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Juma KM, Murakami Y, Morimoto K, Takita T, Kojima K, Suzuki K, Yanagihara I, Ikuta S, Fujiwara S, Yasukawa K. Achieving unprecedented stability in lyophilized recombinase polymerase amplification with thermostable pyruvate kinase from Thermotoga maritima. J Biosci Bioeng 2024; 138:29-35. [PMID: 38719683 DOI: 10.1016/j.jbiosc.2024.04.003] [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: 01/01/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 06/11/2024]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. Considering the onsite use of RPA reagents, lyophilized RPA reagents with long storage stability are highly desired. In this study, as one of the approaches to solve this problem, we attempted to use a thermostable pyruvate kinase (PK). PK gene was isolated from a thermophilic bacterium Thermotoga maritima (Tma-PK). Tma-PK was expressed in Escherichia coli and purified from the cells. Tma-PK exhibited higher thermostability than human PK. The purified Tma-PK preparation was applied to RPA as an ATP-regenerating enzyme. Liquid RPA reagent with Tma-PK exhibited the same performance as that with human PK. Lyophilized RPA reagent with Tma-PK exhibited higher performance than that with human PK. Combined with our previous results of RPA reagents of thermostable Pol from a thermophilic bacterium, Aeribacillus pallidus, the results in this study suggest that thermostable enzymes are preferable to mesophilic ones as a component in lyophilized RPA reagents.
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuto Murakami
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka 565-0871, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka 594-1101, Japan
| | - Soichiro Ikuta
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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Sun A, Wang L, Zhang Y, Yang X, Su Y, Wu X. Development and Application of a Duplex RT-RPA Assay for the Simultaneous Detection of Cymbidium mosaic virus and Odontoglossum ringspot virus. Viruses 2024; 16:543. [PMID: 38675886 PMCID: PMC11054353 DOI: 10.3390/v16040543] [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: 02/17/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are among the world's most serious and widespread orchid viruses; they often infect orchids, causing devastating losses to the orchid industry. Therefore, it is critical to establish a method that can rapidly and accurately detect viruses in the field using simple instruments, which will largely reduce the further spread of viruses and improve the quality of the orchid industry and is suitable for mass promotion and application at grassroots agrotechnical service points. In this investigation, we established a rapid amplification method for virus detection at 39 °C for 35 min to detect the presence of CymMV and ORSV simultaneously, sensitively, and specifically in orchids. Primers for the capsid protein (CP)-encoding genes of both viruses were designed and screened, and the reaction conditions were optimized. The experimental amplification process was completed in just 35 min at 39 °C. There were no instances of nonspecific amplification observed when nine other viruses were present. The RPA approach had detection limits of 104 and 103 copies for pMD19T-CymMV and pMD19T-ORSV, respectively. Moreover, the duplex RT-RPA investigation confirmed sensitivity and accuracy via a comparison of detection results from 20 field samples with those of a gene chip. This study presents a precise and reliable detection method for CymMV and ORSV using RT-RPA. The results demonstrate the potential of this method for rapid virus detection. It is evident that this method could have practical applications in virus detection processes.
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Affiliation(s)
- Aiqing Sun
- Yunnan Provincial Key Laboratory of Flower Breeding, Flower Research Institute, Yunnan Academy of Agriculture Science, Panlong District, Kunming 650025, China; (A.S.); (Y.Z.); (X.Y.); (Y.S.)
- School of Agriculture, Yunnan University, Chenggong District, Kunming 650091, China
| | - Lihua Wang
- Yunnan Provincial Key Laboratory of Flower Breeding, Flower Research Institute, Yunnan Academy of Agriculture Science, Panlong District, Kunming 650025, China; (A.S.); (Y.Z.); (X.Y.); (Y.S.)
| | - Yiping Zhang
- Yunnan Provincial Key Laboratory of Flower Breeding, Flower Research Institute, Yunnan Academy of Agriculture Science, Panlong District, Kunming 650025, China; (A.S.); (Y.Z.); (X.Y.); (Y.S.)
| | - Xiumei Yang
- Yunnan Provincial Key Laboratory of Flower Breeding, Flower Research Institute, Yunnan Academy of Agriculture Science, Panlong District, Kunming 650025, China; (A.S.); (Y.Z.); (X.Y.); (Y.S.)
| | - Yan Su
- Yunnan Provincial Key Laboratory of Flower Breeding, Flower Research Institute, Yunnan Academy of Agriculture Science, Panlong District, Kunming 650025, China; (A.S.); (Y.Z.); (X.Y.); (Y.S.)
| | - Xuewei Wu
- School of Agriculture, Yunnan University, Chenggong District, Kunming 650091, China
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Nakowong P, Chatchawal P, Chaibun T, Boonapatcharoen N, Promptmas C, Buajeeb W, Lee SY, Jearanaikoon P, Lertanantawong B. Detection of high-risk HPV 16 genotypes in cervical cancers using isothermal DNA amplification with electrochemical genosensor. Talanta 2024; 269:125495. [PMID: 38043336 DOI: 10.1016/j.talanta.2023.125495] [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: 08/21/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/05/2023]
Abstract
Cervical cancer emerges as the third most prevalent types of malignancy among women on a global scale. Cervical cancer is significantly associated with the persistent infection of human papillomavirus (HPV) type 16. The process of diagnosing is crucial in order to prevent the progression of a condition into a malignant state. The early detection of cervical cancer through initial stage screening is of the utmost significance in both the prevention and effective management of this disease. The present detection methodology is dependent on quantitative polymerase chain reaction (qPCR), which necessitates the use of a costly heat cycler instrument. In this study, we report the development of an electrochemical DNA biosensor integrated with an isothermal recombinase polymerase amplification (RPA) reaction for the detection and identification of the high-risk HPV-16 genotype. The electrochemical biosensor exhibited a high degree of specificity and sensitivity, as evidenced by its limit of detection (LOD) of 0.23 copies/μL of HPV-16 DNA. The validity of this electrochemical platform was confirmed through the analysis of 40 cervical tissues samples, and the findings were consistent with those obtained through polymerase chain reaction (PCR) testing. Our straightforward electrochemical detection technology and quick turnaround time at 75 min make the assay suitable for point-of-care testing in low-resource settings.
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Affiliation(s)
- Panisara Nakowong
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Patutong Chatchawal
- Center of Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, KhonKaen University, KhonKaen, 40002, Thailand; Center for Innovation and Standard for Medical Technology and Physical Therapy (CISMaP), KhonKaen University, KhonKaen, 40002, Thailand
| | - Thanyarat Chaibun
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Nimaradee Boonapatcharoen
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chamras Promptmas
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Waranun Buajeeb
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Mahidol University, Bangkok, 10400, Thailand
| | - Su Yin Lee
- Faculty of Applied Sciences, AIMST University, 08100, Semeling, Kedah, Malaysia; Centre of Excellence for Omics-Driven Computational Biodiscovery (ComBio), AIMST University, Bedong, 08100, Malaysia
| | - Patcharee Jearanaikoon
- Center of Research and Development of Medical Diagnosis Laboratories, Faculty of Associated Medical Sciences, KhonKaen University, KhonKaen, 40002, Thailand; Center for Innovation and Standard for Medical Technology and Physical Therapy (CISMaP), KhonKaen University, KhonKaen, 40002, Thailand
| | - Benchaporn Lertanantawong
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Yin W, Zhuang J, Li J, Xia L, Hu K, Yin J, Mu Y. Digital Recombinase Polymerase Amplification, Digital Loop-Mediated Isothermal Amplification, and Digital CRISPR-Cas Assisted Assay: Current Status, Challenges, and Perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303398. [PMID: 37612816 DOI: 10.1002/smll.202303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/29/2023] [Indexed: 08/25/2023]
Abstract
Digital nucleic acid detection based on microfluidics technology can quantify the initial amount of nucleic acid in the sample with low equipment requirements and simple operations, which can be widely used in clinical and in vitro diagnosis. Recently, isothermal amplification technologies such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats-CRISPR associated proteins (CRISPR-Cas) assisted technologies have become a hot spot of attention and state-of-the-art digital nucleic acid chips have provided a powerful tool for these technologies. Herein, isothermal amplification technologies including RPA, LAMP, and CRISPR-Cas assisted methods, based on digital nucleic acid microfluidics chips recently, have been reviewed. Moreover, the challenges of digital isothermal amplification and possible strategies to address them are discussed. Finally, future directions of digital isothermal amplification technology, such as microfluidic chip and device manufacturing, multiplex detection, and one-pot detection, are outlined.
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Affiliation(s)
- Weihong Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Jianjian Zhuang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310006, P. R. China
| | - Jiale Li
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Kai Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
- School of information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
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Homklinkaew P, Phatthanakunanan S, Jala S, Boonsoongnern A, Lertwatcharasarakul P. Development of a recombinase-aided amplification method combined with lateral flow dipstick assay to detect Porcine circovirus type 2. Vet World 2023; 16:2313-2320. [PMID: 38152256 PMCID: PMC10750741 DOI: 10.14202/vetworld.2023.2313-2320] [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: 07/17/2023] [Accepted: 10/16/2023] [Indexed: 12/29/2023] Open
Abstract
Background and Aim Porcine circovirus type 2 (PCV2) is a pathogenic virus that suppresses the immune system of pigs, impacting their health and causing economic losses. Rapid diagnostic tools for early detection of PCV2 are critical to disease prevention and control. Several molecular techniques have been established for detecting PCV2 but costly equipment and time-consuming methods are unsuitable for field inspection. In this study, we developed a recombinase-aided amplification combined with lateral flow dipstick (RAA-LFD) assay to compare with polymerase chain reaction (PCR) and quantitative PCR (qPCR) in detecting PCV2 in suspected field samples. Materials and Methods To amplify RAA products, 15 primer pairs were designed from the conserved region of the open reading frame (ORF) 1 gene based on multiple alignments of eight PCV2 genotypes. The most efficient primer pair and conditions for the RAA-LFD assay were tested and selected. Limit of detection, repeatability, and reproducibility were determined using the constructed plasmid. DNA was extracted from positive samples for specificity testing as well as from 100 field samples to compare the detection of the RAA-LFD assay with PCR and qPCR. Results The F1/R1 primer pair was chosen and labeled with fluorescein isothiocyanate at the 5' end of the forward primer and with biotin at the 5' end of the reverse primer. The limit of detection of the RAA-LFD assay was 10 copies/μL at 38°C for 30 min. The RAA-LFD assay was repeatable and reproducible, with no cross-reaction with PCV3, Actinobacillus pleuropneumoniae, Porcine epidemic diarrhea virus, Classical swine fever virus, Porcine reproductive and respiratory syndrome virus - North America strain (PRRSV-US) and Porcine reproductive and respiratory syndrome virus - European strain (PRRSV-EU). Based on testing with 100 samples, the developed RAA showed 100% specificity and 90.56% and 85.71% sensitivity when compared to PCR and qPCR, respectively Cohen's kappa coefficients showed a good agreement with the established techniques. Conclusion The RAA-LFD assay targeting the ORF1 gene was highly sensitive, specific, quick, and simple to perform in the field.
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Affiliation(s)
- Ploypassorn Homklinkaew
- Animal Health and Biomedical Sciences Study Program, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Sakuna Phatthanakunanan
- Kamphaeng Saen Veterinary Diagnostic Center, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Siriluk Jala
- Kamphaeng Saen Veterinary Diagnostic Center, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Alongkot Boonsoongnern
- Department of Farm Resources and Production Medicine, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Preeda Lertwatcharasarakul
- Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
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Zhang N, Li C, Dou X, Du Y, Tian F. Test Article for automation purposes. Crit Rev Anal Chem 2023; 53:1969-1989. [PMID: 37881955 DOI: 10.1080/10408347.2022.2042999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.
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Affiliation(s)
- Ning Zhang
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Chao Li
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Xuechen Dou
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Yaohua Du
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Feng Tian
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
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Hifumi T, Tanaka T, Sato M, Akioka K, Fujimata C, Miyoshi N. Rapid detection of alveolar echinococcosis in hepatic nodules of horses by recombinase polymerase amplification assay. Vet Anim Sci 2023; 20:100291. [PMID: 36936549 PMCID: PMC10015249 DOI: 10.1016/j.vas.2023.100291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Alveolar echinococcosis in slaughtered horses remains a public health issue. This study aimed to develop a Recombinase polymerase amplification (RPA) assay targeting the mitochondrial NADH dehydrogenase subunit 5 (Nad5) gene of Echinococcus multilocularis for the rapid detection of equine alveolar echinococcosis. Thirty-six hepatic solid nodules obtained from each horse (n = 36) were evaluated based on histopathological examination and Nad5-targeted PCR and then submitted to the RPA assay. The results of the developed RPA assay were 94.4% consistent with those of Nad5 PCR and Cohen's kappa coefficient value was 0.89 statistically, indicating high agreement. In addition, the RPA assay using the plasmid samples was one hundredfold more sensitive than PCR testing. Consequently, these results suggest that the performance of the RPA assay developed in this study is equal to that of conventional PCR testing.
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Affiliation(s)
- Tatsuro Hifumi
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Corresponding author.
| | - Miho Sato
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kohei Akioka
- Kumamoto Prefectural Meat Inspection Center, 1314 Sosaki, Shichijo-machi, Kikuchi, Kumamoto 861-1344, Japan
| | - Chiaki Fujimata
- Kumamoto Prefectural Meat Inspection Center, 1314 Sosaki, Shichijo-machi, Kikuchi, Kumamoto 861-1344, Japan
| | - Noriaki Miyoshi
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Varghese J, De Silva I, Millar DS. Latest Advances in Arbovirus Diagnostics. Microorganisms 2023; 11:1159. [PMID: 37317133 DOI: 10.3390/microorganisms11051159] [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: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Abstract
Arboviruses are a diverse family of vector-borne pathogens that include members of the Flaviviridae, Togaviridae, Phenuviridae, Peribunyaviridae, Reoviridae, Asfarviridae, Rhabdoviridae, Orthomyxoviridae and Poxviridae families. It is thought that new world arboviruses such as yellow fever virus emerged in the 16th century due to the slave trade from Africa to America. Severe disease-causing viruses in humans include Japanese encephalitis virus (JEV), yellow fever virus (YFV), dengue virus (DENV), West Nile virus (WNV), Zika virus (ZIKV), Crimean-Congo hemorrhagic fever virus (CCHFV), severe fever with thrombocytopenia syndrome virus (SFTSV) and Rift Valley fever virus (RVFV). Numerous methods have been developed to detect the presence of these pathogens in clinical samples, including enzyme-linked immunosorbent assays (ELISAs), lateral flow assays (LFAs) and reverse transcriptase-polymerase chain reaction (RT-PCR). Most of these assays are performed in centralized laboratories due to the need for specialized equipment, such as PCR thermal cyclers and dedicated infrastructure. More recently, molecular methods have been developed which can be performed at a constant temperature, termed isothermal amplification, negating the need for expensive thermal cycling equipment. In most cases, isothermal amplification can now be carried out in as little as 5-20 min. These methods can potentially be used as inexpensive point of care (POC) tests and in-field deployable applications, thus decentralizing the molecular diagnosis of arboviral disease. This review focuses on the latest developments in isothermal amplification technology and detection techniques that have been applied to arboviral diagnostics and highlights future applications of these new technologies.
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Affiliation(s)
- Jano Varghese
- Genetic Signatures, 7 Eliza Street, Newtown, Sydney 2042, Australia
| | - Imesh De Silva
- Genetic Signatures, 7 Eliza Street, Newtown, Sydney 2042, Australia
| | - Douglas S Millar
- Genetic Signatures, 7 Eliza Street, Newtown, Sydney 2042, Australia
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Rapid, sensitive, and specific, low-resource molecular detection of Hendra virus. One Health 2023. [DOI: 10.1016/j.onehlt.2023.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
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Liu J, Huang T, Mao Y, Soteyome T, Liu G, Seneviratne G, Kjellerup BV, Xu Z. Development and application of multiple polymerase spiral reaction (PSR) assays for rapid detection of methicillin resistant Staphylococcus aureus and toxins from rice and flour products. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Tharakan S, Faqah O, Asghar W, Ilyas A. Microfluidic Devices for HIV Diagnosis and Monitoring at Point-of-Care (POC) Settings. BIOSENSORS 2022; 12:949. [PMID: 36354458 PMCID: PMC9687700 DOI: 10.3390/bios12110949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Human immunodeficiency virus (HIV) is a global epidemic; however, many individuals are able to obtain treatment and manage their condition. Progression to acquired immunodeficiency syndrome (AIDS) occurs during late-stage HIV infection, which compromises the immune system, making it susceptible to infections. While there is no cure, antiretroviral therapy can be used provided that detection occurs, preferably during the early phase. However, the detection of HIV is expensive and resource-intensive when tested with conventional methods, such as flow cytometry, polymerase chain reaction (PCR), or enzyme-linked immunosorbent assays (ELISA). Improving disease detection in resource-constrained areas requires equipment that is affordable, portable, and can deliver rapid results. Microfluidic devices have transformed many benchtop techniques to on-chip detection for portable and rapid point-of-care (POC) testing. These devices are cost-effective, sensitive, and rapid and can be used in areas lacking resources. Moreover, their functionality can rival their benchtop counterparts, making them efficient for disease detection. In this review, we discuss the limitations of currently used conventional HIV diagnostic assays and provide an overview of potential microfluidic technologies that can improve HIV testing in POC settings.
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Affiliation(s)
- Shebin Tharakan
- Bio-Nanotechnology and Biomaterials (BNB) Lab, New York Institute of Technology, Old Westbury, NY 11568, USA
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY 11568, USA
| | - Omair Faqah
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Waseem Asghar
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Azhar Ilyas
- Bio-Nanotechnology and Biomaterials (BNB) Lab, New York Institute of Technology, Old Westbury, NY 11568, USA
- Department of Electrical and Computer Engineering, New York Institute of Technology, Old Westbury, NY 11568, USA
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12
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Lai FY, Chang KC, Chang CS, Wang PH. Development of a Rapid Sex Identification Method for Newborn Pigeons Using Recombinase Polymerase Amplification and a Lateral-Flow Dipstick on Farm. Animals (Basel) 2022; 12:ani12212969. [PMID: 36359091 PMCID: PMC9656852 DOI: 10.3390/ani12212969] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/26/2022] Open
Abstract
Simple Summary The sex of a bird is important for aviculture, scientific research, and conservation. Sex identification is usually not easy, even if the bird’s appearances and sex organs are examined more closely. In monomorphic birds—or most birds during young, molecular sexing—there is a requirement for a fast and accurate identification method. We have designed a pair of DNA primers that is unique to the W chromosome of pigeon, which was unique to the female; further, RPA and LFD are combined for the purposes of a portable field detection for a sex identification method for birds (i.e., pigeons). The minimal-equipped on-farm approach was tested on pigeon sexing and the results have been 100% correct, so far. The concept of this study could spread to any kind of bird to meet the needs and achieve the goals of bird studies and businesses. Abstract According to pigeon racing rules in Taiwan, the pigeon raiser must decide which juveniles will be chosen as soon as possible. Differentiating the sex of young pigeons based on appearances, and other traditional methods, can be time-consuming and require several pieces of equipment. Recombinase polymerase amplification (RPA) combined with a lateral-flow dipstick (LFD) could further simplify the presentation of amplification results. A designed reverse primer and probe were labeled with biotin and FAM (fluorescein), respectively, to serve as ligands in the LFD. With the addition of a designed forward primer, the RPA-LFD can be used to perform sex identification of pigeon DNA. The optimal conditions were determined to require at least 6.3 pg of the DNA template, a temperature of 37 °C, and a reaction time of at least 20 min. Under these conditions, the test band area on the strip appeared as a dark color if the sample contained female template DNA, whereas the male DNA samples did not produce any test signal in any of the conditions. The results of random samples using RPA-LFD under the optimal conditions agreed with the results of the same samples determined by PCR-agarose gel electrophoresis. The approach in this study represents a rapid and accurate method for pigeon sexing.
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Affiliation(s)
- Fang-Yu Lai
- Key Laboratory of Animal Genetics, Breeding and Bioresources, Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 10672, Taiwan
| | - Kuang-Chih Chang
- Avance Technology Co., Ltd., 10F., No. 1, Ln. 83, Sec. 1, Guangfu Rd., Sanchong Dist., New Taipei City 24158, Taiwan
| | - Chi-Sheng Chang
- Department of Animal Science, Chinese Culture University, No. 55, Hwa-Kang Rd., Yang-Ming-Shan, Taipei City 11114, Taiwan
| | - Pei-Hwa Wang
- Key Laboratory of Animal Genetics, Breeding and Bioresources, Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei City 10672, Taiwan
- Correspondence: ; Tel.: +886-02-3366-4164; Fax: +886-02-2372-4070
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Wang YL, Zhang X, Wang Q, Liu PX, Tang W, Guo R, Zhang HY, Chen ZG, Han XG, Jiang W. Rapid and visual detection of Staphylococcus aureus in milk using a recombinase polymerase amplification-lateral flow assay combined with immunomagnetic separation. J Appl Microbiol 2022; 133:3741-3754. [PMID: 36073301 DOI: 10.1111/jam.15811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/27/2022]
Abstract
AIMS The aim of this study was to develop a novel approach using lateral flow recombinase polymerase amplification (RPA-LF) combined with immunomagnetic separation (IMS) for the rapid detection of Staphylococcus aureus in milk. METHODS AND RESULTS Under optimum conditions, the average capture efficiency values (CEs) for S. aureus strains (104 CFU ml-1 ) was above 95.0% in PBST and ~80% in milk within 45 min with 0.7 mg immunomagnetic beads. The RPA-LF assay, which comprised DNA amplification via RPA at 39°C for 10 min and visualization of the amplicons through LF strips for 5 min, detected S. aureus within 15 min. The method only detected S. aureus and did not show cross-reaction with other bacteria, exhibiting a high level of specificity. Sensitivity experiments confirmed a detection limit of RPA-LF assay as low as 600 fg reaction-1 for the S. aureus genome (corresponding to approximately 36 CFU of S. aureus), which was about 16.7-fold more sensitive than that of the conventional PCR method. When RPA-LF was used in combination with IMS to detect S. aureus inoculated into artificially contaminated milk, it exhibited a detection limit of approximately 40 CFU reaction-1 . CONCLUSIONS The newly developed IMS-RPA-LF method enabled detection of S. aureus at levels as low as 40 CFU reaction-1 in milk samples without culture enrichment for an overall testing time of only 70 min. SIGNIFICANCE AND IMPACT OF THE STUDY The newly developed IMS-RPA-LF assay effectively combines sample preparation, amplification, and detection into a single platform. Because of its high sensitivity, specificity, and speed, the IMS-RPA-LF assay will have important implications for the rapid detection of S. aureus in contaminated food.
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Affiliation(s)
- Ya-Lei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xin Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Quan Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Peng-Xuan Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wei Tang
- Department of Electronic Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Rong Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hai-Yang Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhao-Guo Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xian-Gan Han
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Wei Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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14
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Chou MY, Luo J, Clarke BB, Murphy JA, Zhang N, Vines PL, Koch PL. Rapid Detection of the Recently Identified Turfgrass Pathogen Magnaporthiopsis meyeri-festucae Using Recombinase Polymerase Amplification. PLANT DISEASE 2022; 106:2441-2446. [PMID: 35188416 DOI: 10.1094/pdis-08-21-1732-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Magnaporthiopsis meyeri-festucae is a recently identified root-infecting pathogen of fine fescue (Festuca spp.) turfgrasses. Although it is phylogenetically similar to other root-infecting turfgrass pathogens such as M. poae, management of M. meyeri-festucae is distinct and highlights the need for fast and accurate identification. The objective of this study was to develop a rapid detection method for M. meyeri-festucae using recombinase polymerase amplification (RPA) to assist turfgrass managers in identifying the disease in the field and facilitate further epidemiological research on the pathogen. Three isolates of M. meyeri-festucae and eight isolates from four related Magnaporthiopsis species were used to test the specificity of the RPA assay targeting M. meyeri-festucae. Rapid visualization of the RPA assay results using a mixture of purified amplicon and SYBR-Safe fluorescence emitting asymmetrical cyanine dye showed that the assay was effective at detecting M. meyeri-festucae on turfgrass roots with no observed incidence of false positives or false negatives. The assay also differentiated between M. meyeri-festucae and other Magnaporthiopsis species, although overall sensitivity was lower compared with a PCR-based method. The RPA assay successfully detected M. meyeri-festucae following inoculation onto and grinding of turfgrass roots, indicating possible use as a rapid field diagnostic tool for turfgrass managers. The fast and accurate RPA M. meyeri-festucae detection method presented here will be used for additional field and laboratory applications that will help improve the management of this emerging pathogen.
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Affiliation(s)
- Ming-Yi Chou
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Jing Luo
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Bruce B Clarke
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - James A Murphy
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Phillip L Vines
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Paul L Koch
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
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15
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Prasad M, Milton A, Menon V, Ghatak S, Srinivas K, Momin K, Vineesha S, Das S, Sen A, Latha C, Sunil B, Jolly D. Saltatory rolling circle amplification assay for simple and visual detection of Listeria monocytogenes in milk and milk products. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105498] [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]
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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17
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Xu JH, Kang L, Yuan B, Feng ZH, Li SQ, Wang J, Wang YR, Xin WW, Gao S, Li JX, Sun YS, Wang JL, Yuan Y. Development and evaluation of a rapid RPA/CRISPR-based detection of Francisella tularensis. Front Microbiol 2022; 13:901520. [PMID: 36033876 PMCID: PMC9399789 DOI: 10.3389/fmicb.2022.901520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Francisella tularensis is a dangerous pathogen that causes an extremely contagious zoonosis in humans named tularemia. Given its low-dose morbidity, the potential to be fatal, and aerosol spread, it is regarded as a severe threat to public health. The US Centers for Disease Control and Prevention (CDC) has classified it as a category A potential agent for bioterrorism and a Tier 1 Select Agent. Herein, we combined recombinase polymerase amplification (RPA) with CRISPR/Cas12a system to select the F. tularensis target gene (TUL4), creating a two-pronged rapid and ultrasensitive diagnostic method for detecting F. tularensis. The real-time RPA (RT-RPA) assay detected F. tularensis within 10 min at a sensitivity of 5 copies/reaction, F. tularensis genomic DNA of 5 fg, and F. tularensis of 2 × 102 CFU/ml; the RPA-CRISPR/Cas12a assay detects F. tularensis within 40 min at a sensitivity of 0.5 copies/reaction, F. tularensis genomic DNA of 1 fg, and F. tularensis of 2 CFU/ml. Furthermore, the evaluation of specificity showed that both assays were highly specific to F. tularensis. More importantly, in a test of prepared simulated blood and sewage samples, the RT-RPA assay results were consistent with RT-PCR assay results, and the RPA-CRISPR/Cas12a assay could detect a minute amount of F. tularensis genomic DNA (2.5 fg). There was no nonspecific detection with blood samples and sewage samples, giving the tests a high practical application value. For example, in on-site and epidemic areas, the RT-RPA was used for rapid screening and the RPA-CRISPR/Cas12a assay was used for more accurate diagnosis.
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Affiliation(s)
- Jian-Hao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zi-Han Feng
- Department of Disease Control and Prevention, The No. 96609 Hospital of Chinese People's Liberation Army, Yinchuan, China
| | - Shi-Qing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ya-Ru Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Wen-Wen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jia-Xin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yan-Song Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- *Correspondence: Yan-Song Sun
| | - Jing-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Jing-Lin Wang
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Yuan Yuan
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Pewlaoo S, Phanthong S, Kong-Ngoen T, Santajit S, Tunyong W, Buranasinsup S, Kaeoket K, Thavorasak T, Pumirat P, Sookrung N, Chaicumpa W, Indrawattana N. Development of a Rapid Reverse Transcription-Recombinase Polymerase Amplification Couple Nucleic Acid Lateral Flow Method for Detecting Porcine Epidemic Diarrhoea Virus. BIOLOGY 2022; 11:biology11071018. [PMID: 36101399 PMCID: PMC9312133 DOI: 10.3390/biology11071018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Porcine epidemic diarrhea virus infection is an important acute diarrheal disease of swine especially in infected piglets can caused severe diarrhea, dehydration with difficulty in digesting milk curd, leading to death. The diagnosis of this viral infection is essential for monitoring and managing the disease. There is surprisingly little evidence such as easy rapid detection in the field. In this study, we developed rapid the reverse transcription-recombinase polymerase amplification couple nucleic acid lateral flow for Porcine epidemic diarrhea virus detection targeted the membrane gene in the genome sequence of the virus. Herein, the results shown that the established assay is simple and rapid, increases high sensitivity and specificity, and can be applied in the field. Abstract Porcine epidemic diarrhea virus (PEDV) infection is an important acute diarrheal disease of swine that results in economic and industrial losses worldwide. The clinical manifestations in infected piglets are severe diarrhea, dehydration with milk curd indigestion, leading to death. The diagnosis of PEDV is essential for monitoring and managing the disease. PEDV can be detected and identified by serology and the nucleic acid of the virus in clinical samples. Therefore, a novel isothermal amplification and detection technique, reverse transcription-recombinase polymerase amplification couple nucleic acid lateral flow (RT-RPA-NALF) was developed for the rapid detection of PEDV. Qualitative reverse transcription-polymerase chain reaction (RT-qPCR) was established as the gold standard assay to compare results. Specific primer pairs and probes were designed, and RT-RPA conditions were optimized to amplify the M gene of PEDV. The established RT-RPA-NALF assay could finish in 25 min at a temperature of 42 °C and the amplicon interpreted by visual detection. The developed RT-RPA-NALF assay was specific to the M gene of PEDV, did not detect other common swine diarrhea pathogens, and showed minimal detection at 102 TCID50/mL PEDV. The RT-RPA-NALF assay can detect PEDV in 5 simulated fecal samples. Furthermore, in 60 clinical fecal samples, the results of RT-RPA-NALF correlated with RT-qPCR assay, which provides sensitivity of 95.65% and specificity of 100%, with a coincident rate of 98.33%. The rapid RT-RPA-NALF is simple and rapid, increases high sensitivity, and can be used in the field.
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Affiliation(s)
- Seatthanan Pewlaoo
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Siratcha Phanthong
- Siriraj Center of Research Excellence in Allergy and Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.P.); (N.S.)
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.T.); (W.C.)
| | - Thida Kong-Ngoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Sirijan Santajit
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand;
- Research Center in Tropical Pathobiology, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Witawat Tunyong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Shutipen Buranasinsup
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Kampon Kaeoket
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Techit Thavorasak
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.T.); (W.C.)
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
| | - Nitat Sookrung
- Siriraj Center of Research Excellence in Allergy and Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.P.); (N.S.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.T.); (W.C.)
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (S.P.); (T.K.-N.); (W.T.); (P.P.)
- Correspondence: ; Tel.: +66-2-354-9100 (ext. 1598)
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19
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Liu F, Zhang C, Wang Y, Chen G. A review of the current and emerging detection methods of marine harmful microalgae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152913. [PMID: 34999066 DOI: 10.1016/j.scitotenv.2022.152913] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
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20
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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]
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21
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Chen M, Huang T, Du M, Bai X, Soteyome T, Yuan L, Bai C, Lan H, Hong W, Peng F, Fu X, Peng G, Liu L, Kjellerup BV, Xu Z. Establishment and application of a rapid visual detection method for Listeria monocytogenes based on polymerase spiral reaction (PSR). Bioengineered 2022; 13:7860-7867. [PMID: 35298350 PMCID: PMC9208488 DOI: 10.1080/21655979.2022.2044262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 02/05/2023] Open
Abstract
Listeria monocytogenes is a common foodborne pathogen that presents in various food products, posing important threat to public health. The aim of this study was to establish a rapid and sensitive method with visualization to detect L. monocytogenes based on polymerase spiral reaction (PSR). Primers targeting conserved hlyA gene sequence of L. monocytogenes were designed based on bioinformatics analyses on the current available L. monocytogenes genomes. The isothermal amplification PSR can be completed under constant temperature (65ᵒC) within 60 min with high specificity and sensitivity. Twenty-five reference strains were used to evaluate the specificity of the developed reaction. The results showed that the sensitive of the reaction for L. monocytogenes in purified genomic DNA and artificially contaminated food samples were 41 pg/μL and 103 CFU/mL, respectively. It was 100-fold more sensitive than conventional PCR. In conclusion, this novel PSR method is rapid, cost-efficient, timesaving, and applicable on artificially contaminated food samples, providing broad prospects into the detection of foodborne microbes with the promising on-site inspection.
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Affiliation(s)
- Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Tengyi Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Min Du
- Gmu-gibh Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaoxi Bai
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, Guangdong, China
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu, China
| | - Caiying Bai
- Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Haifeng Lan
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Hong
- Gmu-gibh Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fang Peng
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Fu
- Gmu-gibh Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Gongyong Peng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- CONTACT Gongyong Peng ; State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Zhenbo Xu
| | - Liyan Liu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, Guangdong, China
| | - Birthe V. Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Zhenbo Xu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, Guangdong, China
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
- National Institute of Fundamental Studies, Kandy, Sri Lanka
- CONTACT Gongyong Peng ; State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Zhenbo Xu
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22
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Zhang N, Li C, Dou X, Du Y, Tian F. Overview and Future Perspectives of Microfluidic Digital Recombinase Polymerase Amplification (dRPA). Crit Rev Anal Chem 2022; 52:1969-1989. [PMID: 35201910 DOI: 10.1080/10408347.2022.2042669] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.
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Affiliation(s)
- Ning Zhang
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Chao Li
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Xuechen Dou
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Yaohua Du
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
| | - Feng Tian
- Institute of Medical Support Technology, Academy of Military Science, Tianjin, China
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23
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Wang H, Ding X, Sun W, Chen Z, Bai L, Liang H, Liu Y, Zhang W, Wang G, Yang G, Mauk MG, Cui Y, Chen L. Recombinase polymerase amplification assay for rapid detection of Seneca Valley Virus. Anal Biochem 2022; 642:114564. [DOI: 10.1016/j.ab.2022.114564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 11/01/2022]
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Huang QJ, Chen Y, Liu H, St-Hilaire S, Gao S, MacKinnon B, Zhu SQ, Wen ZQ, Jia P, Zheng XC. Establishment of a real-time Recombinase Polymerase Amplification (RPA) for the detection of decapod iridescent virus 1 (DIV1). J Virol Methods 2021; 300:114377. [PMID: 34826518 DOI: 10.1016/j.jviromet.2021.114377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
A rapid and simple real-time recombinase polymerase amplification (RPA) assay was developed to detect decapod iridescent virus 1 (DIV1). The assay was developed using optimized primers and probes designed from the conserved sequence of the DIV1 major capsid protein (MCP) gene. Using the optimized RPA assay, the DIV1 test was completed within 20 min at 39 ℃. The RPA assay was specific to DIV1 with a detection limit of 2.3 × 101 copies/reaction and there was no cross-reactivity with the other aquatic pathogens (WSSV, IHHNV, NHPB, VpAHPND, EHP, IMNV, YHV-1 and GAV) tested. Four out of 45 field-collected shrimp samples tested positive for DIV1 by real-time RPA. The same assay results were obtained by both methods. Thus, the real-time RPA assay developed could be a simple, rapid, sensitive, reliable and affordable method for the on-site diagnosis of DIV1 infection and has significant potential in helping to control DIV1 infections and reduce economic losses to the shrimp industry.
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Affiliation(s)
- Qian-Jun Huang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong
| | - Yu Chen
- University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hong Liu
- Shenzhen Customs, Shenzhen, 518054, China
| | - Sophie St-Hilaire
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong
| | - Shuai Gao
- Northeast Agricultural University, HarBin, 150030, China
| | - Brett MacKinnon
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong
| | | | | | - Peng Jia
- Shenzhen Customs, Shenzhen, 518054, China
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Kobialka RM, Ceruti A, Bergmann M, Hartmann K, Truyen U, Abd El Wahed A. Molecular Detection of Feline Coronavirus Based on Recombinase Polymerase Amplification Assay. Pathogens 2021; 10:pathogens10101237. [PMID: 34684186 PMCID: PMC8538120 DOI: 10.3390/pathogens10101237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Feline coronavirus (FCoV) is endemic in cat populations worldwide. Persistently, subclinically infected cats play a significant role in spreading the infection. Testing fecal samples of cats may facilitate efforts to decrease the viral burden within a population. Real-time RT-PCR is highly sensitive and specific for the detection of FCoV but must be performed in a fully equipped laboratory. A simple and accurate assay is needed to identify FCoV at the point-of-need. The aim of this study was to develop a rapid FCoV detection assay based on isothermal amplification technology, i.e., reverse transcription-recombinase polymerase amplification (RT-RPA). Primers were designed to target the highly conserved 3′ untranslated region of the 7b gene. Running on a constant temperature of 42 °C, reverse transcription as well as DNA amplification and detection was achieved in a maximum of 15 min. A probit analysis revealed a detection limit of 58.5 RNA copies/reaction. For cross-detection, nucleic acids from 19 viruses were tested. Both RT-RPA and real-time RT-PCR showed cross-detection with canine coronavirus and transmissible gastroenteritis virus, but not with other pathogens. To evaluate clinical performance, RNA was extracted from 39 fecal samples from cats. All samples were tested simultaneously with real-time RT-PCR resulting in a RT-RPA sensitivity and specificity of 90.9% and 100%, respectively. RT-RPA can be considered a promising simple method for rapid detection of FCoV.
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Affiliation(s)
- Rea Maja Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (R.M.K.); (A.C.); (U.T.)
| | - Arianna Ceruti
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (R.M.K.); (A.C.); (U.T.)
| | - Michelle Bergmann
- Clinic of Small Animal Medicine, LMU, 80539 Munich, Germany; (M.B.); (K.H.)
| | - Katrin Hartmann
- Clinic of Small Animal Medicine, LMU, 80539 Munich, Germany; (M.B.); (K.H.)
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (R.M.K.); (A.C.); (U.T.)
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany; (R.M.K.); (A.C.); (U.T.)
- Correspondence: ; Tel.: +49-341-97-38-153
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Dehghan Esmat Abadi M, Motalebzadeh H, Barati M, Yaghobi M. Designing Two Synthetic Constructs for Real Time PCR Detection of Francisella tularensis and Ebola Virus. Avicenna J Med Biotechnol 2021; 13:92-97. [PMID: 34012525 PMCID: PMC8112141 DOI: 10.18502/ajmb.v13i2.5528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: Generally, timely diagnosis of micro-organisms is very important to prevent many diseases. Many methods can detect micro-organisms like culture-based methods and molecular methods. The molecular methods are usually preferred because they provide fast and reliable results. In some cases, microbial strains are not accessible, and there is no safety to work with them; therefore, synthetic constructs which are designed according to the available sequences in databases can be used as a positive control for detection of them. Methods: In this study, a synthetic construct was designed for molecular detection of Francisella tularensis (F. tularensis) and the Ebola virus by multiplex real-time PCR reaction. For this, sequences were taken from databases and then multiple alignments were done by software. Also, conventional PCR and two models of real-time PCR (SYBR green and TaqMan) were applied. Finally, multiplex real-time PCR was performed. Results: The synthetic construct was designed and used for conventional PCR and multiplex PCR. The results of common PCR showed a single band at 148 bp and 167 bp in 1.5% agarose gel stained by ethidium bromide for F. tularensis and Ebola virus, respectively. Also, a dual-band at 148 and 167 bp was observed in multiplex PCR. Results of real-time PCR showed a limit of detection about 0.1 pg of plasmid/μl. Conclusion: In conclusion, the designed construct can be used as a positive control for an accurate diagnosis of these micro-organisms without any biological danger for laboratory staff. So, this method is useful for diagnosis of these agents in food, water, and blood samples.
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Affiliation(s)
| | - Hesam Motalebzadeh
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Barati
- Department of Genetics, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammadali Yaghobi
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
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Zhai J, Wang L, Qiao X, Zhao J, Wang X, He X. Detection of Neisseria gonorrhoeae and Chlamydia trachomatis infections in pregnant women by multiplex recombinase polymerase amplification. PLoS One 2021; 16:e0251119. [PMID: 33945580 PMCID: PMC8096098 DOI: 10.1371/journal.pone.0251119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/20/2021] [Indexed: 01/15/2023] Open
Abstract
Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the main pathogenic microorganisms causing sexually transmitted infections. In this study, a multiplex thermostable recombinase polymerase amplification-lateral flow detection (RPA-LFD) assay was established, and the reaction conditions such as the ratio of primer concentration, magnesium ion concentration, amplification time and template DNA concentration in the multiplex RPA reaction were optimized. The optimized multiplex RPA-LFD method was used to detect both CT and NG positive control plasmids, and it was found that the LFD could be used to obtain visible results when the plasmid copy number was only 200. The sensitivity of the multiplex RPA-LFD method used for clinical samples was 85.62 (95% CI at 53.66–97.29) for NG detection and 90.90 (95% CI at 57.12–99.52) for CT detection.
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Affiliation(s)
- Jingjing Zhai
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
| | - Limin Wang
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
- * E-mail:
| | - Xiaoliang Qiao
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
| | - Jianping Zhao
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
| | - Xuexia Wang
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
| | - Xiaohong He
- Department of Clinical Laboratory, Women and Infants Hospital of Zhengzhou, Zhengzhou, China
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Chen K, Ma B, Li J, Chen E, Xu Y, Yu X, Sun C, Zhang M. A Rapid and Sensitive Europium Nanoparticle-Based Lateral Flow Immunoassay Combined with Recombinase Polymerase Amplification for Simultaneous Detection of Three Food-Borne Pathogens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094574. [PMID: 33925871 PMCID: PMC8123443 DOI: 10.3390/ijerph18094574] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/25/2022]
Abstract
Food-borne pathogens have become an important public threat to human health. There are many kinds of pathogenic bacteria in food consumed daily. A rapid and sensitive testing method for multiple food-borne pathogens is essential. Europium nanoparticles (EuNPs) are used as fluorescent probes in lateral flow immunoassays (LFIAs) to improve sensitivity. Here, recombinase polymerase amplification (RPA) combined with fluorescent LFIA was established for the simultaneous and quantitative detection of Listeria monocytogenes, Vibrio parahaemolyticus, and Escherichia coliO157:H7. In this work, the entire experimental process could be completed in 20 min at 37 °C. The limits of detection (LODs) of EuNP-based LFIA–RPA were 9.0 colony-forming units (CFU)/mL for Listeria monocytogenes, 7.0 CFU/mL for Vibrio parahaemolyticus, and 4.0 CFU/mL for Escherichia coliO157:H7. No cross-reaction could be observed in 22 bacterial strains. The fluorescent LFIA–RPA assay exhibits high sensitivity and good specificity. Moreover, the average recovery of the three food-borne pathogens spiked in food samples was 90.9–114.2%. The experiments indicate the accuracy and reliability of the multiple fluorescent test strips. Our developed EuNP-based LFIA–RPA assay is a promising analytical tool for the rapid and simultaneous detection of multiple low concentrations of food-borne pathogens.
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Affiliation(s)
- Kai Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Biao Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Jiali Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Erjing Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Ying Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, EuSwedish 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; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
- Correspondence: ; Tel.: +86-571-8691-4476; Fax: +86-571-8691-4510
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A Multi-Country, Single-Blinded, Phase 2 Study to Evaluate a Point-of-Need System for Rapid Detection of Leishmaniasis and Its Implementation in Endemic Settings. Microorganisms 2021; 9:microorganisms9030588. [PMID: 33809332 PMCID: PMC7999011 DOI: 10.3390/microorganisms9030588] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/17/2022] Open
Abstract
With the advancement of isothermal nucleic acid amplification techniques, detection of the pathogenic DNA in clinical samples at point-of-need is no longer a dream. The newly developed recombinase polymerase amplification (RPA) assay incorporated in a suitcase laboratory has shown promising diagnostic efficacy over real-time PCR in detection of leishmania DNA from clinical samples. For broader application of this point-of-need system, we undertook a current multi-country diagnostic evaluation study towards establishing this technique in different endemic settings which would be beneficial for the ongoing elimination programs for leishmaniasis. For this study purpose, clinical samples from confirmed visceral leishmaniasis (VL) and post-kala-azar dermal leishmaniasis (PKDL) patients were subjected to both real-time PCR and RPA assay in Bangladesh, India, and Nepal. Further skin samples from confirmed cutaneous leishmaniasis (CL) patients were also included from Sri Lanka. A total of 450 clinical samples from VL patients, 429 from PKDL patients, 47 from CL patients, and 322 from endemic healthy/healthy controls were under investigation to determine the diagnostic efficacy of RPA assay in comparison to real-time PCR. A comparative sensitivity of both methods was found where real-time PCR and RPA assay showed 96.86% (95% CI: 94.45–98.42) and 88.85% (95% CI: 85.08–91.96) sensitivity respectively in the diagnosis of VL cases. This new isothermal method also exhibited promising diagnostic sensitivity (93.50%) for PKDL cases, when a skin sample was used. Due to variation in the sequence of target amplicons, RPA assay showed comparatively lower sensitivity (55.32%) than that of real-time PCR in Sri Lanka for the diagnosis of CL cases. Except for India, the assay presented absolute specificity in the rest of the sites. Excellent concordance between the two molecular methods towards detection of leishmania DNA in clinical samples substantiates the application of RPA assay incorporated in a suitcase laboratory for point-of-need diagnosis of VL and PKDL in low resource endemic settings. However, further improvisation of the method is necessary for diagnosis of CL.
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Zhao L, Wang J, Sun XX, Wang J, Chen Z, Xu X, Dong M, Guo YN, Wang Y, Chen P, Gao W, Geng Y. Development and Evaluation of the Rapid and Sensitive RPA Assays for Specific Detection of Salmonella spp. in Food Samples. Front Cell Infect Microbiol 2021; 11:631921. [PMID: 33718280 PMCID: PMC7946851 DOI: 10.3389/fcimb.2021.631921] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella spp. is among the main foodborne pathogens which cause serious foodborne diseases. An isothermal real-time recombinase polymerase amplification (RPA) and lateral flow strip detection (LFS RPA) were used to detect Salmonella spp. targeting the conserved sequence of invasion protein A (invA). The Real-time RPA was performed in a portable florescence scanner at 39°C for 20 min. The LFS RPA was performed in an incubator block at 39°C for 15 min, under the same condition that the amplifications could be inspected by the naked eyes on the LFS within 5 min. The detection limit of Salmonella spp. DNA using real-time RPA was 1.1 × 101 fg, which was the same with real-time PCR but 10 times higher than that of LFS RPA assay. Moreover, the practicality of discovering Salmonella spp. was validated with artificially contaminated lamb, chicken, and broccoli samples. The analyzing time dropped from 60 min to proximately 5–12 min on the basis of the real-time and LFS RPA assays compared with the real-time PCR assay. Real-time and LFS RPA assays’ results were equally reliable. There was no cross-reactivity with other pathogens in both assays. In addition, the assays had good stability. All of these helped to show that the developed RPA assays were simple, rapid, sensitive, credible, and could be a potential point-of-need (PON) test required mere resources.
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Affiliation(s)
- Liwei Zhao
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Jianchang Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiao Xia Sun
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Jinfeng Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Zhimin Chen
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs, Shijiazhuang, China
| | - Xiangdong Xu
- School of Public Health, Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
| | - Mengyuan Dong
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Ya-Nan Guo
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yuanyuan Wang
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Pingping Chen
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Weijuan Gao
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yunyun Geng
- Heibei Key Laboratory of Chinese Medicine Research on Cardiocerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, China
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El-Tholoth M, Mauk MG, Elnaker YF, Mosad SM, Tahoun A, El-Sherif MW, Lokman MS, Kassab RB, Abdelsadik A, Saleh AA, Elmahallawy EK. Molecular Characterization and Developing a Point-of-Need Molecular Test for Diagnosis of Bovine Papillomavirus (BPV) Type 1 in Cattle from Egypt. Animals (Basel) 2020; 10:E1929. [PMID: 33096600 PMCID: PMC7588879 DOI: 10.3390/ani10101929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/11/2022] Open
Abstract
Bovine papillomatosis is a viral disease of cattle causing cutaneous warts. A diagnosis of this viral infection is very mandatory for combating the resulting economic losses. Given the limited data available about bovine papillomavirus (BPV) in Egypt, the present study involved the molecular diagnosis of bovine papillomavirus type-1 (BPV-1), -2, -4, -5, and -10 in cattle presenting cutaneous warts on the head and neck from New Valley Province, Egypt. The phylogenetic analysis of the detected types of BPV was also performed, followed by developing a point-of-need molecular assay for the rapid identification of identified BPV types. In this regard, a total of 308 cattle from private farms in Egypt were clinically examined, of which 13 animals presented cutaneous warts due to suspected BPV infection. The symptomatic animals were treated surgically, and biopsies from skin lesions were collected for BPV-1, -2, -4, -5, and -10 molecular identification using polymerase chain reaction (PCR). The presence of BPV-1 DNA was confirmed in 11 collected samples (84.6%), while BPV-2, -4, -5, and -10 were not detected. Sequencing of the PCR products suggested the Egyptian virus is closely related to BPV found in India. An isothermal nucleic acid amplification test (NAAT) with labeled primers specific for the BPV-1 L1 gene sequence, and based on recombinase polymerase amplification (RPA), in combination with a lateral flow strip assay for the detection of RPA products, was developed and tested. The point-of-need molecular assay demonstrated a diagnostic utility comparable to PCR-based testing. Taken together, the present study provides interesting molecular data related to the occurrence of BPV-1 in Egypt and reveals the genetic relatedness of the Egyptian BPV-1 with BPV-1 found in buffalo in India. In addition, a simple, low-cost combined test was also validated for diagnosis of the infection. The present study suggests the necessity of future investigations about the circulating strains of the virus among the cattle in Egypt to assess their genetic relatedness and better understand the epidemiological pattern of the disease.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.E.-T.); (S.M.M.)
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Health Sciences Division, Veterinary Sciences Program, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, UAE
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Yasser F. Elnaker
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, The New Valley University, El-Karga 72511, New Valley, Egypt;
| | - Samah M. Mosad
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.E.-T.); (S.M.M.)
| | - Amin Tahoun
- Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelshkh University, Kafrelsheikh 33511, Egypt;
| | - Mohamed W. El-Sherif
- Department of Surgery, Anesthesiology and Radiology, Faculty of Veterinary Medicine, The New Valley University, El-Karga 72511, New Valley, Egypt;
| | - Maha S. Lokman
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdul Aziz University, Alkharj 11942, Saudi Arabia;
- Department of Zoology and Entomology, Faculty of Science, Helwan University, 11795 Cairo, Egypt;
| | - Rami B. Kassab
- Department of Zoology and Entomology, Faculty of Science, Helwan University, 11795 Cairo, Egypt;
- Department of Biology, Faculty of Science and Arts, Al Baha University, Almakhwah, Al Baha 1988, Saudi Arabia
| | - Ahmed Abdelsadik
- Zoology Department, Faculty of Science, Aswan University, Aswan 81528, Egypt;
| | - Ayman A. Saleh
- Department of Animal Wealth Development, Genetics and Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Ehab Kotb Elmahallawy
- Department of Biomedical Sciences, University of Leon, 24071 León, Spain
- Department of Zoonoses, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt
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Kim NK, Kim SM, Jeong RD. Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid and Sensitive Detection of Barley Yellow Dwarf Virus in Oat. THE PLANT PATHOLOGY JOURNAL 2020; 36:497-502. [PMID: 33082734 PMCID: PMC7542026 DOI: 10.5423/ppj.nt.08.2020.0148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 05/24/2023]
Abstract
Barley yellow dwarf virus (BYDV) is an economically important plant pathogen that causes stunted growth, delayed heading, leaf yellowing, and purple leaf tip, thereby reducing the yields of cereal crops worldwide. In the present study, a reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed for the detection of BYDV in oat leaf samples. The RT-RPA assay involved incubation at an isothermal temperature (42°C) and could be performed rapidly in 5 min. In addition, no cross-reactivity was observed to occur with other cereal-infecting viruses, and the method was 100 times more sensitive than conventional reverse transcription polymerase chain reaction. Furthermore, the assay was validated for the detection of BYDV in both field-collected oat leaves and viruliferous aphids. Thus, the RT-RPA assay developed in the present study represents a simple, rapid, sensitive, and reliable method for detecting BYDV in oats.
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Affiliation(s)
- Na-Kyeong Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
| | - Sang-Min Kim
- Crop Foundation Research Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
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33
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Rapid detection of peach latent mosaic viroid by reverse transcription recombinase polymerase amplification. Mol Cell Probes 2020; 53:101627. [DOI: 10.1016/j.mcp.2020.101627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022]
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34
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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.
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Appelt S, Faber M, Köppen K, Jacob D, Grunow R, Heuner K. Francisella tularensis Subspecies holarctica and Tularemia in Germany. Microorganisms 2020; 8:microorganisms8091448. [PMID: 32971773 PMCID: PMC7564102 DOI: 10.3390/microorganisms8091448] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022] Open
Abstract
Tularemia is a zoonotic disease caused by Francisella tularensis a small, pleomorphic, facultative intracellular bacterium. In Europe, infections in animals and humans are caused mainly by Francisella tularensis subspecies holarctica. Humans can be exposed to the pathogen directly and indirectly through contact with sick animals, carcasses, mosquitoes and ticks, environmental sources such as contaminated water or soil, and food. So far, F. tularensis subsp. holarctica is the only Francisella species known to cause tularemia in Germany. On the basis of surveillance data, outbreak investigations, and literature, we review herein the epidemiological situation-noteworthy clinical cases next to genetic diversity of F. tularensis subsp. holarctica strains isolated from patients. In the last 15 years, the yearly number of notified cases of tularemia has increased steadily in Germany, suggesting that the disease is re-emerging. By sequencing F. tularensis subsp. holarctica genomes, knowledge has been added to recent findings, completing the picture of genotypic diversity and geographical segregation of Francisella clades in Germany. Here, we also shortly summarize the current knowledge about a new Francisella species (Francisella sp. strain W12-1067) that has been recently identified in Germany. This species is the second Francisella species discovered in Germany.
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Affiliation(s)
- Sandra Appelt
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany; (S.A.); (D.J.); (R.G.)
| | - Mirko Faber
- Gastrointestinal Infections, Zoonoses and Tropical Infections (Division 35), Department for Infectious Disease Epidemiology, Robert Koch Institute, 13353 Berlin, Germany;
| | - Kristin Köppen
- Cellular Interactions of Bacterial Pathogens, ZBS 2, Robert Koch Institute, 13353 Berlin, Germany;
| | - Daniela Jacob
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany; (S.A.); (D.J.); (R.G.)
| | - Roland Grunow
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, 13353 Berlin, Germany; (S.A.); (D.J.); (R.G.)
| | - Klaus Heuner
- Cellular Interactions of Bacterial Pathogens, ZBS 2, Robert Koch Institute, 13353 Berlin, Germany;
- Correspondence: ; Tel.: +49-301-8754-2226
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Jia T, Yu Y, Wang Y. A recombinase polymerase amplification-based lateral flow strip assay for rapid detection of genogroup II noroviruses in the field. Arch Virol 2020; 165:2767-2776. [PMID: 32949263 DOI: 10.1007/s00705-020-04798-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]
Abstract
Human norovirus is the leading cause of viral gastroenteritis worldwide. Rapid detection facilitates management of disease outbreaks, but field diagnosis is difficult to achieve due to the lack of reliable and portable methods. Recombinase polymerase amplification (RPA) is a robust isothermal amplification method that is capable of rapidly amplifying and detecting nucleic acids using simple equipment. In this study, RPA combined with lateral flow (LF) strips specific for human genogroup II (GII) noroviruses was established and evaluated. The assay specifically detects purified GII noroviruses as well as RNA in boiled human stool samples, with a sensitivity of 50 norovirus genome copies per reaction. The whole detection procedure of the one-step RT-RPA-LF is completed within 20 min, which is eight times faster than that of the standard real-time RT-PCR. The RT-RPA-LF method described here is suitable for rapid field diagnosis of all GII noroviruses in human stool samples.
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Affiliation(s)
- Tianhui Jia
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China.
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Jang WS, Lim DH, Nam J, Mihn DC, Sung HW, Lim CS, Kim J. Development of a multiplex isothermal amplification molecular diagnosis method for on-site diagnosis of influenza. PLoS One 2020; 15:e0238615. [PMID: 32915821 PMCID: PMC7485819 DOI: 10.1371/journal.pone.0238615] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/20/2020] [Indexed: 01/30/2023] Open
Abstract
Influenza, which is an acute respiratory disease caused by the influenza virus, represents a worldwide public health and economic problem owing to the significant morbidity and mortality caused by its seasonal epidemics and pandemics. Sensitive and convenient methodologies for the detection of influenza viruses are important for clinical care and infection control as well as epidemiological investigations. Here, we developed a multiplex reverse transcription loop-mediated isothermal amplification (RT-LAMP) with quencher/fluorescence oligonucleotides connected by a 5' backward loop (LF or LB) primer for the detection of two subtypes of influenza viruses: Influenza A (A/H1 and A/H3) and influenza B. The detection limits of the multiplex RT-LAMP assay were 103 copies and 102 copies of RNA for influenza A and influenza B, respectively. The sensitivities of the multiplex influenza A/B/IC RT-LAMP assay were 94.62% and 97.50% for influenza A and influenza B clinical samples, respectively. The specificities of the multiplex influenza A/B/IC RT-LAMP assay were 100% for influenza A, influenza B, and healthy clinical samples. In addition, the multiplex influenza A/B/IC RT-LAMP assay had no cross-reactivity with other respiratory viruses.
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Affiliation(s)
- Woong Sik Jang
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Da Hye Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Do-CiC Mihn
- Department of Diagnostic Immunology, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Haan Woo Sung
- Department of Veterinary Microbiology, College of Veterinary Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeeyong Kim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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Liu S, Huang G, Gong Y, Jin X, Meng Y, Peng Y, Zhao J, Li X, Li Q. Rapid and accurate detection of carbapenem-resistance gene by isothermal amplification in Acinetobacter baumannii. BURNS & TRAUMA 2020; 8:tkaa026. [PMID: 32905076 PMCID: PMC7462923 DOI: 10.1093/burnst/tkaa026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/16/2020] [Accepted: 06/02/2020] [Indexed: 11/15/2022]
Abstract
Background Acinetobacter baumannii (A. baumannii) is one of the pivotal pathogens responsible for nosocomial infections, especially in patients with low immune response, and infection with carbapenem-resistant A. baumannii has been increasing in recent years. Rapid and accurate detection of carbapenem-resistance genes in A. baumannii could be of immense help to clinical staff. Methods In this study, a 15-μL reaction system for recombinase polymerase amplification (RPA) was developed and tested. We collected 30 clinical isolates of A. baumannii from the Burn Institute of Southwest Hospital of Third Military Medical University (Army Medical University) for 6 months and tested antibiotic susceptibility using the VITEK 2 system. A. baumannii was detected based on the blaOXA-51 gene by PCR, qPCR and 15 μL-RPA, respectively. Sensitivity and specificity were evaluated. In addition, PCR and 15 μL-RPA data for detecting the carbapenem-resistance gene blaOXA-23 were comparatively assessed. Results The detection limit of the blaOXA-51 gene by 15 μL RPA was 2.86 CFU/ml, with sensitivity comparable to PCR and qPCR. No positive amplification signals were detected in non-Acinetobacter isolates, indicating high specificity. However, only 18 minutes were needed for the 15 μL RPA assay. Furthermore, an antibiotic susceptibility test showed that up to 90% of A. baumannii strains were resistant to meropenem and imipenem; 15 μL RPA data for detecting blaOXA-23 showed that only 10% (n = 3) of A. baumannii isolates did not show positive amplification signals, and the other 90% of (n = 27) isolates were positive, corroborating PCR results. Conclusion We demonstrated that the new 15 μL RPA assay for detecting blaOXA-23 in A. baumannii is faster and simpler than qPCR and PCR. It is a promising alternative molecular diagnostic tool for rapid and effective detection of A. baumannii and drug-resistance genes in the field and point-of-care testing.
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Affiliation(s)
- Shuang Liu
- Department of Plastic & Burns Surgery, The Affiliated Hospital of Southwest Medical University, Tai Ping Street, Luzhou, 646000, China
| | - Guangtao Huang
- Institute of Burn Research, Southwest Hospital, The Army Medical University, Gao Tan Yan Street, Chongqing, 400038, China
| | - Yali Gong
- Institute of Burn Research, Southwest Hospital, The Army Medical University, Gao Tan Yan Street, Chongqing, 400038, China
| | - Xiaojun Jin
- Department of Emergency, The First Affiliated Hospital, Zhejiang University School of Medicine, Qingchun Road, Hangzhou, 310003, China
| | - Yudan Meng
- Department of Plastic & Burns Surgery, The Affiliated Hospital of Southwest Medical University, Tai Ping Street, Luzhou, 646000, China
| | - Yizhi Peng
- Institute of Burn Research, Southwest Hospital, The Army Medical University, Gao Tan Yan Street, Chongqing, 400038, China
| | - Junning Zhao
- Sichuan Translational Medicine Center of Chinese Medicine, Sichuan Academy of Chinese Medical Sciences, Ren Min Nan Lu Road, Chengdu, 610041, China
| | - Xiaolu Li
- School of Medicine, Chengdu University, Xindu Avenue, Chengdu 610106, China
| | - Qin Li
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Tai Ping Street, Luzhou, 646000, China
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Gao X, Liu X, Zhang Y, Wei Y, Wang Y. Rapid and visual detection of porcine deltacoronavirus by recombinase polymerase amplification combined with a lateral flow dipstick. BMC Vet Res 2020; 16:130. [PMID: 32381014 PMCID: PMC7203717 DOI: 10.1186/s12917-020-02341-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/22/2020] [Indexed: 01/19/2023] Open
Abstract
Background Porcine Deltacoronavirus (PDCoV) is a newly emerging Coronavirus that was first identified in 2012 in Hong Kong, China. Since then, PDCoV has subsequently been reported worldwide, causing a high number of neonatal piglet deaths and significant economic losses to the swine industry. Therefore, it is necessary to establish a highly sensitive and specific method for the rapid diagnosis of PDCoV. Results In the present study, a highly sensitive and specific diagnostic method using recombinase polymerase amplification combined with a lateral flow dipstick (LFD-RPA) was developed for rapid and visual detection of PDCoV. The system can be performed under a broad range of temperature conditions from 10 to 37 °C, and the detection of PDCoV can be completed in 10 min at 37 °C. The sensitivity of this assay was 10 times higher than that of conventional PCR with a lower detection limit of 1 × 102 copies/µl of PDCoV. Meanwhile, the LFD-RPA assay specifically amplified PDCoV, while there was no cross-amplification with other swine-associated viruses, including Porcine epidemic diarrhea virus (PEDV), Transmissible gastroenteritis virus (TGEV), Porcine kobuvirus (PKoV), Foot and mouth disease virus (FMDV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine circovirus type 2 (PCV2), Classical swine fever virus (CSFV) and Seneca valley virus (SVV). The repeatability of the test results indicated that this assay had good repeatability. In addition, 68 clinical samples (48 fecal swab specimens and 20 intestinal specimens) were further tested by LFD-RPA and RT-PCR assay. The positive rate of LFD-RPA clinical samples was 26.47% higher than that of conventional PCR (23.53%). Conclusions The LFD-RPA assay successfully detected PDCoV in less than 20 min in this study, providing a potentially valuable tool to improve molecular detection for PDCoV and to monitor the outbreak of PDCoV, especially in low-resource areas and laboratories.
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Affiliation(s)
- Xiang Gao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Xinsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Yongguang Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Yonglu Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
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Abstract
Although highly active antiretroviral therapy (HAART) has been introduced over twenty years ago to treat Human Immunodeficiency Virus (HIV) positive patients, acquired immunodeficiency syndrome (AIDS) is still one of the deadliest diseases found worldwide. AIDS prevalence and mortality rates are usually more pronounced in resource-constrained countries than in the developed world. The lack of trained medical technicians, sophisticated diagnostic equipment, and the overall scarcity of medical infrastructures have severely impacted HIV/AIDS diagnostics, which hinders the initiation and periodic monitoring of antiretroviral therapy (ART). Currently, available HIV viral load assays are not well-suited for resource-limited settings due to their high cost and a requirement for medical/technical infrastructures. In this paper, we review current and emerging diagnostic assays for HIV detection, with a focus on point-of-care (POC) based immunoassays for viral load measurement, drug resistance, and HIV recurrence. We also discuss the limitations of the available HIV assays and highlight the technological advancements in cellphone, paper, and flexible material-based assays which have the potential to improve HIV diagnosis and monitoring, thus assisting with the management of the disease.
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Affiliation(s)
- Md Alamgir Kabir
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA.,Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL, USA
| | - Hussein Zilouchian
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL, USA
| | - Massimo Caputi
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Waseem Asghar
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA.,Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL, USA.,Department of Biological Sciences (courtesy appointment), Florida Atlantic University, Boca Raton, FL, USA
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Liu H, Wang J, Li P, Bai L, Jia J, Pan A, Long X, Cui W, Tang X. Rapid detection of P–35S and T-nos in genetically modified organisms by recombinase polymerase amplification combined with a lateral flow strip. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106775] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chen Z, Huang J, Zhang F, Zhou Y, Huang H. Detection of shrimp hemocyte iridescent virus by recombinase polymerase amplification assay. Mol Cell Probes 2019; 49:101475. [PMID: 31655105 DOI: 10.1016/j.mcp.2019.101475] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Shrimp hemocyte iridescent virus (SHIV), which was first identified in white leg shrimp (Litopenaeus vannamei) in China in 2014, can cause extensive shrimp mortality and major economic losses in the shrimp farming industry in China. In this study, a novel real-time isothermal recombinase polymerase amplification (RPA) assay was developed using a TwistAmp exo kit for SHIV detection. First, five primers and a probe were designed for the major capsid protein gene (GenBank: KY681039.1) according to the TwistDx manual; next, the optimal primers were selected by a comparison experiment. The primers and probe were specific for SHIV and did not react with shrimp white spot syndrome virus (WSSV), shrimp infectious hypodermal and hematopoietic necrosis virus (IHHNV), shrimp enterocytozoon hepatopenaei (EHP), and macrobrachium rosenbergii nodavirus (MrNV) samples, as well as pathogens of acute hepatopancreatic necrosis disease (AHPND). The RPA assay reached a detection limit of 11 copies per reaction according to probit regression analysis. In addition, RPA assay detected the positive plasmid samples at concentration of 1000 copies/μL within 16.04 ± 0.72 min at a single low operation temperature (39 °C). The results proved that the proposed RPA method was an accurate, sensitive, affordable, and rapid detection tool that can be suitably applied for the diagnosis of SHIV in field conditions and in resource-poor settings.
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Affiliation(s)
- Zhengwei Chen
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China; Center of Engineering Training, Zhejiang University of Science and Technology, Hangzhou, P.R. China.
| | - Jun Huang
- College of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Fang Zhang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China.
| | - Yang Zhou
- College of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, P.R. China
| | - Huijie Huang
- Laboratory of Information Optics and Optoelectronic Technology, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, P.R. China; University of Chinese Academy of Sciences, Beijing, P.R. China.
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Kim NY, Lee HJ, Jeong RD. A portable detection assay for Apple stem pitting virus using reverse transcription-recombinase polymerase amplification. J Virol Methods 2019; 274:113747. [PMID: 31580840 DOI: 10.1016/j.jviromet.2019.113747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 09/20/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023]
Abstract
A molecular diagnostic assay for the rapid, sensitive and specific detection of Apple stem pitting virus (ASPV) in infected samples, utilizing reverse transcription-recombinase polymerase amplification (RT-RPA) at an isothermal constant temperature of 42 °C and the designed target-specific primers, was developed. The RT-RPA assay was able to be used in ASPV-infected leaves, rootstocks and fruits. Sensitivity tests, using ASPV transcripts, showed that the RT-RPA with the ASPV-specific primers was more sensitive than the conventional RT-PCR, with a detection limit of 1 fg/μL of RNA. In addition, the reaction time for the amplification of ASPV was shortened to as little as 1 min. The assay was highly specific and did not give a positive reaction to other viruses infecting pears. Moreover, the amplified genomic fragment of ASPV produced by the assay could be determined within 4 min using a portable capillary gel electrophoresis system. The entire process, excluding the extraction of total RNA, could be completed in 5 min using portable equipment in the field. This is the first report of utilizing an RT-RPA assay to detect a pear tree virus and the assay could be used both in the laboratory and in the field for ASPV detection.
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Affiliation(s)
- Nam-Yeon Kim
- Department of Applied Biology and AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61185, Republic of Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology and AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61185, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology and AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61185, Republic of Korea.
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Recombinase polymerase amplification-nucleic acid lateral flow immunoassays for Newcastle disease virus and infectious bronchitis virus detection. Mol Biol Rep 2019; 46:6391-6397. [PMID: 31549369 PMCID: PMC7089497 DOI: 10.1007/s11033-019-05085-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022]
Abstract
Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) are two poultry pathogens affecting the respiratory tract of chickens, and cause major economic losses in the industry. Rapid detection of these viruses is crucial to inform implementation of appropriate control measures. The objective of our study is developing a simple, rapid and field applicable recombinase polymerase amplification (RPA)–nucleic acid lateral flow (NALF) immunoassay for detection of NDV and IBV. Isothermal amplification of the matrix protein (M) gene of NDV and the nucleoprotein (N) gene of IBV was implemented via recombinase polymerase amplification at 38 °C for 40 min and 20 min, respectively using modified labeled primers. NALF device used in this study utilizes antibodies for detection of labeled RPA amplicons. The results revealed that RPA-NALF immunoassays can detect both viruses after 40 min at 38 °C and only NDV after 20 min. The limit of detection (LOD) was 10 genomic copies/RPA reaction. The assays results on clinical samples collected from diseased chicken farms demonstrated a good performance in comparison with quantitative real time reverse transcription polymerase chain reaction (qRT-PCR). The assays established in this study can facilitate rapid, on-site molecular diagnosis of suspected cases of ND and IB viral infections as the results can be detected by the naked eye without the need for measuring fluorescence. Furthermore, the NALF device could be adapted to detect other infectious agents.
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Qin L, Nan W, Wang Y, Zhang Y, Tan P, Chen Y, Mao K, Chen Y. A novel approach for detection of brucella using a real-time recombinase polymerase amplification assay. Mol Cell Probes 2019; 48:101451. [PMID: 31541671 DOI: 10.1016/j.mcp.2019.101451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/15/2019] [Accepted: 09/17/2019] [Indexed: 10/26/2022]
Abstract
Brucella, the etiological agent of brucellosis, is an important zoonosis pathogen worldwide. Brucella infects humans and various domestic and wild animals, and represents a great threat to public health and animal husbandry. In the present study, we developed a real-time recombinase polymerase amplification (RPA) assay for the detection of Brucella. The assay targeted the bcsp31 gene of Brucella, and an RPA exo probe and a pair of primers were selected for assay validation. RPA sensitivity and specificity were evaluated using plasmid standards, Brucella representative strains, and non-Brucella strains. The RPA assay achieved a detection limit of 17 molecules in 95% of cases based on probit analysis, and could successfully distinguish 18 representative Brucella strains (B. abortus biovars 1, 2, 3, 4, 5, 6, 7 and 9, B. melitensis biovars 1, 2 and 3, B. suis biovars 1, 2, 3 and 4, B. canis, B. neotomae and B. ovis), and four Brucella vaccine strains (A19, S19, S2 and M5). A total of 52 Brucella field strains were detected by real-time PCR and RPA in parallel, and compared with real-time PCR, the sensitivity of the RPA assay was 94% (49/52). Thus, this RPA assay may be a rapid, sensitive, and specific tool for the prevention and control of Brucellosis.
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Affiliation(s)
- Lide Qin
- Laboratory of Diagnositics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Wenlong Nan
- Laboratory of Diagnositics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Yong Wang
- Laboratory of Diagnositics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China; College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, China
| | - Yueyong Zhang
- Laboratory of Diagnositics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China
| | - Pengfei Tan
- Laboratory of Diagnositics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China; College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu, 225009, China
| | - Yuqi Chen
- Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu Province, 215123, China
| | - Kairong Mao
- China Institute of Veterinary Drug Control, 8 Zhongguanchun South Street, Beijing, 100081, China
| | - Yiping Chen
- Laboratory of Diagnositics Development, China Animal Health and Epidemiology Center, 369 Nanjing Road, Qingdao, Shandong, 266032, China.
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Wu L, Ye L, Wang Z, Cui Y, Wang J. Utilization of recombinase polymerase amplification combined with a lateral flow strip for detection of Perkinsus beihaiensis in the oyster Crassostrea hongkongensis. Parasit Vectors 2019; 12:360. [PMID: 31340841 PMCID: PMC6657052 DOI: 10.1186/s13071-019-3624-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/19/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Perkinsosis, a disease caused by the protist Perkinsus, is responsible for mass mortalities of many molluscan species worldwide. The rapid, early and accurate detection of Perkinsus infection is necessary to react to outbreaks, and manage disease transmission. Current methods for diagnosis of Perkinsus spp. are time-consuming or require professional equipment and experienced personnel, rendering them unsuitable for field application. Recombinase polymerase amplification (RPA) assay is a highly sensitive and selective isothermal amplification technique that operates at temperatures of 37-42 °C, requires minimal sample preparation, and is capable of amplifying as low as 1-10 target DNA copies in less than 20 minutes. METHODS We report a novel RPA assay that amplifies the internal transcriber spacer (ITS) region of P. beihaiensis, which, followed by rapid detection of amplicons using a lateral flow (LF) strip, enables easy visualization of results by the naked eye. RESULTS The LF-RPA assay successfully amplified P. beihaiensis DNA using a set of primers of 20-25 bp in length. After incubation at 37 °C for 25 min, results were read within 5 min by the naked eye on a lateral flow strip. Our LF-RPA assay was comparably sensitive to qPCR assay, and capable of detecting as few as 26 copies of P. beihaiensis DNA. Cross-amplification occurred with other two Perkinsus species, P. olseni and P. chesapeaki, but not with other potential pathogen taxa in culture environments. We compared the performance of LF-RPA, conventional PCR and qPCR assays on 60 oyster samples. While LF-RPA assay results were 86.2% as sensitive, 77.4% as specific, and generally in agreement with those of conventional PCR results, they were more (93.3%) sensitive, (86.7%) specific, and agreed better with qPCR assay results. Future research should focus on developing simple DNA extraction methods that do not require professional laboratories and complicated extraction procedures, to facilitate application of this LF-RPA assay in the field. CONCLUSIONS Our LF-RPA assay provides a rapid and efficient method for detecting species of Perkinsus. This novel assay has potential to be used in field applications.
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Affiliation(s)
- Lin Wu
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
- Shanghai Ocean University, Shanghai, 201306 China
| | - Lingtong Ye
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
| | - Zhaorui Wang
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
- College of Fisheries, Tianjin Agricultural University, Tianjin, 300384 China
| | - Yingyi Cui
- Zhongshan Center for Animal Disease Prevention and Control, Zhongshan, 528455 Guangdong China
| | - Jiangyong Wang
- Key Laboratory of Aquatic Product Processing; Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300 China
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Nelson MM, Waldron CL, Bracht JR. Rapid molecular detection of macrolide resistance. BMC Infect Dis 2019; 19:144. [PMID: 30755177 PMCID: PMC6373131 DOI: 10.1186/s12879-019-3762-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emerging antimicrobial resistance is a significant threat to human health. However, methods for rapidly diagnosing antimicrobial resistance generally require multi-day culture-based assays. Macrolide efflux gene A, mef(A), provides resistance against erythromycin and azithromycin and is known to be laterally transferred among a wide range of bacterial species. METHODS We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. To validate these results we performed broth dilution assays to assess antimicrobial resistance to erythromycin and ampicillin (a negative control). RESULTS We validate the detection of mef(A) in raw lysates of Streptococcus pyogenes, S. pneumoniae, S. salivarius, and Enterococcus faecium bacterial lysates within 7-10 min of assay time. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. The assay was unaffected by single-nucleotide polymorphisms within divergent mef(A) gene sequences, strengthening its utility as a robust diagnostic tool. CONCLUSIONS This finding opens the door to implementation of rapid genomic diagnostics in a clinical setting, while providing researchers a rapid, cost-effective tool to track antibiotic resistance in both pathogens and commensal strains.
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Affiliation(s)
- Megan M. Nelson
- Department of Biology, American University, Washington, DC 20016 USA
| | | | - John R. Bracht
- Department of Biology, American University, Washington, DC 20016 USA
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Frimpong M, Ahor HS, Wahed AAE, Agbavor B, Sarpong FN, Laing K, Wansbrough-Jones M, Phillips RO. Rapid detection of Mycobacterium ulcerans with isothermal recombinase polymerase amplification assay. PLoS Negl Trop Dis 2019; 13:e0007155. [PMID: 30707706 PMCID: PMC6373974 DOI: 10.1371/journal.pntd.0007155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/13/2019] [Accepted: 01/14/2019] [Indexed: 01/05/2023] Open
Abstract
Background Access to an accurate diagnostic test for Buruli ulcer (BU) is a research priority according to the World Health Organization. Nucleic acid amplification of insertion sequence IS2404 by polymerase chain reaction (PCR) is the most sensitive and specific method to detect Mycobacterium ulcerans (M. ulcerans), the causative agent of BU. However, PCR is not always available in endemic communities in Africa due to its cost and technological sophistication. Isothermal DNA amplification systems such as the recombinase polymerase amplification (RPA) have emerged as a molecular diagnostic tool with similar accuracy to PCR but having the advantage of amplifying a template DNA at a constant lower temperature in a shorter time. The aim of this study was to develop RPA for the detection of M. ulcerans and evaluate its use in Buruli ulcer disease. Methodology and principal findings A specific fragment of IS2404 of M. ulcerans was amplified within 15 minutes at a constant 42°C using RPA method. The detection limit was 45 copies of IS2404 molecular DNA standard per reaction. The assay was highly specific as all 7 strains of M. ulcerans tested were detected, and no cross reactivity was observed to other mycobacteria or clinically relevant bacteria species. The clinical performance of the M. ulcerans (Mu-RPA) assay was evaluated using DNA extracted from fine needle aspirates or swabs taken from 67 patients in whom BU was suspected and 12 patients with clinically confirmed non-BU lesions. All results were compared to a highly sensitive real-time PCR. The clinical specificity of the Mu-RPA assay was 100% (95% CI, 84–100), whiles the sensitivity was 88% (95% CI, 77–95). Conclusion The Mu-RPA assay represents an alternative to PCR, especially in areas with limited infrastructure. Current diagnostic methods to detect M. ulcerans suffer from delayed time-to-results in most endemic countries by the prolonged period of time for the shipment and storage of samples to a distant, centralized laboratory. The M. ulcerans recombinase polymerase amplification assay (Mu-RPA) is a new, rapid diagnostic test developed for the detection of M. ulcerans infection, known commonly as Buruli ulcer, a chronic, debilitating, necrotizing disease of the skin and soft tissues. This assay is suitable for use on a portable detection device, with the potential to be used for quick diagnosis at the point of need, providing timely results to health workers at Buruli ulcer treatment clinics.
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Affiliation(s)
- Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- * E-mail:
| | - Hubert Senanu Ahor
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, Georg-August University, Goettingen, Germany
| | - Bernadette Agbavor
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Francisca Naana Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kenneth Laing
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| | - Mark Wansbrough-Jones
- Institute for Infection and Immunity, St. George’s University of London, London, United Kingdom
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Li J, Macdonald J, von Stetten F. Review: a comprehensive summary of a decade development of the recombinase polymerase amplification. Analyst 2019; 144:31-67. [DOI: 10.1039/c8an01621f] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RPA is a versatile complement or replacement of PCR, and now is stepping into practice.
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Affiliation(s)
- Jia Li
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
| | - Joanne Macdonald
- Inflammation and Healing Research Cluster
- Genecology Research Centre
- School of Science and Engineering
- University of the Sunshine Coast
- Australia
| | - Felix von Stetten
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
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