL OF FISH DISEASES 2022; 45:1065-1071. [PMID: 35467756 DOI: 10.1111/jfd.13629] [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: 02/14/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Viral diseases of fish cause significant economic losses in the aquaculture industry. Viral haemorrhagic septicemia virus (VHSV) is one of the most important viral diseases that affects more than 80 fish species. Detection of the disease, especially in the field, is critical to managing disease prevention and control programmes. Recombinase polymerase amplification (RPA) is an isothermal method with a very short amplification period and a single incubation temperature ranging from 37 to 42°C, which is a good alternative to the polymerase chain reaction (PCR). This study aimed to develop an RPA assay as sensitive as a real-time RT-PCR to detect VHSV. For this purpose, primers and probes are designed for the same targeted region of gG of VHSV. The ssRNA standards were prepared to find the detection limits of the assay. Detection limits were found ten-fold differences between real-time RT-PCR and real-time RT-RPA. While the detection limit of the RT-PCR was found as 95.5 viral RNA molecules/reaction in 95% probit value, the detection limit of RT-RPA was found as 943.75 viral RNA molecules/reaction in 95% probit value using ssRNA standards. These results show that RPA is a suitable test for VHSV Ie detection.
Collapse
Affiliation(s)
- Cuneyt Tamer
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | | | - Hanne Nur Kurucay
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Harun Albayrak
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Manfred Weidmann
- Medizinische Hochschule Brandenburg Theodor Fontane, Senftenberg, Germany
| |
Collapse
|
17
|
Development and Application of a Visual Duck Meat Detection Strategy for Molecular Diagnosis of Duck-Derived Components. Foods 2022; 11:foods11131895. [PMID: 35804711 PMCID: PMC9266182 DOI: 10.3390/foods11131895] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
To make meat adulteration detection systems faster, simpler and more efficient, we established a duck-derived meat rapid detection Recombinase Polymerase Amplification (dRPA) method by using interleukin 2 (IL-2) from nuclear genomic DNA as the target gene to design specific primers. We tested the dRPA detection system by comparing its sensitivity and specificity using real-time fluorescent PCR technology. By adjusting the ratio of reagents, this method shortens the time of DNA extraction and visualizes results in combination with colloidal gold immunoassay strips. Our results demonstrate that this dRPA method could specifically detect duck-derived components with a sensitivity of up to 23 copies/μL and the accuracy of the results is consistent with real-time fluorescent PCR. Additionally, dRPA can detect at least 1% of the duck meat content by mixing beef and mutton with duck meat in different proportions, which was verified by spot-check market samples. These results can be visualized with colloidal gold immunoassay strips with the same accuracy as real-time fluorescent RPA. dRPA can complete detection within 30 min, which shortens existing detection time and quickly visualizes the detection results on-site. This lays the groundwork for future large-scale standardized duck origin detection.
Collapse
|
18
|
Wang R, Li Y, Pang Y, Zhang F, Li F, Luo S, Qian C. VIR-CRISPR: Visual in-one-tube ultrafast RT-PCR and CRISPR method for instant SARS-CoV-2 detection. Anal Chim Acta 2022; 1212:339937. [PMID: 35623788 PMCID: PMC9100291 DOI: 10.1016/j.aca.2022.339937] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 02/07/2023]
Abstract
Until now, corona virus disease 2019 (COVID-19) remained to be an enormous threat for global health. As one viral illness induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), versatile, rapid and sensitive method for SARS-CoV-2 detection in early stage is urgently needed. Here, we reported an ultrasensitive and visual in-one-tube detection method which could be accomplished within half an hour from sampling-to-result. By integrating all reactions in one tube, liquid handling steps were omitted and amplicon contamination could be totally avoided. Magnetic beads were employed to achieve the fast extraction of viral nucleic acid and increase the sensitivity. Using portable thermocycler and blue light, the fluorescent results could be directly observed by naked eyes. The proposed method is of higher specificity and sensitivity, nearly at single molecule level. More important, results demonstrated 100% positive detection rate for 40 clinical samples, which was consistent with standard RT-PCR. Thus, our method is considerably simple, rapid, sensitive and accurate, holding great promise for the instant detecting of viruses including SARS-CoV-2 and the next generation of molecular diagnosis.
Collapse
Affiliation(s)
- Rui Wang
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China,Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China
| | - Yongfang Li
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China,Corresponding author
| | - Yanan Pang
- Changhai Hospital, Second Military Medical University, Shanghai, 200433, China,Corresponding author
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Fuyou Li
- Department of Chemistry & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, 200433, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China,Corresponding author
| | - Chunyan Qian
- Clinical Laboratory, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 311100, China,School of Life Sciences, Fudan University, Shanghai, 200438, China,Corresponding author. Clinical Laboratory, Linping Campus, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 311100, China
| |
Collapse
|
19
|
Stringer OW, Li Y, Bossé JT, Forrest MS, Hernandez-Garcia J, Tucker AW, Nunes T, Costa F, Mortensen P, Velazquez E, Penny P, Rodriguez-Manzano J, Georgiou P, Langford PR. Rapid Detection of Actinobacillus pleuropneumoniae From Clinical Samples Using Recombinase Polymerase Amplification. Front Vet Sci 2022; 9:805382. [PMID: 35400111 PMCID: PMC8990124 DOI: 10.3389/fvets.2022.805382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/25/2022] [Indexed: 11/30/2022] Open
Abstract
Actinobacillus pleuropneumoniae (APP) is the causative agent of porcine pleuropneumonia, resulting in high economic impact worldwide. There are currently 19 known serovars of APP, with different ones being predominant in specific geographic regions. Outbreaks of pleuropneumonia, characterized by sudden respiratory difficulties and high mortality, can occur when infected pigs are brought into naïve herds, or by those carrying different serovars. Good biosecurity measures include regular diagnostic testing for surveillance purposes. Current gold standard diagnostic techniques lack sensitivity (bacterial culture), require expensive thermocycling machinery (PCR) and are time consuming (culture and PCR). Here we describe the development of an isothermal point-of-care diagnostic test - utilizing recombinase polymerase amplification (RPA) for the detection of APP, targeting the species-specific apxIVA gene. Our APP-RPA diagnostic test achieved a sensitivity of 10 copies/μL using a strain of APP serovar 8, which is the most prevalent serovar in the UK. Additionally, our APP-RPA assay achieved a clinical sensitivity and specificity of 84.3 and 100%, respectively, across 61 extracted clinical samples obtained from farms located in England and Portugal. Using a small subset (n = 14) of the lung tissue samples, we achieved a clinical sensitivity and specificity of 76.9 and 100%, respectively) using lung imprints made on FTA cards tested directly in the APP-RPA reaction. Our results demonstrate that our APP-RPA assay enables a suitable rapid and sensitive screening tool for this important veterinary pathogen.
Collapse
Affiliation(s)
- Oliver W. Stringer
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Janine T. Bossé
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Juan Hernandez-Garcia
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Tiago Nunes
- Ceva Animal Health Ltd., Saúde Animal, Algés, Portugal
| | | | | | | | - Paul Penny
- Ceva Animal Health Ltd., Amersham, United Kingdom
| | - Jesus Rodriguez-Manzano
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| |
Collapse
|
20
|
Development and Application of Recombinase Polymerase Amplification Assays for Rapid Detection of Escherichia coli O157 in Food. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
21
|
Cassedy A, Della Bartola M, Parle-McDermott A, Mullins E, O'Kennedy R. A one-step reverse transcription recombinase polymerase amplification assay for lateral flow-based visual detection of PVY. Anal Biochem 2021; 642:114526. [PMID: 34922917 DOI: 10.1016/j.ab.2021.114526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022]
Abstract
Potato virus Y (PVY) is an abundant and damaging virus which reduces crop yield and marketability. Accurate detection of this economically important virus both in-field and in seed potato is considered essential in the control of PVY spread. Current detection methods are focused on immunodetection and PCR-based methods, however, identification of PVY through isothermal amplification is a promising avenue for developing accessible, on-site diagnostics with quick turnaround times. In this work, a rapid recombinase polymerase amplification assay was developed which could readily amplify PVY nucleic acids with good sensitivity and specificity. Additionally, this assay was shown to be capable of amplification directly from RNA in a one-step amplification process, without the need for prior reverse transcription. The assay was coupled with lateral flow technology to provide a rapid visual confirmation of amplification. This nucleic-acid lateral flow immunoassay could feasibly be employed in-field, or at any location where testing is required, to aid in the detection and control of PVY.
Collapse
Affiliation(s)
- Arabelle Cassedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | | | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, Carlow, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Hamad Bin Khalifa University, Education City, Doha, Qatar; Qatar Foundation, Education City, Doha, Qatar.
| |
Collapse
|
22
|
Xiao X, Lin Z, Huang X, Lu J, Zhou Y, Zheng L, Lou Y. Rapid and Sensitive Detection of Vibrio vulnificus Using CRISPR/Cas12a Combined With a Recombinase-Aided Amplification Assay. Front Microbiol 2021; 12:767315. [PMID: 34745075 PMCID: PMC8566878 DOI: 10.3389/fmicb.2021.767315] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/04/2021] [Indexed: 12/19/2022] Open
Abstract
Vibrio vulnificus is an important zoonotic and aquatic pathogen and can cause vibriosis in humans and aquatic animals (especially farmed fish and shrimp species). Rapid and sensitive detection methods for V. vulnificus are still required to diagnose human vibriosis early and reduce aquaculture losses. Herein, we developed a rapid and sensitive diagnostic method comprising a recombinase-aided amplification (RAA) assay and the CRISPR/Cas12a system (named RAA-CRISPR/Cas12a) to detect V. vulnificus. The RAA-CRISPR/Cas12a method allows rapid and sensitive detection of V. vulnificus in 40 min without a sophisticated instrument, and the limit of detection is two copies of V. vulnificus genomic DNA per reaction. Meanwhile, the method shows satisfactory specificity toward non-target bacteria and high accuracy in the spiked blood, stool, and shrimp samples. Therefore, our proposed rapid and sensitive V. vulnificus detection method, RAA-CRISPR/Cas12a, has great potential for early diagnosis of human vibriosis and on-site V. vulnificus detection in aquaculture and food safety control.
Collapse
Affiliation(s)
- Xingxing Xiao
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ziqin Lin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xianhui Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Jinfang Lu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yan Zhou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
23
|
Guaman-Bautista LP, Moreta-Urbano E, Oña-Arias CG, Torres-Arias M, Kyriakidis NC, Malcı K, Jonguitud-Borrego N, Rios-Solis L, Ramos-Martinez E, López-Cortés A, Barba-Ostria C. Tracking SARS-CoV-2: Novel Trends and Diagnostic Strategies. Diagnostics (Basel) 2021; 11:1981. [PMID: 34829328 PMCID: PMC8621220 DOI: 10.3390/diagnostics11111981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic has had an enormous impact on economies and health systems globally, therefore a top priority is the development of increasingly better diagnostic and surveillance alternatives to slow down the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In order to establish massive testing and contact tracing policies, it is crucial to have a clear view of the diagnostic options available and their principal advantages and drawbacks. Although classical molecular methods such as RT-qPCR are broadly used, diagnostic alternatives based on technologies such as LAMP, antigen, serological testing, or the application of novel technologies such as CRISPR-Cas for diagnostics, are also discussed. The present review also discusses the most important automation strategies employed to increase testing capability. Several serological-based diagnostic kits are presented, as well as novel nanotechnology-based diagnostic methods. In summary, this review provides a clear diagnostic landscape of the most relevant tools to track COVID-19.
Collapse
Affiliation(s)
- Linda P. Guaman-Bautista
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Erick Moreta-Urbano
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Claudia G. Oña-Arias
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador; (L.P.G.-B.); (E.M.-U.); (C.G.O.-A.)
| | - Marbel Torres-Arias
- Immunology and Virology Laboratory, Department of Life Science and Agriculture, Universidad de las Fuerzas Armadas, Quito 171103, Ecuador;
| | - Nikolaos C. Kyriakidis
- Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas, Quito 170125, Ecuador;
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9LE, UK; (K.M.); (N.J.-B.); (L.R.-S.)
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH8 9LE, UK
| | - Espiridion Ramos-Martinez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 4510, Mexico;
| | - Andrés López-Cortés
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170147, Ecuador;
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170901, Ecuador
| |
Collapse
|
24
|
Tortajada-Genaro LA, Maquieira A. Multiple recombinase polymerase amplification and low-cost array technology for the screening of genetically modified organisms. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
25
|
Cantera JL, White HN, Forrest MS, Stringer OW, Belizario VY, Storey HL, de Hostos EL, de los Santos T. Sensitive and semiquantitative detection of soil-transmitted helminth infection in stool using a recombinase polymerase amplification-based assay. PLoS Negl Trop Dis 2021; 15:e0009782. [PMID: 34516554 PMCID: PMC8459997 DOI: 10.1371/journal.pntd.0009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 09/23/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Soil-transmitted helminths (STHs) are parasitic nematodes that inhabit the human intestine. They affect more than 1.5 billion people worldwide, causing physical and cognitive impairment in children. The global strategy to control STH infection includes periodic mass drug administration (MDA) based on the results of diagnostic testing among populations at risk, but the current microscopy method for detecting infection has diminished sensitivity as the intensity of infection decreases. Thus, improved diagnostic tools are needed to support decision-making for STH control programs. Methodology We developed a nucleic acid amplification test based on recombinase polymerase amplification (RPA) technology to detect STH in stool. We designed primers and probes for each of the four STH species, optimized the assay, and then verified its performance using clinical stool samples. Principal findings Each RPA assay was as sensitive as a real-time polymerase chain reaction (PCR) assay in detecting copies of cloned target DNA sequences. The RPA assay amplified the target in DNA extracted from human stool samples that were positive for STH based on the Kato-Katz method, with no cross-reactivity of the non-target genomic DNA. When tested with clinical stool samples from patients with infections of light, moderate, and heavy intensity, the RPA assays demonstrated performance comparable to that of real-time PCR, with better results than Kato-Katz. This new rapid, sensitive and field-deployable method for detecting STH infections can help STH control programs achieve their goals. Conclusions Semi-quantitation of target by RPA assay is possible and is comparable to real-time PCR. With proper instrumentation, RPA assays can provide robust, semi-quantification of STH DNA targets as an alternative field-deployable indicator to counts of helminth eggs for assessing infection intensity. More than 1.5 billion people are infected with parasitic intestinal worms called soil-transmitted helminths. Infection is transmitted by helminth eggs in human feces, which contaminate soil in areas with poor sanitation. Adverse health effects include physical and cognitive impairment in children. A key strategy to control infection is periodic mass drug administration for populations with a high prevalence of disease based on the results of diagnostic testing. The current microscopy method for detecting infection, however, has limited ability to detect disease as the intensity of infection decreases with repeated mass drug administration. To address limitations of current diagnostic methods, we developed a novel technique to diagnose infections, including those at very low levels of intensity, by detecting helminth DNA in stool samples. Our initial studies suggest that the new diagnostic technique reliably detects the presence of intestinal worms, even at low intensities of infection, and may be more useful than currently available diagnostic tools for guiding the use of periodic mass drug administration to eliminate disease in low-resource settings.
Collapse
Affiliation(s)
| | | | | | | | - Vicente Y. Belizario
- Department of Parasitology, College of Public Health, University of the Philippines, Ermita, Manila, Philippines
| | | | | | | |
Collapse
|
26
|
Song Z, Yang X, Zhang X, Luan M, Guo B, Liu C, Pan J, Mei S. Rapid and Visual Detection of Meloidogyne hapla Using Recombinase Polymerase Amplification Combined with a Lateral Flow Dipstick Assay. PLANT DISEASE 2021; 105:2697-2703. [PMID: 33267643 DOI: 10.1094/pdis-06-20-1345-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The northern root-knot nematode, Meloidogyne hapla, is a biotrophic parasite that infects many crops and causes severe economic losses worldwide. Rapid and accurate detection of M. hapla is crucial for disease forecasting and control. We developed a recombinase polymerase amplification combined with a lateral flow dipstick (RPA-LFD) assay for rapid detection of M. hapla. The primers and probe were designed based on the effector gene 16D10 sequence and were highly specific to M. hapla. The RPA reaction was performed at a wide range of temperatures from 25 to 45°C within 5 to 25 min, and the amplicon was visualized directly on the LFD within 5 min. The detection limits of the RPA-LFD assay were 10-3 females and 10-2 second-stage juveniles/0.5 g of soil, which was 10 times more sensitive than the conventional PCR assay. In addition, the RPA-LFD assay can detect M. hapla from infested plant roots and soil samples, and the entire detection process can be completed within 1.5 h. These results indicate that the RPA-LFD assay is a simple, rapid, specific, sensitive, and visual method that can be used for rapid detection of M. hapla in the field and in resource-limited conditions.
Collapse
Affiliation(s)
- Zhiqiang Song
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Xiaowei Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Bing Guo
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Chunjie Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Jiangpeng Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| | - Shiyong Mei
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China
| |
Collapse
|
27
|
Development of an on-spot and rapid recombinase polymerase amplification assay for Aspergillus flavus detection in grains. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
28
|
Li H, Feng J, Wang Y, Liu G, Chen X, Fu L. Instant and Multiple DNA Extraction Method by Microneedle Patch for Rapid and on-Site Detection of Food Allergen-Encoding Genes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6879-6887. [PMID: 34105975 DOI: 10.1021/acs.jafc.1c01077] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA-based detection methods are highly promising for risk assessment in the food sector, such as tracing the existence of food allergens. However, due to the complexity of food matrices, cumbersome protocols are often needed to isolate the DNA components, which hinder the achievement of rapid and on-site detection. Herein, an instant and multiple DNA extraction method was developed based on the poly(vinyl alcohol) microneedle (MN) patch. With simple press and peel-off operations within 1 min, samples suitable for DNA-based analysis such as polymerase chain reaction (PCR) could be collected. By further combining with the recombinase polymerase amplification assay, rapid screening of the allergenic risks in complex samples such as shrimp ball and cheesecake could be achieved within 30 min. The MN-based DNA extraction method not only was a potential alternative to the traditional DNA extraction method but provided a transformative approach in realizing rapid, on-site detection of foodborne hazards in collaborating with fast DNA-based assays.
Collapse
Affiliation(s)
- Huan Li
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Jiesi Feng
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Yanbo Wang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| | - Guangming Liu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen 361021, P. R. China
| | - Xiaojing Chen
- College of Electrical and Electronic Engineering, Wenzhou University, Wenzhou 325035, P. R. China
| | - Linglin Fu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, P. R. China
| |
Collapse
|
29
|
Rapid detection of multidrug-resistant tuberculosis based on allele-specific recombinase polymerase amplification and colorimetric detection. PLoS One 2021; 16:e0253235. [PMID: 34115793 PMCID: PMC8195408 DOI: 10.1371/journal.pone.0253235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) poses a serious threat to TB control. Early diagnosis and proper treatment are essential factors to limit the spread of the disease. The existing molecular tests for MDR-TB usually require specific instruments, steady power supply, and routine maintenance, which might be obstacles for low-resource settings. This study aimed to develop allele-specific isothermal recombinase polymerase amplification (allele-specific RPA) to simultaneously detect the most common mutations in the rpoB gene at codons 516, 526, and 531, which are associated with rifampicin resistance, and in the katG gene at codon 315, which is related to isoniazid resistance. Allele-specific primers targeting four major mutations, rpoB516, rpoB526, rpoB531, and katG315, were constructed and used in individual RPA reactions. The RPA amplicons were endpoints detected by the naked eye immediately after applying SYBR Green I. The optimised RPA assay was evaluated with the Mycobacterium tuberculosis wild-type strain H37Rv and 141 clinical M. tuberculosis isolates. The results revealed that allele-specific RPA combined with SYBR Green I detection (AS-RPA/SYBR) detected these four major mutations with 100% sensitivity and specificity relative to DNA sequencing. The limits of detection for these particular mutations with AS-RPA/SYBR were 5 ng. As a result of the outstanding performance of AS-RPA/SYBR, including its easy setup, speed, lack of a specific instrument requirement, and lack of cross-reaction with other bacteria, this technique may be integrated for the molecular diagnosis of MDR-TB, especially in low-resource settings.
Collapse
|
30
|
Liu L, Hu R, Li C, Li X, Ni W, Yao R, Zhang M, Li H, Xu Y, Ullah Y, Hu S. Rapid visual detection of FecB gene expression in sheep. Open Life Sci 2021; 15:902-911. [PMID: 33817277 PMCID: PMC7874556 DOI: 10.1515/biol-2020-0091] [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: 03/04/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 11/15/2022] Open
Abstract
Sheep play an important role in agricultural production and people's lives, and fecundity is one of the most important economic traits of sheep for sheep breeders. The Booroola fecundity (FecB) gene has a certain correlation with litter size in sheep. Therefore, this study aims to detect FecB expression quickly, accurately and visually. Here, we used the nucleic acid dye SYBR Green I to detect FecB with the amplification refractory mutation system (ARMS), which can efficiently, rapidly, economically and visually detect FecB expression in sheep. After ARMS polymerase chain reaction (PCR), SYBR Green I was directly added to the ARMS products, and whether the sheep carried FecB was judged by directly observing the color change in the PCR tube. Homozygous (BB) or heterozygous (B+) samples with FecB mutation were bright green, while wild type (++) samples without FecB were orange yellow. This study suggested that this method has 100% accuracy and 0.5 ng/µL sensitivity. To our knowledge, this is the first report that shows the integration of the ARMS with SYBR Green I to detect FecB expression in sheep visually.
Collapse
Affiliation(s)
- Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China.,College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| |
Collapse
|
31
|
Zheng Y, Hu P, Ren H, Wang H, Cao Q, Zhao Q, Li H, Zhang H, Liu Z, Li Y, Wang C, Liu Z, Lu S. RPA-SYBR Green I based instrument-free visual detection for pathogenic Yersinia enterocolitica in meat. Anal Biochem 2021; 621:114157. [PMID: 33705723 DOI: 10.1016/j.ab.2021.114157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 10/22/2022]
Abstract
Pathogenic Yersinia (Y.) enterocolitica is the primary causative agent of Yersiniosis, with outbreaks in numerous countries around the world, and causes diarrhea and vomiting in animals and humans. Therefore, an instrument-free and convenient nucleic acid visualization method, RPA-SYBR Green I, was established, which combines recombinase polymerase amplification (RPA) with the fluorescent dye SYBR Green I for the detection of the adhesion gene ail in pathogenic Y. enterocolitica. After optimization of a series of conditions such as primer concentration, the detection of pathogenic Y. enterocolitica could be finally completed within about 20 min (from DNA extraction to observation of results) at an isothermal temperature of 39°C. RPA-SYBR Green I had no cross-reactivity with other bacteria and the detection limit was 101 CFU/μL, with sensitivity equal to that of conventional PCR. The method established in this paper and conventional PCR identified a total of 5 spiked samples and 15 meat samples stored in refrigerated, and it was concluded that there was 100% consistency between the two methods. Overall, RPA-SYBR Green I is a visual and facilitate detection assay that can accurately discover pathogenic Y. enterocolitica.
Collapse
Affiliation(s)
- Yu Zheng
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Pan Hu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Honglin Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Han Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Qi Cao
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Qiang Zhao
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Hanxiao Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Hailing Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Zhanxu Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Yansong Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Cong Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Zengshan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Shiying Lu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
| |
Collapse
|
32
|
Pumford EA, Lu J, Spaczai I, Prasetyo ME, Zheng EM, Zhang H, Kamei DT. Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics. Biosens Bioelectron 2020; 170:112674. [PMID: 33035900 PMCID: PMC7529604 DOI: 10.1016/j.bios.2020.112674] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023]
Abstract
Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.
Collapse
Affiliation(s)
- Elizabeth A Pumford
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Jiakun Lu
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Iza Spaczai
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Matthew E Prasetyo
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Elaine M Zheng
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Hanxu Zhang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Daniel T Kamei
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
33
|
Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
Collapse
Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
34
|
Establishment of Recombinase Polymerase Amplification assay for rapid and sensitive detection of Orientia tsutsugamushi in Southeast Asia. Acta Trop 2020; 210:105541. [PMID: 32492397 DOI: 10.1016/j.actatropica.2020.105541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 11/20/2022]
Abstract
Scrub typhus, caused by Orientia tsutsugamushi, is a common fever in parts of Southern and Southeast Asia. As delayed diagnosis of scrub typhus leads to inappropriate treatment and high mortality rates, of up to 70%, sensitive and rapid detection of O. tsutsugamushi is required for timely and appropriate treatment. Molecular assays, such as PCR and real-time PCR, have been shown to be more sensitive than conventional immunoassay, however, they are only available in centralized laboratories. In contrast to PCR assays, Recombinase Polymerase Amplification (RPA) is conducted under a constant temperature ranging from 24°C to 45°C. Therefore, this technology is very promising for nucleic acid testing in the field, and in resource-limited areas. An RPA assay for the detection of O. tsutsugamushi based on the target gene encoding for the 47 kDa outer membrane protein has been reported, but the primer and probe sequences of this assay are suboptimal for detection of the majority of recently published sequences of O. tsutsugamushi isolates from Southeast Asia. We have established a real-time RPA assay with primer and probe sequences that are optimized for most Southeast Asia's isolates of O. tsutsugamushi. As a result, the new RPA assay showed better performance than the previous assay in detecting O. tsutsugamushi in clinical samples of scrub typhus cases found in Vietnam. The specificity of RPA assay was also evaluated using genomic DNA from microorganisms commonly encountered in the differential diagnosis of scrub typhus, and blood samples from healthy controls and O. tsutsugamushi negative confirmed cases.
Collapse
|
35
|
Direct detection of methicillin-resistant in Staphylococcus spp. in positive blood culture by isothermal recombinase polymerase amplification combined with lateral flow dipstick assay. World J Microbiol Biotechnol 2020; 36:162. [PMID: 32989593 DOI: 10.1007/s11274-020-02938-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
Abstract
Methicillin-resistant staphylococci (MRS) are important antimicrobial-resistant pathogens in sepsis. Conventional blood cultures take 24-72 h. The polymerase chain reaction (PCR)-based methods give faster results (2-3 h) but need expensive thermal cyclers. We therefore developed an isothermal recombinase polymerase amplification (RPA) combined with lateral flow dipstick (LFD) assay for rapid detection of MRS in spiked blood culture samples. Fifty-six clinical isolates including 38 mecA-carrying staphylococci and 18 non-mecA-carrying organisms as confirmed by PCR methods were studied. RPA primer set and probe specific for mecA gene (encoding penicillin-binding protein 2a) were designed. RPA reaction was carried out under isothermal condition (45 °C) within 20 min and read by LFD in 5 min. The RPA-LFD provided 92.1% (35/38) sensitivity for identifying MRS in positive blood culture samples, and no cross-amplification was found (100% specificity). This test failed to detect three mecA-carrying S.sciuri isolates. The detection limits of RPA-LFD method for identifying MRS were equal to those of PCR method. The RPA-LFD is simple, fast, and user-friendly. This method could detect the mecA gene directly from the positive blood culture samples without requirement for special equipment. This method would be useful for appropriate antibiotic therapy and infection control, particularly in a low-resource setting.
Collapse
|
36
|
Kanitchinda S, Srisala J, Suebsing R, Prachumwat A, Chaijarasphong T. CRISPR-Cas fluorescent cleavage assay coupled with recombinase polymerase amplification for sensitive and specific detection of Enterocytozoon hepatopenaei. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 27:e00485. [PMID: 32577410 PMCID: PMC7301165 DOI: 10.1016/j.btre.2020.e00485] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/08/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022]
Abstract
Enterocytozoon hepatopenaei (EHP) is a parasite that infects pacific whiteleg shrimp, Penaeus vannamei, causing growth retardation and uneven size distributions that lead to severe losses in shrimp productivity. Routine monitoring is crucial to timely prevention and management of EHP, but field-deployable diagnostic kits for EHP are still scarce. Here, we proposed the use of recombinase polymerase amplification (RPA) and CRISPR-Cas12a fluorescence assay, henceforth RPA-Cas12a, for detection of EHP. Targeting ptp2 gene, RPA-Cas12a could detect as few as 50 copies of DNA and showed no reactivity with closely related microsporidia. The entire procedure could be performed at a temperature close to 37 °C within 1 h. Naked eye visualization was possible with UV/blue-light excitation or lateral flow detection. Thus, RPA-Cas12a is a rapid, sensitive and specific detection platform that requires no sophisticated equipment and shows promise for on-site surveillance of EHP.
Collapse
Key Words
- CRISPR, clustered regularly interspaced short palindromic repeats
- CRISPR-Cas12a
- Cas, CRISPR-associated protein
- EHP, Enterocytozoon hepatopenaei
- Eca, Enterospora canceri
- Enterocytozoon hepatopenaei
- FB, FAM-ssDNA-Biotin reporter
- FQ, fluorescent-quencher reporter
- Her, Hepatospora eriocheir
- IHHNV, infectious hypodermal and hematopoietic necrosis virus
- LFD, lateral flow dipstick
- Lateral flow detection
- NTC, no-template control
- PAM, protospacer adjacent motif
- RPA
- RPA, recombinase polymerase amplification
- RPA-Cas12a, RPA coupled with Cas12a cleavage assay
- SWP-PCR, nested PCR targeting swp
- WSSV, white spot syndrome virus
- ptp2, polar tube protein 2
- swp, spore wall protein
Collapse
Affiliation(s)
- Suthasinee Kanitchinda
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Jiraporn Srisala
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group (AAQG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Road, Bangkok 10400, Thailand
| | - Rungkarn Suebsing
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group (AAQG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Road, Bangkok 10400, Thailand
| | - Anuphap Prachumwat
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group (AAQG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Road, Bangkok 10400, Thailand
| | - Thawatchai Chaijarasphong
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| |
Collapse
|
37
|
Wang X, Chen Y, Chen X, Peng C, Wang L, Xu X, Wu J, Wei W, Xu J. A highly integrated system with rapid DNA extraction, recombinase polymerase amplification, and lateral flow biosensor for on-site detection of genetically modified crops. Anal Chim Acta 2020; 1109:158-168. [PMID: 32252899 DOI: 10.1016/j.aca.2020.02.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 01/29/2023]
Abstract
With the large-scale planting of genetically modified (GM) crops, the development of a rapid and convenient method for on-site monitoring GM crops is needed. In this study, a duplex recombinase polymerase amplification (DRPA)-based, quick and simple detection system is presented for on-site detection of GM crops. In this system, a rapid DNA extraction method, a DRPA, and a lateral flow biosensor (LFB) are integrated to allow for rapid DNA extraction and amplification, and fast visualization of the detection results. Using the rapid DNA extraction method, high-quality DNA suitable for RPA and polymerase chain reaction (PCR) was quickly isolated from various crops within 5 min. Utilizing the optimal DRPA assay, the universal screening sequences (Cauliflower mosaic virus 35S promoter [35S] and Agrobacterium tumefaciens NOS terminator [NOS]) were rapidly and simultaneously amplified with high selectivity and sensitivity. The sensitivity threshold of the DRPA assay was ∼10 copies for GM soybean genomic DNA and 100 ng DNA of 0.1% GM soybean. In combination with the LFB in an enclosed cassette, the entire detection process was performed in approximately 20-30 min and eliminated the carryover contamination. No special or expensive equipment was needed for the detection process. The system was successfully applied and validated for on-site detection of GM rice, demonstrating its suitability for on-site testing of GM crops and high potential for application to other fields, especially in low-resource regions that require rapid detection of DNA targets.
Collapse
Affiliation(s)
- Xiaofu Wang
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, 310021, China
| | - Yu Chen
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; College of Chemistry and Life Science, Shenyang Normal University, Shenyang, 110034, China
| | - Xiaoyun Chen
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cheng Peng
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, 310021, China
| | - Liu Wang
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Wei Wei
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou, 310021, China
| | - Junfeng Xu
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
38
|
Wang X, Xie S, Chen X, Peng C, Xu X, Wei W, Ma T, Cai J, Xu J. A rapid and convenient method for on-site detection of MON863 maize through real-time fluorescence recombinase polymerase amplification. Food Chem 2020; 324:126821. [PMID: 32361093 DOI: 10.1016/j.foodchem.2020.126821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 11/16/2022]
Abstract
As large-scale planting of genetically modified (GM) crops increases, the development of a rapid and convenient method for on-site detection of GM crops is important. We combined the advantages of recombinase polymerase amplification (RPA) and fluorescence detection to establish a rapid, sensitive, specific, and simple detection platform for on-site detection of MON863 maize. Test samples were added directly to the platform after simple pre-treatment with a DNA extraction-free method. Results were obtained through real-time monitoring with a portable instrument, which facilitated sample-in/answer-out on-site detection. The entire detection process, including sample preparation, RPA and identification of amplification results, was accomplished in approximately 10 min. Furthermore, the detection was achieved with a simple and inexpensive portable device. This method has high potential for application in other fields requiring rapid detection of DNA targets, such as in field research, resource-limited areas, and science education.
Collapse
Affiliation(s)
- Xiaofu Wang
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, China
| | - Shilong Xie
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Biology and Food Engineering School, Fuyang Normal University, Fuyang 236037, China
| | - Xiaoyun Chen
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, China
| | - Cheng Peng
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, China
| | - Xiaoli Xu
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, China
| | - Wei Wei
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, China
| | - Tongfu Ma
- Biology and Food Engineering School, Fuyang Normal University, Fuyang 236037, China
| | - Jian Cai
- Biology and Food Engineering School, Fuyang Normal University, Fuyang 236037, China
| | - Junfeng Xu
- State Key Laboratory for Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture of China, Hangzhou 310021, China.
| |
Collapse
|
39
|
Ma B, Li J, Chen K, Yu X, Sun C, Zhang M. Multiplex Recombinase Polymerase Amplification Assay for the Simultaneous Detection of Three Foodborne Pathogens in Seafood. Foods 2020; 9:E278. [PMID: 32138267 PMCID: PMC7143093 DOI: 10.3390/foods9030278] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 12/24/2022] Open
Abstract
Foodborne pathogens can cause foodborne illness. In reality, one food sample may carry more than one pathogen. A rapid, sensitive, and multiple target method for bacteria detection is crucial in food safety. For the simultaneous detection of Staphylococcus aureus, Vibrio parahaemolyticus, and Salmonella Enteritidis, multi-objective recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD) was developed in this study. The whole process, including amplification and reading, can be completed in 15 min at 37 °C. The detection limits were 2.6 × 101 CFU/mL for Staphylococcus aureus, 7.6 × 101 CFU/mL for Vibrio parahaemolyticus, and 1.29 × 101 CFU/mL for Salmonella Enteritidis. Moreover, colored signal intensities on test lines were measured by a test strip reader to achieve quantitative detection for Staphylococcus aureus (R2 = 0.9903), Vibrio parahaemolyticus (R2 = 0.9928), and Salmonella Enteritidis (R2 = 0.9945). In addition, the method demonstrated good recoveries (92.00%-107.95%) in the testing of spiked food samples. Therefore, the multiplex LFD-RPA assay is a feasible method for the rapid, sensitive, and quantitative detection of bacterial pathogens in seafood.
Collapse
Affiliation(s)
- Biao Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (B.M.); (J.L.); (K.C.); (X.Y.)
| | - Jiali Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (B.M.); (J.L.); (K.C.); (X.Y.)
| | - Kai Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (B.M.); (J.L.); (K.C.); (X.Y.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (B.M.); (J.L.); (K.C.); (X.Y.)
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Science (SLU), SE-75007 Uppsala, Sweden;
| | - Mingzhou Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (B.M.); (J.L.); (K.C.); (X.Y.)
| |
Collapse
|
40
|
Wang Y, Chen R, Nie X, Zhong Z, Li C, Li K, Huang W, Fu X, Liu J, Nie B. Rapid and sensitive detection of potato virus Y by isothermal reverse transcription-recombinase polymerase amplification assay in potato. Mol Cell Probes 2020; 50:101505. [PMID: 31904418 DOI: 10.1016/j.mcp.2019.101505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/13/2019] [Accepted: 12/27/2019] [Indexed: 12/24/2022]
Abstract
In this study, an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) assay was developed for the efficient and accurate detection of potato virus Y (PVY) under isothermal conditions. This RT-RPA assay was more efficient than the conventional reverse transcription-polymerase chain reaction (RT-PCR) assay as the amplification reaction can be completed in less than 20 min. Moreover, unlike PCR that requires a thermocycler to carry out the DNA amplification through specific temperature phases, RPA assay could be performed under an isothermal condition at a temperature ranging from 25 to 40 °C. A simple instrumentation such as a heating block or a water bath or even anon-instrumental condition such as human hands or a benchtop inside/outside a room during the summer could satisfy the temperature requirement of RPA. The sensitivity of this assay was equivalent to that of the conventional RT-PCR, and the virus can be detected in a minimum of 2 pg of total RNA extracted from the PVY infected potato leaf tissues. The efficacy of the newly developed RT-RPA was then evaluated using field potato leaf and dormancy-broken sprout samples upon enzyme-linked immunosorbent assay (ELISA) screening. Of the 164 PVY-ELISA-positive samples, RT-RPA detected 157 whereas simplex RT-PCR detected 160 and multiplex RT-PCR detected 154. Of the 74 randomly selected PVY-ELISA-negative samples, RT-RPA, simplex RT-PCR and multiplex RT-PCR led to 1, 1 and 0 positive detections, receptively. Overall, RT-RPA and the two RT-PCR assays as well as ELISA exhibited an agreement of 96.6-98.7%, thus demonstrating the suitability of RT-RPA for large scale detection of PVY, irrespective of the strain type of the virus.
Collapse
Affiliation(s)
- Ying Wang
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruhao Chen
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianzhou Nie
- Fredericton Research and Development Center, Agriculture and Agri-Food Canada, 850 Lincoln Road, P. O. Box 20280, Fredericton, New Brunswick, E3B4Z7, Canada
| | - Ziyang Zhong
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyan Li
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kun Li
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Huang
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingyu Fu
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Liu
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bihua Nie
- National Center for Vegetable Improvement (Central China), Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
41
|
Wang Y, Wang X, Gailing O, Xi D. Visual detection of Fusarium proliferatum based on dual-cycle signal amplification and T5 exonuclease. RSC Adv 2020; 10:35131-35135. [PMID: 35515665 PMCID: PMC9056896 DOI: 10.1039/d0ra06559e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022] Open
Abstract
A novel visual detection of Fusarium proliferatum species through recombinase polymerase amplification and rolling circle amplification was established. Single-stranded circle DNA was produced based on one strand of RPA product, which used as a template for rolling circle amplification. Schematic illustration of RPA-RCA-assisted dual amplification for visual detection of F. proliferatum.![]()
Collapse
Affiliation(s)
- Ying Wang
- College of Life Science
- Linyi University
- Linyi 276005
- People's Republic of China
- Faculty of Forest Sciences and Forest Ecology
| | - Xiaoqiang Wang
- Plant Protection Research Center
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences
- Qingdao 266101
- People's Republic of China
| | - Oliver Gailing
- Faculty of Forest Sciences and Forest Ecology
- University of Göttingen
- Göttingen 37077
- Germany
| | - Dongmei Xi
- College of Life Science
- Linyi University
- Linyi 276005
- People's Republic of China
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J. Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 2019; 1099:1-15. [PMID: 31986265 DOI: 10.1016/j.aca.2019.11.056] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022]
Abstract
Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.
Collapse
Affiliation(s)
- Mengyao Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ye
- Zhijiangnan Think Tank, Zhejiang Institute of Science and Technology Information, Hangzhou, 310006, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
| |
Collapse
|
44
|
Chen D, Zhang M, Ma M, Hai H, Li J, Shan Y. A novel electrochemical DNA biosensor for transgenic soybean detection based on triple signal amplification. Anal Chim Acta 2019; 1078:24-31. [PMID: 31358225 DOI: 10.1016/j.aca.2019.05.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 11/17/2022]
Abstract
A novel electrochemical DNA biosensor was developed and MON89788 of soybean transgenic gene sequence was detected based on a strategy of rolling circle amplification (RCA) and gold nanoparticle cube (AuNPC)-labeled multiple probes. First, the mercapto-modified capture DNA was immobilized on the surface of the Fe3O4@Au magnetic nanoparticles via an Au-S bond, and the capture DNA was opened and complementarily hybridized with the target DNA to form a double-stranded DNA. In the 10 × reaction buffer, Exonuclease III (ExoIII) specifically recognized and sheared the double-stranded DNA to release the target DNA, which led to the next round of reaction. Afterward, AuNP cube-loaded ssDNA (AuNPC/DNA) was added with the rolling circle reaction with the help of Phi29 DNA polymerase and T4 ligase. Finally, [Ru(NH3)6]3+ was attracted directly by the anionic phosphate of ssDNA via electrostatic interaction. The determination was carried out by using chronocoulometry (CC), and the CC signal was recorded. The mass amount of DNA strands extended infinitely on the AuNPs cube and numerous [Ru(NH3)6]3+ were absorbed, thus the detected signal was highly amplified. The corresponding CC signal showed a good linear relationship with the logarithm of the target DNA concentration in the range of 1 × 10-16 to 1 × 10-7 mol L-1, with a detection limit of 4.5 × 10-17 mol L-1. Specific gene sequence of MON89788 in soybean samples was determined, and the recoveries ranged from 97.3% to 102.0%. This sensor is one of the most sensitive sensors for genetic sequence assessment at present. Moreover, it demonstrates good selectivity, stability, and reproducibility.
Collapse
Affiliation(s)
- Dongli Chen
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China
| | - Meng Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China
| | - Mingyi Ma
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China
| | - Hong Hai
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China; Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, Guangxi, 541004, China.
| | - Jianping Li
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China; Guangxi Key Laboratory of Electrochemical and Magnetochemical Function Materials, Guangxi, 541004, China.
| | - Yang Shan
- College of Chemistry and Bioengineering, Guilin University of Technology, Guangxi, 541004, China
| |
Collapse
|
45
|
Yang B, Fang X, Kong J. In Situ Sampling and Monitoring Cell-Free DNA of the Epstein-Barr Virus from Dermal Interstitial Fluid Using Wearable Microneedle Patches. ACS APPLIED MATERIALS & INTERFACES 2019; 11:38448-38458. [PMID: 31554395 DOI: 10.1021/acsami.9b12244] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using polymerase chain reaction and genotyping, Epstein-Barr virus cell-free DNA (EBV Cf DNA) was detectable in interstitial fluid (ISF). Microneedles offer a minimally invasive approach to capture such Cf DNA. However, a key challenge of microneedles lies in the ability to specifically isolate biomarkers within a short time. We introduced a hydrogel microneedle patch for rapid and easy capture of EBV Cf DNA from ISF in situ around 15 min, with a maximum capture efficiency of 93.6%. Then, quantification of EBV Cf DNA was achieved by electrochemical recombinase polymerase amplification wearable flexible microfluidics, with a detection limit of 3.7 × 102 copies/μL. Animal tests supported the performance of microneedles for EBV Cf DNA capture. Collectively, these data showed that the microneedle patch may have broad implications for patients with Cf DNA-related disease and cancer metastasis in minimally invasive manners.
Collapse
Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| |
Collapse
|
46
|
Wang B, Wang R, Wang D, Wu J, Li J, Wang J, Liu H, Wang Y. Cas12aVDet: A CRISPR/Cas12a-Based Platform for Rapid and Visual Nucleic Acid Detection. Anal Chem 2019; 91:12156-12161. [PMID: 31460749 DOI: 10.1021/acs.analchem.9b01526] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bei Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Rui Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Daqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Huihui Liu
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China
| |
Collapse
|
47
|
Yang B, Kong J, Fang X. Bandage-like wearable flexible microfluidic recombinase polymerase amplification sensor for the rapid visual detection of nucleic acids. Talanta 2019; 204:685-692. [PMID: 31357353 DOI: 10.1016/j.talanta.2019.06.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/05/2019] [Accepted: 06/08/2019] [Indexed: 12/21/2022]
Abstract
With the development of flexible advanced materials and microfluidic technology, wearable biosensors provide a new strategy for the continuous monitoring of health. In this study, a novel bandage-like wearable flexible microfluidic recombinase polymerase amplification (RPA) sensor was constructed for the rapid and visual detection of nucleic acids. This wearable sensor is triggered by human body heat (30°C-37 °C) and allows for visual nucleic acid (a conserved nucleic acid fragments of zika virus) detection within 10 min. The sensor displays good sensitivity and selectivity, with a detection limit of 10 copies/μL. The wearable sensor has exhibited well-defined accuracy when applied to testing clinical serum samples. In addition, the wearable RPA sensor was proved to be feasible by human trials under different daily activities. This wearable sensor of nucleic acids will probably be of great significance in the field of online pathogen detection for wounds, for tumour biomarker diagnosis, and for the detection of epidermal cell molecular lesions.
Collapse
Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
| |
Collapse
|
48
|
Abudayyeh OO, Gootenberg JS, Kellner MJ, Zhang F. Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13. CRISPR J 2019; 2:165-171. [PMID: 31225754 PMCID: PMC7001462 DOI: 10.1089/crispr.2019.0011] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nucleic acid detection is vital for agricultural applications including trait detection during breeding, pest surveillance, and pathogen identification. Here, we use a modified version of the CRISPR-based nucleic acid detection platform SHERLOCK to quantify levels of a glyphosate resistance gene in a mixture of soybeans and to detect multiple plant genes in a single reaction. SHERLOCK is rapid (∼15 min), quantitative, and portable, and can process crude soybean extracts as input material for minimal nucleic acid sample preparation. This field-ready SHERLOCK platform with color-based lateral flow readout can be applied for detection and quantitation of genes in a range of agricultural applications.
Collapse
Affiliation(s)
- Omar O. Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts; Departments of Harvard Medical School, Boston, Massachusetts
- Brain and Cognitive Science, Harvard Medical School, Boston, Massachusetts
- Biological Engineering, and Harvard Medical School, Boston, Massachusetts
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Jonathan S. Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts; Departments of Harvard Medical School, Boston, Massachusetts
- Brain and Cognitive Science, Harvard Medical School, Boston, Massachusetts
- Biological Engineering, and Harvard Medical School, Boston, Massachusetts
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Max J. Kellner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts; Departments of Harvard Medical School, Boston, Massachusetts
- Brain and Cognitive Science, Harvard Medical School, Boston, Massachusetts
- Biological Engineering, and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
49
|
Zhao G, He H, Wang H. Use of a recombinase polymerase amplification commercial kit for rapid visual detection of Pasteurella multocida. BMC Vet Res 2019; 15:154. [PMID: 31101109 PMCID: PMC6525368 DOI: 10.1186/s12917-019-1889-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Pasteurella multocida (P. multocida) is a bacterium that causes bovine respiratory disease (BRD) and haemorrhagic septicaemia (HS) in cattle, buffaloes and bison. Rapid point-of-care diagnosis or regular testing of Pasteurellosis, therefore, could contribute greatly to early detection, and screening infected animal is important. Up to now, there are no published reports on the use of recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD) for P. multocida detection. Results This study proposes a promising isothermal detection method for P. multocida with the potential to be developed as an on-site test for Pasteurellosis. The method includes an RPA combined with LFD. First, the analytical sensitivity and specificity of P. multocida RPA-LFD were tested. The RPA-LFD, performed at 39 °C, successfully detected P. multocida DNA in 30 min, with a detection limit of up to 120 copies per reaction. Then, the practicability of RPA-LFD was analysed using 62 nasal swabs and 33 fresh lungs samples from 17 different dairy farms. Compared to real-time quantitative PCR (qPCR), the RPA-LFD assay yielded a clinical specificity of 95.15%, positive predictive value (PPV) of 95.15% and 0.958 kappa coefficient. Compared with the culture method, it achieved 100% sensitivity, 67.20% specificity and a 0.572 kappa coefficient. Conclusions These results combined with the simple conditions required for the performance of the RPA-LFD assay, have demonstrated the effectiveness and practicability of the method for development into a regular on-site protocol for the diagnosis of Pasteurellosis.
Collapse
Affiliation(s)
- Guimin Zhao
- Ruminant Disease Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Lixia District, Jinan, 250014, Shandong Province, China
| | - Hongbin He
- Ruminant Disease Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Lixia District, Jinan, 250014, Shandong Province, China.
| | - Hongmei Wang
- Ruminant Disease Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Lixia District, Jinan, 250014, Shandong Province, China.
| |
Collapse
|
50
|
Strobbia P, Ran Y, Crawford BM, Cupil-Garcia V, Zentella R, Wang HN, Sun TP, Vo-Dinh T. Inverse Molecular Sentinel-Integrated Fiberoptic Sensor for Direct and in Situ Detection of miRNA Targets. Anal Chem 2019; 91:6345-6352. [PMID: 30916925 DOI: 10.1021/acs.analchem.9b01350] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular advances have been made in analysis systems for a wide variety of applications ranging from biodiagnostics, biosafety, bioengineering, and biofuel research applications. There are, however, limited practical tools necessary for in situ and accurate detection of nucleic acid targets during field work. New technology is needed to translate these molecular advances from laboratory settings into the real-life practical monitoring realm. The exquisite characteristics (e.g., sensitivity and adaptability) of plasmonic nanosensors have made them attractive candidates for field-ready sensing applications. Herein, we have developed a fiber-based plasmonic sensor capable of direct detection (i.e., no washing steps required) of nucleic acid targets, which can be detected simply by immerging the sensor in the sample solution. This sensor is composed of an optical fiber that is decorated with plasmonic nanoprobes based on silver-coated gold nanostars (AuNS@Ag) to detect target nucleic acids using the surface-enhanced Raman scattering (SERS) sensing mechanism of nanoprobes referred to as inverse molecular sentinels (iMS). These fiber-optrodes can be reused for several detection-regeneration cycles (>6). The usefulness and applicability of the iMS fiber-sensors was tested by detecting target miRNA in extracts from leaves of plants that were induced to have different expression levels of miRNA targets. These fiber-optrodes enable direct detection of miRNA in plant tissue extract without the need for complex assays by simply immersing the fiber in the sample solution. The results indicate the fiber-based sensors developed herein have the potential to be a powerful tool for field and in situ analysis of nucleic acid samples.
Collapse
Affiliation(s)
- Pietro Strobbia
- Fitzpatrick Institute for Photonics , Duke University , Durham , North Carolina 27708 , United States
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Yang Ran
- Fitzpatrick Institute for Photonics , Duke University , Durham , North Carolina 27708 , United States
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology , Jinan University , Guangzhou 510632 , China
| | - Bridget M Crawford
- Fitzpatrick Institute for Photonics , Duke University , Durham , North Carolina 27708 , United States
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Vanessa Cupil-Garcia
- Fitzpatrick Institute for Photonics , Duke University , Durham , North Carolina 27708 , United States
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Rodolfo Zentella
- Department of Biology , Duke University , Durham , North Carolina 27708 , United States
| | - Hsin-Neng Wang
- Fitzpatrick Institute for Photonics , Duke University , Durham , North Carolina 27708 , United States
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
| | - Tai-Ping Sun
- Department of Biology , Duke University , Durham , North Carolina 27708 , United States
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics , Duke University , Durham , North Carolina 27708 , United States
- Department of Biomedical Engineering , Duke University , Durham , North Carolina 27708 , United States
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| |
Collapse
|