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Sun L, Cheng Y, Fei D, Ma Y, Ma M, Li M. Establishment of a reverse transcription-recombinase polymerase amplification-lateral flow dipstick method for the dual detection of Israeli acute paralysis virus and chronic bee paralysis virus. Front Microbiol 2024; 15:1389313. [PMID: 38817969 PMCID: PMC11137664 DOI: 10.3389/fmicb.2024.1389313] [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: 02/21/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Abstract
Introduction As an important social insect, honey bees play crucial roles in agricultural production, sustainable development of agricultural production, and the balance of the natural environment. However, in recent years, Israeli acute paralysis virus (IAPV) and chronic bee paralysis virus (CBPV), the main pathogens of bee paralysis, have continuously harmed bee colonies and caused certain losses to the beekeeping industry. Some beekeeping farms are located in wild or remote mountainous areas, and samples from these farms cannot be sent to the laboratory for testing in a timely manner, thereby limiting the accurate and rapid diagnosis of the disease. Methods and results In this study, we used a reverse transcription-recombinase polymerase amplification-lateral flow dipstick (RT-RPA-LFD) method for the dual detection of IAPV and CBPV. RPA primers and LFD detection probes were designed separately for their conserved genes. Primers and probes were screened, and the forward and reverse primer ratios, reaction times, and temperatures were optimized. According to the results of the optimization tests, the optimal reaction temperature for RT-RPA is 37°C, and when combined with LFD, detection with the naked eye requires <20 min. The developed RPA-LFD method specifically targets IAPV and CBPV and has no cross-reactivity with other common bee viruses. In addition, the minimum detection limit of the RT-RPA-LFD method is 101 copies/μL. Conclusion Based this study, this method is suitable for the detection of clinical samples and can be used for field detection of IAPV and CBPV.
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Affiliation(s)
- Li Sun
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Yu Cheng
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Dongliang Fei
- Experimental Animal Center of Jinzhou Medical University, Jinzhou, China
| | - Yueyu Ma
- Experimental Animal Center of Jinzhou Medical University, Jinzhou, China
| | - Mingxiao Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
| | - Ming Li
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, China
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Jiang L, Zhang G, Wang P, Niu X, Liu Q, Zhang S, Gao W, Li Y. Simultaneous detection of bovine viral diarrhea virus (BVDV) and bovine herpesvirus 1 (BoHV-1) using recombinase polymerase amplification. Sci Rep 2024; 14:10169. [PMID: 38702375 PMCID: PMC11068760 DOI: 10.1038/s41598-024-56869-7] [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: 01/15/2024] [Accepted: 03/12/2024] [Indexed: 05/06/2024] Open
Abstract
Bovine viral diarrhea virus (BVDV) is considered to be the most common agent of severe diarrhea in cattle worldwide, causing fever, diarrhea, ulcers, and abortion. Bovine herpesvirus 1 (BoHV-1) is also a major bovine respiratory disease agent that spreads worldwide and causes extensive damage to the livestock industry. Recombinase polymerase amplification (RPA) is a novel nucleic acid amplification method with the advantages of high efficiency, rapidity and sensitivity, which has been widely used in the diagnosis of infectious diseases. A dual RPA assay was developed for the simultaneous detection of BVDV and BoHV-1. The assay was completed at a constant temperature of 37 °C for 30 min. It was highly sensitive and had no cross-reactivity with other common bovine viruses. The detection rate of BVDV RPA in clinical samples (36.67%) was higher than that of PCR (33.33%), the detection rate of BoHV-1 RPA and PCR were equal. Therefore, the established dual RPA assay for BVDV and BoHV-1 could be a potential candidate for use as an immediate diagnostic.
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Affiliation(s)
- Lingling Jiang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Gang Zhang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Pu Wang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Xiaoxia Niu
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Qiang Liu
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Sinong Zhang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Weifeng Gao
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Yong Li
- School of Life Sciences, Ningxia University, Yinchuan, China.
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China.
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Bian Z, Liu W, Jin J, Hao Y, Jiang L, Xie Y, Zhang H. Development of a recombinase polymerase amplification assay with lateral flow dipstick (RPA-LFD) for rapid detection of Shigella spp. and enteroinvasive Escherichia coli. PLoS One 2022; 17:e0278869. [PMID: 36508428 PMCID: PMC9744308 DOI: 10.1371/journal.pone.0278869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/26/2022] [Indexed: 12/14/2022] Open
Abstract
Shigella spp. and enteroinvasive Escherichia coli (EIEC) are widely distributed and can cause serious food-borne diseases for humans such as dysentery. Therefore, an efficient detection platform is needed to detect Shigella and EIEC quickly and sensitively. In this study, a method called recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) was developed for rapid detection of Shigella and EIEC. RPA primers and LFD detection probes were designed for their shared virulence gene ipaH. Primers and probes were screened, and the primer concentration, and reaction time and temperature were optimized. According to the optimization results, the RPA reaction should be performed at 39°C, and when combined with LFD, it takes less than 25 min for detection with the naked eye. The developed RPA-LFD method specifically targets gene ipaH and has no cross-reactivity with other common food-borne pathogens. In addition, the minimum detection limit of RPA-LFD is 1.29×102 copies/μL. The detection of food sample showed that the RPA-LFD method was also verified for the detection of actual samples.
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Affiliation(s)
- Zheng Bian
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Wenbo Liu
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Junhua Jin
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Yanling Hao
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Linshu Jiang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yuanhong Xie
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Hongxing Zhang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
- * E-mail:
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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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5
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Guo Y, Wang Y, Fan Z, Zhao X, Bergmann SM, Dong H, Jin Y, Sun D, Mai Q, Liu W, Zeng W. Establishment and evaluation of qPCR and real-time recombinase-aided amplification assays for detection of largemouth bass ranavirus. JOURNAL OF FISH DISEASES 2022; 45:1033-1043. [PMID: 35475515 DOI: 10.1111/jfd.13627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Largemouth bass ranavirus disease (LMBVD) caused by largemouth bass ranavirus (LMBV) has resulted in severe economic losses in the largemouth bass (Micropterus salmoides) farming industry in China. Early and accurate diagnosis is the key measure for the prevention and control of LMBVD. In this study, a quantitative polymerase chain reaction (qPCR) and a real-time recombinase-aided amplification (real-time RAA) assay were established for the detection of LMBV. The sensitivity and specificity of these two methods, and the efficacy for detection of LMBV from clinical samples were also evaluated. Results showed that the real-time RAA reaction was completed in <30 min at 39℃ with a detection limit of 58.3 copies, while qPCR reaction required 60 min with a detection limit of 5.8 copies. Both methods were specific for LMBV, where no cross-reactions observed with the other tested fish pathogens. Comparing the amplification results of both assays to the results obtained by virus isolation using 53 clinical tissue samples, results showed that the clinical sensitivity of real-time RAA and qPCR were 93.75% and 100% respectively, and the clinical specificity of both were 100%. Our results showed that qPCR is more suitable for quantitative analysis and accurate detection of LMBV in the laboratory, while real-time RAA is more suitable as a point-of-care diagnostic tool for on-site detection and screening of LMBV under farm conditions and in poorly equipped laboratories.
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Affiliation(s)
- Yanmin Guo
- College of Pharmacy, Heze University, Heze, China
| | - Yahui Wang
- Guangdong Yongshun Biopharmaceutical Co. Ltd., Zhaoqing, China
| | - Zhaobin Fan
- College of Pharmacy, Heze University, Heze, China
| | - Xianlin Zhao
- College of Pharmacy, Heze University, Heze, China
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-InselRiems, Germany
| | - Hanxu Dong
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yuqi Jin
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Dongli Sun
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Qianyi Mai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Weiqiang Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Weiwei Zeng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
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Srisrattakarn A, Panpru P, Tippayawat P, Chanawong A, Tavichakorntrakool R, Daduang J, Wonglakorn L, Lulitanond A. Rapid detection of methicillin-resistant Staphylococcus aureus in positive blood-cultures by recombinase polymerase amplification combined with lateral flow strip. PLoS One 2022; 17:e0270686. [PMID: 35771885 PMCID: PMC9246191 DOI: 10.1371/journal.pone.0270686] [Citation(s) in RCA: 6] [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: 02/20/2022] [Accepted: 06/15/2022] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), is an important bacterium that causes community and healthcare-related infections throughout the world. However, the current conventional detection methods are time-consuming. We therefore developed and evaluated a recombinase polymerase amplification-lateral flow strip (RPA-LF) approach for detection of MRSA in positive blood-culture samples. Sixty positive blood-cultures from a hospital were tested directly without DNA extraction and purification before the amplification reaction. RPA primers and probes were designed for nuc (encoding thermonuclease) and mecA (encoding penicillin-binding protein 2a) genes to diagnose S. aureus and its methicillin-resistance status. The RPA reaction occurred under isothermal conditions (45°C) within 20 min and a result was provided by the LF strip in a further 5 min at room temperature. The evaluation of RPA-LF using blood-culture samples showed 93.3% (14/15) sensitivity for identifying S. aureus, and no cross-amplification was seen [100% (45/45) specificity]. For detection of methicillin resistance, the RPA-LF test provided 100% (16/16) sensitivity and 97.7% (43/44) specificity. The RPA-LF is rapid, highly sensitive, robust and easy to use. It can be used for direct detection of MRSA with no requirement for special equipment.
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Affiliation(s)
- Arpasiri Srisrattakarn
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Pimchanok Panpru
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Patcharaporn Tippayawat
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonwadee Chanawong
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ratree Tavichakorntrakool
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Jureerut Daduang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Lumyai Wonglakorn
- Clinical Microbiology Unit, Srinagarind Hospital, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonlug Lulitanond
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- Department of Medical Technology, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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7
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A panoptic review of techniques for finfish disease diagnosis: The status quo and future perspectives. J Microbiol Methods 2022; 196:106477. [DOI: 10.1016/j.mimet.2022.106477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
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Maekawa S, Pulpipat T, Wang PC, Chen SC. Transcriptome analysis of immune- and iron-related genes after Francisella noatunensis subsp. orientalis infection in Nile tilapia (Oreochromis niloticus). FISH & SHELLFISH IMMUNOLOGY 2021; 111:36-48. [PMID: 33444737 DOI: 10.1016/j.fsi.2020.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Francisella noatunensis subsp. orientalis (Fno) is a gram-negative intracellular bacterium identified in many fish species worldwide, including cultured Nile tilapia (Oreochromis niloticus) in Taiwan. To investigate the gene expression responses to Fno infection, we performed transcriptome analysis of the head kidney and spleen in Nile tilapia using RNA-seq. Total RNA was extracted from the head kidney and spleen of infected (Fno-injected) and uninfected (control) tilapia at 1-day and 2-days post-infection, and RNA-seq was performed using the Illumina HiSeq™ 4000 platform. After de novo assembly, a total of 106,534 transcripts were detected. These transcripts were annotated and categorized into a total of 7171 genes based on the KEGG pathway database. Differentially expressed genes (DEGs) were significantly (2-fold difference comparing Fno and PBS groups at each time point) enriched in the immune-related pathways, including the following: complement and coagulation cascades, cytokine-cytokine receptor interaction, hematopoietic cell lineage, lysosome, phagosome. We identified the upregulation of inflammatory cytokine-, apoptosis-, and neutrophil-related genes, and downregulation of complement- and lymphocyte-related genes. Additionally, we found the induction of natural resistance-associated macrophage protein 1 (NRAMP1) and heme responsive gene-1 (HRG1). Anemia of inflammation, caused by intracellular iron storage in spleen after Fno infection, was also observed. This study provides natural disease control strategies against Fno infection in tilapia. It is suggested that intercellular iron storage is a host protection strategy.
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Affiliation(s)
- Shun Maekawa
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan; International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan; General Research Service Centre, National Pingtung University of Science and Technology, Pingtung, Taiwan.
| | - Theeraporn Pulpipat
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan; International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan.
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Göpfert L, Elsner M, Seidel M. Isothermal haRPA detection of bla CTX-M in bacterial isolates from water samples and comparison with qPCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:552-557. [PMID: 33410433 DOI: 10.1039/d0ay02000a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Antibiotic resistant bacteria complicate infection treatment worldwide. Rapid and inexpensive detection of the current occurrence of antibiotic resistant bacteria in surface and irrigation water as well as treated wastewater is essential to minimize exposure and further spread. To reduce cost and analysis time compared to current qPCR (quantitative polymerase chain reaction), isothermal nucleic acid amplification tests are promising bioanalytical methods which can be integrated in simplified molecular biological detection systems. This study establishes heterogeneous asymmetric recombinase polymerase amplification (haRPA) for the detection of antibiotic resistance genes in water. After DNA extraction of bacteria cultivated from water, the target DNA for blaCTX-M cluster 1 was amplified at 39 °C for 40 min on a microfluidic DNA chip. The amplified DNA on each spot was quantified by a flow-based chemiluminescence reaction. Even though slightly less sensitive than conventional qPCR, the haRPA method was successful in identifying the blaCTX-M cluster 1 in bacterial isolates with a limit of detection of 0.013 ng μL-1. In a proof-of-principle study, 37 bacterial isolates from environmental water samples were classified according to blaCTX-M cluster 1 occurrence and gave 100% agreement in cross-reference with PCR. Importantly, haRPA allows for a quick in-field monitoring at low incubation temperatures and by an easy visual readout. This study paves the path to establish haRPA as a quick on-site monitoring option for antibiotic resistance gene occurrence without the need for a thermal cycling device or long data processing.
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Affiliation(s)
- Lisa Göpfert
- Institute of Hydrochemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistr. 17, 81377 Munich, Germany.
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Aman R, Mahas A, Marsic T, Hassan N, Mahfouz MM. Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA-CRISPR/Cas12a Assay. Front Microbiol 2020; 11:610872. [PMID: 33391239 PMCID: PMC7773598 DOI: 10.3389/fmicb.2020.610872] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/30/2020] [Indexed: 12/25/2022] Open
Abstract
Most viruses that infect plants use RNA to carry their genomic information; timely and robust detection methods are crucial for efficient control of these diverse pathogens. The RNA viruses, potexvirus (Potexvirus, family Alphaflexiviridae), potyvirus (Potyvirus, family Potyviridae), and tobamovirus (Tobamovirus, family Virgaviridae) are among the most economically damaging pathogenic plant viruses, as they are highly infectious and distributed worldwide. Their infection of crop plants, alone or together with other viruses, causes severe yield losses. Isothermal nucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and others have been harnessed for the detection of DNA- and RNA-based viruses. However, they have a high rate of non-specific amplification and other drawbacks. The collateral activities of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease Cas systems such as Cas12 and Cas14 (which act on ssDNA) and Cas13 (which acts on ssRNA) have recently been exploited to develop highly sensitive, specific, and rapid detection platforms. Here, we report the development of a simple, rapid, and efficient RT- RPA method, coupled with a CRISPR/Cas12a-based one-step detection assay, to detect plant RNA viruses. This diagnostic method can be performed at a single temperature in less than 30 min and integrated with an inexpensive commercially available fluorescence visualizer to facilitate rapid, in-field diagnosis of plant RNA viruses. Our developed assay provides an efficient and robust detection platform to accelerate plant pathogen detection and fast-track containment strategies.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Norhan Hassan
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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11
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Ma L, Shi H, Zhang M, Song Y, Zhang K, Cong F. Establishment of a Real-Time Recombinase Polymerase Amplification Assay for the Detection of Avian Reovirus. Front Vet Sci 2020; 7:551350. [PMID: 33195523 PMCID: PMC7536300 DOI: 10.3389/fvets.2020.551350] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
Avian reovirus (ARV) infection results in multiple disease manifestations in chicken. A rapid detection method will contribute to early diagnosis and control of the virus infection. The recombinase polymerase amplification (RPA) technology is a nucleic acid amplification method which is experiencing rapid development. In present study, a real-time reverse transcription (RT)-RPA assay was developed for the detection of ARV. The limit of detection of the real-time RT-RPA was 102 copies/μL of ARV genomic RNA standard in 95% of cases. The RT-RPA assay also exhibited remarkable specificity. When the nucleic acids of CRV and other common avian pathogens were subjected to the RT-RPA test, only ARV tested positive, all the other pathogens tested negative. Furthermore, the practicality of the RT-RPA assay in field was confirmed by testing 86 clinical samples. The clinical samples were also detected by qRT-PCR. The detection result by RT-RPA was 96.5% agreement with that of qRT-PCR. As a result of the simplicity and convenience of the assay with high sensitivity and specificity, the probe-based RT-RPA will be an alternative diagnostic assay for the detection of ARV in resource-limited settings.
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Affiliation(s)
- Lei Ma
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China.,Henan Joint International Research Laboratory of Veterinary Biologics Research and Application, Academician Workstation of Animal Disease Control and Nutrition Immunity in Henan Province, Anyang, China
| | - Hongfei Shi
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, China-UK-NYNU-RRes Joint Libratory of Insect Biology, Nanyang Normal University, Nanyang, China
| | - Mingliang Zhang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China.,Henan Joint International Research Laboratory of Veterinary Biologics Research and Application, Academician Workstation of Animal Disease Control and Nutrition Immunity in Henan Province, Anyang, China
| | - Yuwei Song
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China.,Henan Joint International Research Laboratory of Veterinary Biologics Research and Application, Academician Workstation of Animal Disease Control and Nutrition Immunity in Henan Province, Anyang, China
| | - Kunpeng Zhang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China.,Henan Joint International Research Laboratory of Veterinary Biologics Research and Application, Academician Workstation of Animal Disease Control and Nutrition Immunity in Henan Province, Anyang, China
| | - Feng Cong
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
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Kanitchinda S, Srisala J, Suebsing R, Prachumwat A, Chaijarasphong T. CRISPR-Cas fluorescent cleavage assay coupled with recombinase polymerase amplification for sensitive and specific detection of Enterocytozoon hepatopenaei. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 27:e00485. [PMID: 32577410 PMCID: PMC7301165 DOI: 10.1016/j.btre.2020.e00485] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/08/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022]
Abstract
Enterocytozoon hepatopenaei (EHP) is a parasite that infects pacific whiteleg shrimp, Penaeus vannamei, causing growth retardation and uneven size distributions that lead to severe losses in shrimp productivity. Routine monitoring is crucial to timely prevention and management of EHP, but field-deployable diagnostic kits for EHP are still scarce. Here, we proposed the use of recombinase polymerase amplification (RPA) and CRISPR-Cas12a fluorescence assay, henceforth RPA-Cas12a, for detection of EHP. Targeting ptp2 gene, RPA-Cas12a could detect as few as 50 copies of DNA and showed no reactivity with closely related microsporidia. The entire procedure could be performed at a temperature close to 37 °C within 1 h. Naked eye visualization was possible with UV/blue-light excitation or lateral flow detection. Thus, RPA-Cas12a is a rapid, sensitive and specific detection platform that requires no sophisticated equipment and shows promise for on-site surveillance of EHP.
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Key Words
- CRISPR, clustered regularly interspaced short palindromic repeats
- CRISPR-Cas12a
- Cas, CRISPR-associated protein
- EHP, Enterocytozoon hepatopenaei
- Eca, Enterospora canceri
- Enterocytozoon hepatopenaei
- FB, FAM-ssDNA-Biotin reporter
- FQ, fluorescent-quencher reporter
- Her, Hepatospora eriocheir
- IHHNV, infectious hypodermal and hematopoietic necrosis virus
- LFD, lateral flow dipstick
- Lateral flow detection
- NTC, no-template control
- PAM, protospacer adjacent motif
- RPA
- RPA, recombinase polymerase amplification
- RPA-Cas12a, RPA coupled with Cas12a cleavage assay
- SWP-PCR, nested PCR targeting swp
- WSSV, white spot syndrome virus
- ptp2, polar tube protein 2
- swp, spore wall protein
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Affiliation(s)
- Suthasinee Kanitchinda
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
| | - Jiraporn Srisala
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group (AAQG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Road, Bangkok 10400, Thailand
| | - Rungkarn Suebsing
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group (AAQG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Road, Bangkok 10400, Thailand
| | - Anuphap Prachumwat
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology Research Group (AAQG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Road, Bangkok 10400, Thailand
| | - Thawatchai Chaijarasphong
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400, Thailand
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Hu J, Wang Y, Ding H, Jiang C, Geng Y, Sun X, Jing J, Gao H, Wang Z, Dong C. Recombinase polymerase amplification with polymer flocculation sedimentation for rapid detection of Staphylococcus aureus in food samples. Int J Food Microbiol 2020; 331:108691. [PMID: 32534163 DOI: 10.1016/j.ijfoodmicro.2020.108691] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 01/02/2023]
Abstract
Currently, rapid, sensitive, and convenient visual detection methods for Staphylococcus aureus (S. aureus) are scarce. In this study, a novel detection method based on recombinase polymerase amplification (RPA) and polymer flocculation sedimentation (PFS) was developed. Twelve effective primer combinations derived from four forward primers F1, F2, F3, F4, and three reverse primers R1, R2, R3 targeting the nuc gene of S. aureus were designed and screened by a polymerase chain reaction and RPA methods. RPA reaction conditions, including temperature, time, and volume as well as PEG8000 and NaCl concentrations range, were optimized. Moreover, the specificity and sensitivity of the RPA-PFS assay were further analyzed. Finally, the potential use of the RPA-PFS assay was evaluated using artificially S. aureus contaminated food samples, including pork, beef, shrimp, fish, cheese, cabbage, leftover rice, egg, milk, and orange juice. Results showed that the SA5 (F2/R2) combination was the optimal primer candidate. The optimal temperature range, the shortest time and the minimal volume of RPA reaction were 40-42 °C, 10 min and 10 μL, respectively and the optimal PEG8000/NaCl concentrations were 0.2 g/mL and 2.5 M, respectively, for the adsorption between magnetic beads and RPA products. The RPA-PFS method could detect as little as 13 fg genomic DNA of S. aureus and was also specific for five target S. aureus as well as twenty-seven non-target foodborne bacteria. The limit of detection of RPA-PFS for S. aureus in artificially contaminated food samples was 38 CFU/mL (g). Besides, RPA-PFS has directly been judged by the naked eye and has totally taken less than 20 min. In short, the assay RPA-PFS developed in this study is a rapid, sensitive, and specific visual detection method for S. aureus.
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Affiliation(s)
- Jinqiang Hu
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China; Collaborative Innovation Center of Food Production and Safety, Zhengzhou 450000, Henan Province, China; Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Zhengzhou 450000, Henan Province, China.
| | - Yi Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Huimin Ding
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Chunpeng Jiang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Yao Geng
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Xincheng Sun
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Jianzhou Jing
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Hui Gao
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China; International Joint Laboratory of Food Safety, Zhengzhou 450000, Henan Province, China
| | - Zhangcun Wang
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
| | - Caiwen Dong
- School of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan Province, China
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Development of a Sensitive and Rapid Recombinase Polymerase Amplification Assay for Detection of Anaplasma phagocytophilum. J Clin Microbiol 2020; 58:JCM.01777-19. [PMID: 32132189 DOI: 10.1128/jcm.01777-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
Human granulocytic anaplasmosis (HGA) is a tick-borne disease caused by the obligate intracellular Gram-negative bacterium Anaplasma phagocytophilum The disease often presents with nonspecific symptoms with negative serology during the acute phase. Direct pathogen detection is the best approach for early confirmatory diagnosis. Over the years, PCR-based molecular detection methods have been developed, but optimal sensitivity is not achieved by conventional PCR while real-time PCR requires expensive and sophisticated instruments. To improve the sensitivity and also develop an assay that can be used in resource-limited areas, an isothermal DNA amplification assay based on recombinase polymerase amplification (RPA) was developed. To do this, we identified a 171-bp DNA sequence within multiple paralogous copies of msp2 within the genome of A. phagocytophilum Our novel RPA assay targeting this sequence has an analytical limit of detection of one genome equivalent copy of A. phagocytophilum and can reliably detect 125 bacteria/ml in human blood. A high level of specificity was demonstrated by the absence of nonspecific amplification using genomic DNA from human or DNA from other closely-related pathogenic bacteria, such as Anaplasma platys, Ehrlichia chaffeensis, Orientia tsutsugamushi, and Rickettsia rickettsii, etc. When applied to patient DNA extracted from whole blood, this new RPA assay was able to detect 100% of previously diagnosed A. phagocytophilum cases. The sensitivity and rapidness of this assay represents a major improvement for early diagnosis of A. phagocytophilum in human patients and suggest a role for better surveillance in its reservoirs or vectors, especially in remote regions where resources are limited.
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Recent advances in nucleic acid-based methods for detection of helminth infections and the perspective of biosensors for future development. Parasitology 2019; 147:383-392. [PMID: 31840627 DOI: 10.1017/s0031182019001665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pathogenic helminth infections are responsible for severe health problems and economic losses worldwide. Timely and accurate diagnosis of helminth infections is critical for adopting suitable strategies for pathogen control. Here, we review recent advances in nucleic acid-based diagnostic methods, including polymerase chain reaction, quantitative qPCR, loop-mediated isothermal amplification and recombinase polymerase amplification, and discuss their advantages and disadvantages for diagnosing helminth infections. In addition, we highlight recent advances in biosensors for the detection of nucleic acid biomarkers that can potentially be used for the diagnosis of helminth infection.
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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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Zhang TT, Liu MZ, Yin RH, Yao LQ, Liu BS, Chen ZL. Rapid and simple detection of Glaesserella parasuis in synovial fluid by recombinase polymerase amplification and lateral flow strip. BMC Vet Res 2019; 15:294. [PMID: 31412870 PMCID: PMC6694577 DOI: 10.1186/s12917-019-2039-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/02/2019] [Indexed: 01/02/2023] Open
Abstract
Background Glaesserella parasuis (G. parasuis) is an influential pathogen of the pig, which induces high morbidity and mortality in naive pig populations in the pig industry. Accurate and rapid detection of the agent is important for disease control. In this study, a simple recombinase polymerase amplification (RPA) with a Lateral flow (LF) strip (RPA-LF-GPS) was developed to detect G. parasuis. Results The RPA-LF-GPS can specifically detect G. parasuis a limit of 100 CFU from other common related pathogens causing arthritis in the pig. The RPA-LF-GPS assay can use boiled synovial fluid samples as a template with the same sensitivity as other DNA extraction methods. In the detection of clinic positive synovial fluid sample, RPA-LF-GPS is equally sensitive (98.1%) compared with that of PCR (90.4%) (P > 0.05). The whole procedure of the RPA-LF-GPS assay could be finished in 1 hour without professional equipment. Conclusions RPA-LF-GPS assay is a rapid and simple method for point-of-care diagnostic testing for G. parasuis infection.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, No. 120 Dongling road, Shenyang, 110866, China
| | - Meng-Zhi Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, No. 120 Dongling road, Shenyang, 110866, China
| | - Rong-Huan Yin
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, No. 120 Dongling road, Shenyang, 110866, China
| | - Long-Quan Yao
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, No. 120 Dongling road, Shenyang, 110866, China
| | - Bao-Shan Liu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, No. 120 Dongling road, Shenyang, 110866, China.
| | - Ze-Liang Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, No. 120 Dongling road, Shenyang, 110866, China.
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Shahin K, Shinn AP, Metselaar M, Ramirez-Paredes JG, Monaghan SJ, Thompson KD, Hoare R, Adams A. Efficacy of an inactivated whole-cell injection vaccine for nile tilapia, Oreochromis niloticus (L), against multiple isolates of Francisella noatunensis subsp. orientalis from diverse geographical regions. FISH & SHELLFISH IMMUNOLOGY 2019; 89:217-227. [PMID: 30951851 DOI: 10.1016/j.fsi.2019.03.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Francisellosis, induced by Francisella noatunensis subsp. orientalis (Fno), is an emerging bacterial disease representing a major threat to the global tilapia industry. There are no commercialised vaccines presently available against francisellosis for use in farmed tilapia, and the only available therapeutic practices used in the field are either the prolonged use of antibiotics or increasing water temperature. Recently, an autogenous whole cell-adjuvanted injectable vaccine was developed that gave 100% relative percent survival (RPS) in tilapia challenged with a homologous isolate of Fno. In this study, we evaluated the efficacy of this vaccine against challenge with heterologous Fno isolates. Healthy Nile tilapia, Oreochromis niloticus (∼15 g) were injected intraperitoneally (i.p.) with the vaccine, adjuvant-alone or phosphate buffer saline (PBS) followed by an i.p. challenge with three Fno isolates from geographically distinct locations. The vaccine provided significant protection in all groups of vaccinated tilapia, with a significantly higher RPS of 82.3% obtained against homologous challenge, compared to 69.8% and 65.9% with the heterologous challenges. Protection correlated with significantly higher specific antibody responses, and western blot analysis demonstrated cross-isolate antigenicity with fish sera post-vaccination and post-challenge. Moreover, a significantly lower bacterial burden was detected by qPCR in conjunction with significantly greater expression of IgM, IL-1 β, TNF-α and MHCII, 72 h post-vaccination (hpv) in spleen samples from vaccinated tilapia compared to fish injected with adjuvant-alone and PBS. The Fno vaccine described in this study may provide a starting point for development a broad-spectrum highly protective vaccine against francisellosis in tilapia.
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Affiliation(s)
- Khalid Shahin
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK; Aquatic Animal Diseases Lab, Aquaculture Department, National Institute of Oceanography and Fisheries (NIOF), P.O. Box 43511, Suez, Egypt.
| | - Andrew P Shinn
- Fish Vet Group Asia, 21/359 Premjairard Road, Chonburi, 20130, Thailand
| | - Matthijs Metselaar
- Benchmark Animal Health, Bush House, Edinburgh Technopole, Midlothian, Edinburgh, EH26 0BB, UK
| | | | - Sean J Monaghan
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Kim D Thompson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK
| | - Rowena Hoare
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
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Pulpipat T, Lin KH, Chen YH, Wang PC, Chen SC. Molecular characterization and pathogenicity of Francisella noatunensis subsp. orientalis isolated from cultured tilapia (Oreochromis sp.) in Taiwan. JOURNAL OF FISH DISEASES 2019; 42:643-655. [PMID: 30715744 DOI: 10.1111/jfd.12964] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/28/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
Francisella noatunensis subsp. orientalis is a causative agent of systemic granulomatous disease in tilapia. The present study was designed to understand the genetic and phenotypic diversities among Taiwanese Fno isolates obtained from tilapia (n = 17) and green Texas cichlid (Herichthys cyanoguttatus) (n = 1). The enzymatic profiles of the isolates were studied using the API ZYM system. Phylogenetic tree analysis of the 16S rRNA and housekeeping gene and pulsed-field gel electrophoresis (PFGE) were carried out to determine the genotypic characters of all isolates. The phylogenetic tree showed similarity of 99%-100% nucleotide sequences of 16S rRNA and housekeeping genes compared to the Fno references genes from GenBank database. Comparatively, the results revealed an identical profile of enzymatic and PFGE pattern which was distincted from that of F. philomiragia. To understand the pathogenicity, the isolates were intraperitoneal injected to tilapia the gross lesions were observed concomitant with natural outbreak. Median lethal dose upon Nile tilapia and red tilapia were 9.06 × 103 CFU/fish and 2.08 × 102 CFU/fish, respectively. Thus, our data provide understanding the epidemiology of Taiwanese Fno isolates, and help in development of future control and prevention.
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Affiliation(s)
- Theeraporn Pulpipat
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Kuo-Hua Lin
- Animal Protection Office, Taoyuan City, Taiwan
| | | | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Southern Taiwan Fish Diseases Research Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- International Degree Program of Ornamental Fish Technology and Aquatic Animal Health, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung, Taiwan
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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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Ma L, Cong F, Zhu Y, Wu M, Xu F, Huang R, Moore RJ, Guo P. Development of a reverse transcription recombinase polymerase amplification assay for rapid detection of Theiler's murine encephalomyelitis virus. Mol Cell Probes 2018; 41:27-31. [PMID: 30157451 DOI: 10.1016/j.mcp.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/06/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022]
Abstract
Theiler's murine encephalomyelitis virus (TMEV) is one of the most common viral pathogens that circulate widely in captive mouse colonies. A molecular biology detection method would be a useful tool to use in an integrated program to monitor and prevent TMEV infection and transmission. Thus, a reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed to detect TMEV infection. The sensitivity of the RT-RPA assay approached 8 copies per reaction, which is equivalent to the sensitivity of RT-qPCR reactions. This assay did not detect RNA extracts from other murine pathogens included in this study or TMEV negative samples. Brain tissues and contaminated biological materials were used to assess the clinical performance of the RT-RPA. The detection results of RT-RPA and RT-qPCR were very similar, except that a contaminated biological material sample which was positive by RT-qPCR, with a CT value of 38, was negative by RT-RPA. In summary, the developed RT-RPA assay offers a rapid, sensitive and specific alternative method for monitoring of TMEV, especially in resource-limited conditions.
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Affiliation(s)
- Lei Ma
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China
| | - Feng Cong
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China
| | - Yujun Zhu
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China
| | - Miaoli Wu
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China
| | - Fengjiao Xu
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China
| | - Ren Huang
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China
| | - Robert J Moore
- School of Science, RMIT University, Melbourne, Australia
| | - Pengju Guo
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals, Monitoring Institute, Guangzhou, China.
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