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Zhang L, Zhou Q, Liu J, Liu M, Hu J, Bao Z, Wang M. Development of recombinase amplification assays for the rapid detection of infectious myonecrosis virus. J Invertebr Pathol 2024; 205:108143. [PMID: 38810834 DOI: 10.1016/j.jip.2024.108143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/01/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
Infectious myonecrosis virus (IMNV) has affected shrimp farming in many countries, such as northeastern Brazil and southeast Asia, and poses a serious threat to the global shrimp industry. Reverse transcription enzymatic recombinant amplification technology (RT-ERA) is a rapid DNA amplification assay with high specificity in isothermal conditions and has been widely applied to the pathogen's detection. In this study, two novel ERA assays of IMNV, real-time RT-ERA and an RT-ERA combined with lateral flow dipsticks assay (RT-ERA-LFD), were developed and evaluated. The real-time RT-ERA assay could be carried out at 38-42 °C and had the highest end-point fluorescence value and the smallest Ct value at 41 °C. The brightness and width of the detection line were at a maximum at 39 °C and 30 min, and these conditions were selected in RT-ERA-LFD. Both real-time RT-ERA and RT-ERA-LFD produced positive results with IMNV standard plasmids only and showed no cross-reaction with Vibrio parahaemolyticus, which causes acute hepatopancreatic necrosis disease (VpAHPND); white spot syndrome virus (WSSV); infectious hypodermal and hematopoietic necrosis virus (IHHNV); or Ecytonucleospora hepatopenaei (EHP). Meanwhile, we compared the sensitivities of nested RT-PCR, real-time RT-PCR, real-time RT-ERA, and RT-ERA-LFD. The sensitivities of real-time RT-ERA and RT-ERA-LFD were both 101 copies/μL. The detection sensitivities of nested RT-PCR and real-time RT-PCR were 100 and 102 copies/μL, respectively. As a result, two ERA assays were determined to be specific, sensitive, and economical methods for the on-site diagnosis of IMNV infection, showing great potential for the control of IMNV infections.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Qingqian Zhou
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Junjiang Liu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Mengran Liu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China.
| | - Jingjie Hu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Zhenmin Bao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Mengqiang Wang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572024, China; MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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2
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Grammatikos S, Svoliantopoulos I, Gizeli E. Naked-Eye Detection of LAMP-Produced Nucleic Acids in Saliva Using Chitosan-Capped AuNPs in a Single-Tube Assay. Anal Chem 2023; 95:18514-18521. [PMID: 38065570 PMCID: PMC10733902 DOI: 10.1021/acs.analchem.3c03878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a low-technology molecular assay that is highly adaptable to point-of-care (POC) applications. However, achieving sensitive naked-eye detection of the amplified target in a crude sample is challenging. Herein, we report a simple yet highly efficient and sensitive methodology for the colorimetric visualization of a single target copy in saliva using chitosan-capped gold nanoparticles (Chit-AuNPs) synthesized via a green chemistry approach. The presence or absence of free Chit in the Chit-AuNPs solution was shown to affect LAMP colorimetric detection oppositely: the observed stabilization in the negative samples and aggregation in the positive samples in the presence of free Chit were reversed in the case of neat Chit-AuNPs. The mechanism of the two assays was investigated and attributed to electrostatic and depletion effects exerted between the Chit-AuNPs, free Chit, and the solution components. The developed contamination-free, one-tube assay successfully amplified and detected down to 1-5 cfu of Salmonella and 10 copies of SARS-CoV-2 per reaction (25 μL) used, respectively, as model DNA and RNA targets in the presence of 20% saliva, making the method suitable for POC applications. Compared to the commonly used pH-sensitive dyes, Chit-AuNPs are shown to have an enhanced sensitivity toward naked-eye colorimetric observation owing to the direct detection of DNA amplicons. Thus, this is a simple, highly sensitive, fast, and versatile naked-eye detection methodology that could be coupled to any LAMP or RT-LAMP assay, avoiding the need of using complicated sample pretreatments and/or AuNPs long and laborious functionalization processes.
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Affiliation(s)
- Stylianos Grammatikos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Biology, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Ioannis Svoliantopoulos
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Chemistry, University of Crete, Voutes, 70013 Heraklion, Greece
| | - Electra Gizeli
- Institute
of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013 Heraklion, Greece
- Department
of Biology, University of Crete, Voutes, 70013 Heraklion, Greece
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3
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Kumar SS, Jamalpure S, Ahmed AN, Taju G, Vimal S, Majeed SA, Suryakodi S, Rahamathulla S, Paknikar KM, Rajwade JM, Hameed ASS. An Indigenous, Field-Deployable, Lateral Flow Immunochromatographic Assay Rapidly Detects Infectious Myonecrosis in Shrimp, Litopenaeus vannamei. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1110-1124. [PMID: 36242690 DOI: 10.1007/s10126-022-10172-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Shrimp farming is an important socioeconomic activity worldwide. Infectious myonecrosis virus (IMNV) is an important shrimp virus responsible for significant mortality (up to 70%) in Litopenaeus vannamei. We produced recombinant capsid protein (r-IMNV31) and obtained a highly specific antibody, anti-r-IMNV31, which was used in WOAH-approved ELISA and Western blot to detect IMNV. Further, anti-r-IMNV31 was employed in an indigenously developed lateral flow immunoassay (LFA) with gold nanoparticles as a visual label. Using LFA, IMNV could be detected rapidly (20 min) from tissue homogenate with high specificity, reproducibility, and sensitivity (LOD = 103 viral particles). LFA was validated with "gold standard" qRT-PCR using 60 samples with high sensitivity (100%), specificity (86%). A Cohen's kappa coefficient of 0.86 suggested "good agreement" between LFA and qRT-PCR. With a shelf-life of ~ 1 year at ambient temperature, the use of LFA in the on-site detection of IMNV by shrimp farmers will be a reality.
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Affiliation(s)
- S Santhosh Kumar
- Aquatic Animal Health Laboratory (OIE Reference Laboratory for WTD), C. Abdul Hakeem College, ( Thiruvalluvar University), Tamilnadu, 632509, Melvisharam, India
| | - Snehal Jamalpure
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, India
| | - A Nafeez Ahmed
- Aquatic Animal Health Laboratory (OIE Reference Laboratory for WTD), C. Abdul Hakeem College, ( Thiruvalluvar University), Tamilnadu, 632509, Melvisharam, India
| | - G Taju
- Aquatic Animal Health Laboratory (OIE Reference Laboratory for WTD), C. Abdul Hakeem College, ( Thiruvalluvar University), Tamilnadu, 632509, Melvisharam, India
| | - S Vimal
- Saveetha Medical College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai, 602105, India
| | - S Abdul Majeed
- Aquatic Animal Health Laboratory (OIE Reference Laboratory for WTD), C. Abdul Hakeem College, ( Thiruvalluvar University), Tamilnadu, 632509, Melvisharam, India
| | - S Suryakodi
- Aquatic Animal Health Laboratory (OIE Reference Laboratory for WTD), C. Abdul Hakeem College, ( Thiruvalluvar University), Tamilnadu, 632509, Melvisharam, India
| | | | - Kishore M Paknikar
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India
- Indian Institute of Technology, Powai, Mumbai, 400076, India
| | - Jyutika M Rajwade
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India.
- Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, India.
| | - A S Sahul Hameed
- Aquatic Animal Health Laboratory (OIE Reference Laboratory for WTD), C. Abdul Hakeem College, ( Thiruvalluvar University), Tamilnadu, 632509, Melvisharam, India.
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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5
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Filik H, Avan AA. Nanotechnology-based Colorimetric Approaches for Pathogenic Virus Sensing: A review. Curr Med Chem 2021; 29:2691-2718. [PMID: 34269661 DOI: 10.2174/0929867328666210714154051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 11/22/2022]
Abstract
Fast and inexpensive virus identification protocols are paramount to hinder the further extent of pandemic diseases, minimize economic and social damages, and expedite proper clinical rehabilitation. Until now, various biosensors have been fabricated for the identification of pathogenic particles. But, they offer many difficulties. Nanotechnology resolves these difficulties and offers direct identification of pathogenic species in real-time. Among them, nanomaterial based-colorimetric sensing approach of pathogenic viruses by the naked eye has attracted much awareness because of their simplicity, speed, and low cost. In this review, the latest tendencies and advancements are overviewed in detecting pathogenic viruses using colorimetric concepts. We focus on and reconsider the use of distinctive nanomaterials such as metal nanoparticles, carbon nanotubes, graphene oxide, and conducting polymer to form colorimetric pathogenic virus sensors.
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Affiliation(s)
- Hayati Filik
- Istanbul University-Cerrahpaşa, Faculty of Engineering, Department of Chemistry, 34320 Avcılar, Istanbul, Turkey
| | - Asiye Aslıhan Avan
- Istanbul University-Cerrahpaşa, Faculty of Engineering, Department of Chemistry, 34320 Avcılar, Istanbul, Turkey
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6
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Aly SM, Mansour SM, Thabet RY, Mabrok M. Studies on infectious myonecrosis virus (IMNV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) in cultured penaeid shrimp in Egypt. DISEASES OF AQUATIC ORGANISMS 2021; 143:57-67. [PMID: 33570040 DOI: 10.3354/dao03556] [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: 06/12/2023]
Abstract
The present study aimed to diagnose infectious myonecrosis virus (IMNV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) among cultured penaeid shrimp (Penaeus semisulcatus, n = 120) collected from private farms in 2 Egyptian provinces (Damietta and North Sinai) along the Mediterranean coast. The collected shrimp were subjected to clinical examination, histopathology, molecular characterization, and phylogenetic analysis. Most of the shrimp infected with IMNV showed a distinctive appearance resembling cooked shrimp and white necrosis on distal abdominal segments and tail fans. Simultaneously, IHHNV-infected cases displayed opaque abdominal muscles, white milky to buff mottling on the shell, and a pathognomonic runt-deformity syndrome. Histopathological examination of infected specimens revealed muscular edema, hemocyte infiltration, deformities, Zenker's necrosis, and eosinophilic intra-nuclear inclusion bodies (Cowdry type A). PCR results gave predictable amplicon sizes of 139 and 81 bp and confirmed the presence of IMNV and IHHNV with a total prevalence of 37.5 and 25%, respectively. A homology search by BLAST analysis showed that the retrieved isolates putatively belonged to IMNV and IHHNV based on 96.3 to 97% nucleotide identity to the corresponding open reading frame gene of each virus. The phylogenetic analysis clearly showed genetic similarity and cross-lineage between our isolates and other isolates from Egypt, the USA, Brazil, Indonesia, China, Korea, Taiwan, and Ecuador. In conclusion, gross inspection and histopathology may aid in the diagnosis of viral diseases; however, molecular tools are indispensable for confirming a possible infection. The current study recommends strict regulations during live shrimp transportation and implementing health control certificates over all imports and exports, especially in developing countries, including Egypt.
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Affiliation(s)
- Salah M Aly
- Department of Pathology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
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7
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Zhao VXT, Wong TI, Zheng XT, Tan YN, Zhou X. Colorimetric biosensors for point-of-care virus detections. MATERIALS SCIENCE FOR ENERGY TECHNOLOGIES 2020; 3:237-249. [PMID: 33604529 PMCID: PMC7148662 DOI: 10.1016/j.mset.2019.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 05/05/2023]
Abstract
Colorimetric biosensors can be used to detect a particular analyte through color changes easily by naked eyes or simple portable optical detectors for quantitative measurement. Thus, it is highly attractive for point-of-care detections of harmful viruses to prevent potential pandemic outbreak, as antiviral medication must be administered in a timely fashion. This review paper summaries existing and emerging techniques that can be employed to detect viruses through colorimetric assay design with detailed discussion of their sensing principles, performances as well as pros and cons, with an aim to provide guideline on the selection of suitable colorimetric biosensors for detecting different species of viruses. Among the colorimetric methods for virus detections, loop-mediated isothermal amplification (LAMP) method is more favourable for its faster detection, high efficiency, cheaper cost, and more reliable with high reproducible assay results. Nanoparticle-based colorimetric biosensors, on the other hand, are most suitable to be fabricated into lateral flow or lab-on-a-chip devices, and can be coupled with LAMP or portable PCR systems for highly sensitive on-site detection of viruses, which is very critical for early diagnosis of virus infections and to prevent outbreak in a swift and controlled manner.
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Affiliation(s)
- Victoria Xin Ting Zhao
- College of Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Ten It Wong
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xin Ting Zheng
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Xiaodong Zhou
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
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Qin Y, Chen G, Zhang C, Wang Y, Zhou J. Development of loop-mediated isothermal amplification combined with a chromatographic lateral-flow dipstick for rapid detection of Chattonella marina. HARMFUL ALGAE 2019; 89:101666. [PMID: 31672231 DOI: 10.1016/j.hal.2019.101666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/10/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms caused by Chattonella marina recently have caused severe negative effect on coastal economy worldwide, with increased occurrence frequency and scale. It is therefore vital to establish new methods for rapid detection of this alga. In this study, the internal transcribed spacer (ITS) sequence was used as the target gene for molecular detection of C. marina. First, four loop-mediated isothermal amplification (LAMP) primers were designed based on the six regions of ITS, and the LAMP reaction system was established using these primers. Next, a probe was designed to detect the LAMP products by lateral-flow dipstick (LFD). Finally, a new method for rapid and sensitive detection of C. marina that is referred to as LAMP-LFD was established. The LAMP reaction system, amplification time, and amplification temperature were particularly optimized. The optimal parameters are as follows: Mg2+ concentration, 10 mM;dNTP concentration, 1.2 mM;ratio of internal primer concentration to outer primer concentration, 8:1;reaction time, 60 min;and reaction temperature, 60 °C. Both specificity and sensitivity were tested using the optimized LAMP reaction system in combination with LFD (LAMP-LFD). The established LAMP-LFD displayed good specificity and no cross reaction was detected with non-target algal species. The detection limit of LAMP-LFD was 3.4 × 10-4 ng μL-1 (3.4 × 10-4 ng per reaction) for the genomic DNA of target algae, and 1.3 copies μL-1 (1.3 copies per reaction) for the plasmid DNA containing the target ITS. Sensitivity tests using genomic DNA and plasmid DNA as templates consistently revealed that LAMP-LFD is 100 times more sensitive than regular PCR. The established LAMP-LFD was applied to analyze the simulated samples and the results showed that the detection limit of LAMP-LFD could reach 1 cell mL-1. LAMP-LFD also demonstrated good specificity and sensitivity in the analysis of natural samples. The whole procedure of LAMP-LFD could be completed within 1.5 h. Taken together, the LAMP-LFD assay developed here is characterized by simplicity, high specificity and sensitivity, and rapidity and therefore is promising for rapid detection of C. marina.
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Affiliation(s)
- Yue Qin
- 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.
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Jin Zhou
- Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China
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9
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Arunrut N, Kiatpathomchai W, Ananchaipattana C. Development and evaluation of real‐time loop mediated isothermal amplification assay for rapid and sensitive detection ofSalmonellaspp. in chicken meat products. J Food Saf 2018. [DOI: 10.1111/jfs.12564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Narong Arunrut
- Department of Biology, Faculty of Science and TechnologyRajamangala University of Technology Thanyaburi, 39 Muh1 Thanyaburi Pathum Thani Thailand
- Bioengineering and Sensing Technology Laboratory, BIOTECNational Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng Khlong Luang Pathum Thani Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTECNational Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng Khlong Luang Pathum Thani Thailand
| | - Chiraporn Ananchaipattana
- Department of Biology, Faculty of Science and TechnologyRajamangala University of Technology Thanyaburi, 39 Muh1 Thanyaburi Pathum Thani Thailand
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10
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Garrido-Maestu A, Azinheiro S, Carvalho J, Abalde-Cela S, Carbó-Argibay E, Diéguez L, Piotrowski M, Kolen’ko YV, Prado M. Combination of Microfluidic Loop-Mediated Isothermal Amplification with Gold Nanoparticles for Rapid Detection of Salmonella spp. in Food Samples. Front Microbiol 2017; 8:2159. [PMID: 29209283 PMCID: PMC5701617 DOI: 10.3389/fmicb.2017.02159] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/20/2017] [Indexed: 11/16/2022] Open
Abstract
Foodborne diseases are an important cause of morbidity and mortality. According to the World Health Organization, there are 31 main global hazards, which caused in 2010 600 million foodborne illnesses and 420000 deaths. Among them, Salmonella spp. is one of the most important human pathogens, accounting for more than 90000 cases in Europe and even more in the United States per year. In the current study we report the development, and thorough evaluation in food samples, of a microfluidic system combining loop-mediated isothermal amplification with gold nanoparticles (AuNPs). This system is intended for low-cost, in situ, detection of different pathogens, as the proposed methodology can be extrapolated to different microorganisms. A very low limit of detection (10 cfu/25 g) was obtained. Furthermore, the evaluation of spiked food samples (chicken, turkey, egg products), completely matched the expected results, as denoted by the index kappa of concordance (value of 1.00). The results obtained for the relative sensitivity, specificity and accuracy were of 100% as well as the positive and negative predictive values.
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11
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Balbin MM, Lertanantawong B, Suraruengchai W, Mingala CN. Colorimetric detection of caprine arthritis encephalitis virus (CAEV) through loop-mediated isothermal amplification (LAMP) with gold nanoprobes. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.11.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Arunrut N, Kampeera J, Sirithammajak S, Sanguanrut P, Proespraiwong P, Suebsing R, Kiatpathomchai W. Sensitive Visual Detection of AHPND Bacteria Using Loop-Mediated Isothermal Amplification Combined with DNA-Functionalized Gold Nanoparticles as Probes. PLoS One 2016; 11:e0151769. [PMID: 27003504 PMCID: PMC4803327 DOI: 10.1371/journal.pone.0151769] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a component cause of early mortality syndrome (EMS) of shrimp. In 2013, the causative agent was found to be unique isolates of Vibrio parahaemolyticus (VPAHPND) that contained a 69 kbp plasmid (pAP1) carrying binary Pir-like toxin genes PirvpA and PirvpB. In Thailand, AHPND was first recognized in 2012, prior to knowledge of the causative agent, and it subsequently led to a precipitous drop in shrimp production. After VPAHPND was characterized, a major focus of the AHPND control strategy was to monitor broodstock shrimp and post larvae for freedom from VPAHPND by nucleic acid amplification methods, most of which required use of expensive and sophisticated equipment not readily available in a shrimp farm setting. Here, we describe a simpler but equally sensitive approach for detection of VPAHPND based on loop-mediated isothermal amplification (LAMP) combined with unaided visual reading of positive amplification products using a DNA-functionalized, ssDNA-labled nanogold probe (AuNP). The target for the special set of six LAMP primers used was the VPAHPND PirvpA gene. The LAMP reaction was carried out at 65°C for 45 min followed by addition of the red AuNP solution and further incubation at 65°C for 5 min, allowing any PirvpA gene amplicons present to hybridize with the probe. Hybridization protected the AuNP against aggregation, so that the solution color remained red upon subsequent salt addition (positive test result) while unprotected AuNP aggregated and underwent a color change from red to blue and eventually precipitated (negative result). The total assay time was approximately 50 min. The detection limit (100 CFU) was comparable to that of other commonly-used methods for nested PCR detection of VPAHPND and 100-times more sensitive than 1-step PCR detection methods (104 CFU) that used amplicon detection by electrophoresis or spectrophotometry. There was no cross reaction with DNA templates derived from non-AHPND bacteria commonly found in shrimp ponds (including other Vibrio species). The new method significantly reduced the time, difficulty and cost for molecular detection of VPAHPND in shrimp hatchery and farm settings.
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Affiliation(s)
- Narong Arunrut
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jantana Kampeera
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sarawut Sirithammajak
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Piyachat Sanguanrut
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Faculty of Science, Mahidol University, Rama VI road, Bangkok 10400, Thailand
| | - Porranee Proespraiwong
- Aquatic Animal Health Research Center, Charoen Pokphand Foods Pulic CO., LTD. Samutsakorn 74000, Thailand
| | - Rungkarn Suebsing
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
- * E-mail:
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Oh S, Park B, Jung J, Choi G, Lee DC, Kim DH, Seo T. Centrifugal loop-mediated isothermal amplification microdevice for rapid, multiplex and colorimetric foodborne pathogen detection. Biosens Bioelectron 2016; 75:293-300. [DOI: 10.1016/j.bios.2015.08.052] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/22/2015] [Indexed: 01/09/2023]
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Demonstration of a very inexpensive, turbidimetric, real-time, RT-LAMP detection platform using shrimp Laem-Singh virus (LSNV) as a model. PLoS One 2014; 9:e108047. [PMID: 25255231 PMCID: PMC4177868 DOI: 10.1371/journal.pone.0108047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate detection of pathogens under field laboratory conditions is necessary for effective control of veterinary pathogens. Here we describe a prototype, portable, pathogen detection device developed for single tube, real-time, reverse transcription, loop-mediated isothermal amplification (RT-LAMP) using Laem-Singh virus (LSNV) as a model. LSNV is an RNA virus and a component cause of growth retardation in black tiger shrimp. We chose its RNA-dependent RNA polymerase (RdRp) gene as the target for our tests. The basis for detection was measurement of turbidity arising from formation of a white, insoluble magnesium pyrophosphate precipitate byproduct upon amplification of the RdRp target sequence from 100 ng template RNA extracted from shrimp. The measurement device consisted of a heating block to maintain constant temperature in the RT-LAMP reaction for 8 Eppindorf sample tubes, a light-emitting diode (LED) light source providing red light emission at 650 nm wavelength to pass through sample tubes, a light dependent resistance (LDR) photo-detector and a software program to report turbidity events and could potentially be marketed for under US$3000. The device was connected to a computer to display real-time results in a variety of formats. The optimized protocol for LSNV detection consisted of incubation of the sample tubes at 65 °C for 1 h during which turbidity was continuously measured, and quantitative results could be obtained by reaction time measurement. The sensitivity of detection was comparable to that of conventional nested RT-PCR and there was no cross reaction with other common shrimp viruses. The device was used for quantitative measurement of relative copy numbers of LSNV RdRp in 8 shrimp tissues and they were found to be highest in the gills followed in order by the lymphoid organ and hemolymph (p ≤ 0.05). This platform can be easily adapted for detection of other pathogens under field laboratory settings.
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