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Suwannin P, Jangpatarapongsa K, Polpanich D, Alhibshi A, Errachid A, Elaissari A. Enhancing leptospirosis control with nanosensing technology: A critical analysis. Comp Immunol Microbiol Infect Dis 2024; 104:102092. [PMID: 37992537 DOI: 10.1016/j.cimid.2023.102092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Leptospirosis is a serious health problem in tropical areas; thus, animals shed leptospires in the environment. Humans are accidental hosts infected through exposure to contaminating bacteria in the environment. One health strategy can be applied to protect and eliminate leptospirosis because this cooperates and coordinates activities between doctors, veterinarians, and ecologists. However, conventional methods still have limitations. Therefore, the main challenges of leptospirosis control are the high sensing of detection methods to screen and control the pathogens. Interestingly, nano sensing combined with a leptospirosis detection approach can increase the sensitivity and eliminate some limitations. This article reviews nanomaterial development for an advanced leptospirosis detection method, e.g., latex beads-based agglutination test, magnetic nanoparticles enrichment, and gold-nanoparticles-based immunochromatographic assay. Thus, nanomaterials can be functionalized with biomolecules or sensing molecules utilized in various mechanisms such as biosensors. Over the last decade, many biosensors have been developed for Leptospira spp. pathogen and others. The evolution of biosensors for leptospirosis detection was designed for high efficiency and might be an alternative tool. In addition, the high-sensing fabrications are useful for leptospires screening in very low levels, for example, soil or water from the environment.
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Affiliation(s)
- Patcharapan Suwannin
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand; Univ Lyon, University Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, Villeurbanne 69622, France
| | - Kulachart Jangpatarapongsa
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Duangporn Polpanich
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Amani Alhibshi
- Department of Neuroscience Research, Institute of Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Abdelhamid Errachid
- Univ Lyon, University Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, Villeurbanne 69622, France
| | - Abdelhamid Elaissari
- Univ Lyon, University Claude Bernard Lyon-1, CNRS, ISA-UMR 5280, Villeurbanne 69622, France.
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de Guia ACM, Guia MRDUD, Monserate JJ, Salazar JR, Velasco RR, Mingala CN, Quiazon KMA. Detection of Aeromonas hydrophila possessing aerolysin gene using gold nanoparticle probe. J Adv Vet Anim Res 2023; 10:593-598. [PMID: 38370905 PMCID: PMC10868686 DOI: 10.5455/javar.2023.j714] [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: 06/02/2023] [Revised: 08/22/2023] [Accepted: 10/20/2023] [Indexed: 02/20/2024] Open
Abstract
Objective The aerolysin (aerA) is a virulence indicator used to identify the pathogenicity of the Aeromonas strain. Targeting a pathogen's crucial virulence gene for detection is essential, as it determines the potential threat to the host. This study aimed to develop a gold nanoparticle (AuNP) probe for detecting the gene aerA in Aeromonas hydrophila among field samples. Materials and Methods Kidney samples among both healthy and sick Nile tilapias in five provinces of Luzon Island were collected for bacterial analysis. Screening using specific primers targeting aerA was conducted in parallel with testing the AuNPs probe on the same sample set. The positive control provided by BFAR-NFLD, confirmed by polymerase chain reaction (PCR) assay, was used as a positive sample containing the target gene. Results The AuNP probe demonstrated a computed accuracy of 81.32%, sensitivity of 100%, and specificity of 81.26%. Among the 257 reactions, 59 were false positives, while no false negative results were observed. The AuNP probe could detect aerA at levels as low as 30 ng/µl. The low prevalence of the target gene may be attributed to the use of general media instead of specific media like Rimler-Shotts agar. Conclusion The established colorimetric detection method for A. hydrophila with the aerA gene offers a swift alternative to PCR, negating the requirement for advanced equipment like a thermal cycler.
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Affiliation(s)
- Arren Christian M. de Guia
- Livestock Biotechnology Center, Philippine Carabao Center, Science City of Muñoz, The Philippines
- Freshwater Aquaculture Center—College of Fisheries, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Mary Rose D. Uy-de Guia
- Production System and Nutrition Section, Philippine Carabao Center, Science City of Muñoz, The Philippines
| | - Juvy J. Monserate
- Department of Chemistry, College of Science, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Joel R. Salazar
- Department of Chemistry, College of Science, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Ravelina R. Velasco
- Freshwater Aquaculture Center—College of Fisheries, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Claro N. Mingala
- Livestock Biotechnology Center, Philippine Carabao Center, Science City of Muñoz, The Philippines
- Department of Animal Science, College of Agriculture, Institute of Graduate Studies, Central Luzon State University, Science City of Muñoz, The Philippines
| | - Karl Marx A. Quiazon
- Freshwater Aquaculture Center—College of Fisheries, Central Luzon State University, Science City of Muñoz, The Philippines
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Kim SH, Lee SY, Kim U, Oh SW. Diverse methods of reducing and confirming false-positive results of loop-mediated isothermal amplification assays: A review. Anal Chim Acta 2023; 1280:341693. [PMID: 37858542 DOI: 10.1016/j.aca.2023.341693] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 10/21/2023]
Abstract
Loop-mediated isothermal amplification (LAMP), a rapid and sensitive isothermal nucleic acid amplification method, is a promising alternative to other molecular amplification techniques due to its superior specificity and sensitivity. However, due to primer dimerization, LAMP results in nonspecific and nontemplate amplification. And during the amplification confirmation process, there is carry-over contamination. These factors can result in false-positive results that overestimate the amount of DNA, preventing accurate detection. This review outlined several techniques for reducing false-positive LAMP results before amplification and confirming false-positive results after amplification. Before the amplification step, DNA polymerase activity can be decreased with organic additives such as dimethyl sulfoxide, betaine, and pullulan to prevent nonspecific amplification. The enzyme uracil-DNA-glycosylase (UDG) can eliminate false-positive results caused by carry-over contamination, and the hot-start effect with gold nanoparticles can reduce nonspecific amplification. When confirming false-positive results using clustered regularly interspaced short palindromic repeats, guide RNA accurately detects LAMP amplification, allowing differentiation from nonspecific amplification. By confirming amplification, the colorimetric change in the deoxyribozyme (DNAzyme) formed by the reaction of the G-quadruplex sequence of the LAMP amplicon and hemin can distinguish false-positive results. Lateral flow immunoassay can distinguish false-positive results by accurately recognizing hybridized probes to LAMP amplicons.
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Affiliation(s)
- So-Hee Kim
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea
| | - So-Young Lee
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea
| | - Unji Kim
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul, Republic of Korea.
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Retraction: Sensitive Visual Detection of AHPND Bacteria Using Loop-Mediated Isothermal Amplification Combined with DNA-Functionalized Gold Nanoparticles as Probes. PLoS One 2023; 18:e0282453. [PMID: 36827257 PMCID: PMC9956062 DOI: 10.1371/journal.pone.0282453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
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Sun Y, Lu C, Lee C, Tu E, Lin C. Using loop‐mediated isothermal amplification combined with gold nanoparticles for optically rapid detection of shrimp
Vibrio parahaemolyticus
. J Food Saf 2022. [DOI: 10.1111/jfs.13036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu‐Ling Sun
- Aquatic Technology Laboratories Agricultural Technology Research Institute Hsinchu Taiwan
| | - Chug‐Lun Lu
- Aquatic Technology Laboratories Agricultural Technology Research Institute Hsinchu Taiwan
| | - Chia‐Hung Lee
- Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan
| | - En‐I Tu
- Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan
| | - Chih‐Sheng Lin
- Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan
- Department of Biological Science and Technology National Chiao Tung University Hsinchu Taiwan
- Center for Intelligent Drug Systems and Smart Bio‐devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu Taiwan
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Naranitus P, Aiamsa-At P, Sukonta T, Hannanta-Anan P, Chaijarasphong T. Smartphone-compatible, CRISPR-based platforms for sensitive detection of acute hepatopancreatic necrosis disease in shrimp. JOURNAL OF FISH DISEASES 2022; 45:1805-1816. [PMID: 35946585 DOI: 10.1111/jfd.13702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Acute Hepatopancreatic Necrosis Disease (AHPND), caused by bacterial isolates expressing PirAB binary toxins, represents the severest and most economically destructive disease affecting penaeid shrimp. Its rapid disease progression and associated massive mortalities call for vigilant monitoring and early diagnosis, but molecular detection methods that simultaneously satisfy the requirements of sensitivity, specificity, and portability are still scarce. In this work, the CRISPR-Cas12a technology was harnessed for the development of two fluorescent assays compatible with naked-eye visualization. The first assay, AP4-Cas12a, was based on the OIE-recommended AP4 two-tubed nested PCR method and was designed to bypass the time-consuming and potentially hazardous agarose gel electrophoresis step. Using AP4-Cas12a, the detection limit of 10 copies per reaction could be achieved within less than 30 minutes post-PCR. The second assay, RPA-Cas12a, utilized recombinase polymerase amplification (RPA) to rapidly and isothermally amplify the target DNA, followed by amplicon detection by Cas12a, resulting in a protocol that can be completed in less than an hour at a constant temperature of 37°C. The detection limit of RPA-Cas12a is 100 copies of plasmid DNA or 100 fg of bacterial genomic DNA per reaction. Importantly, we validated that both assays are compatible with a previously reported smartphone-based device for facile visualization of fluorescence, thereby providing an affordable option that requires less consumables than lateral flow detection. Using this portable device for readouts, the AP4-Cas12a and RPA-Cas12a methods showed excellent concordance with the AP4-agarose gel electrophoresis approach in the evaluation of clinical samples. Therefore, the developed Cas12a assays have the potential to streamline both in-laboratory and onsite diagnosis of AHPND.
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Affiliation(s)
- Punyaporn Naranitus
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Praphutson Aiamsa-At
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanwarat Sukonta
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pimkhuan Hannanta-Anan
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Thawatchai Chaijarasphong
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
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Donia A, Furqan Shahid M, Hassan SU, Shahid R, Ahmad A, Javed A, Nawaz M, Yaqub T, Bokhari H. Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:364-373. [PMID: 35508752 PMCID: PMC9067896 DOI: 10.1007/s12560-022-09522-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 05/21/2023]
Abstract
Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.
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Affiliation(s)
- Ahmed Donia
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Furqan Shahid
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammer-ul Hassan
- Department of Mechanical Engineering, University of Hong Kong, Pok Fu Lam, Hong Kong, Hong Kong
| | - Ramla Shahid
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
- Kohsar University Murree, Murree, Pakistan
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Distance-based paper device using combined SYBR safe and gold nanoparticle probe LAMP assay to detect Leishmania among patients with HIV. Sci Rep 2022; 12:14558. [PMID: 36028548 PMCID: PMC9418321 DOI: 10.1038/s41598-022-18765-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Asymptomatic visceral leishmaniasis cases increase continuously, particularly among patients with HIV who are at risk to develop further symptoms of leishmaniasis. A simple, sensitive and reliable diagnosis is crucially needed due to risk populations mostly residing in rural communities with limited resources of laboratory equipment. In this study, a highly sensitive and selective determination of Leishmania among asymptomatic patients with Leishmania/HIV co-infection was achieved to simultaneously interpret and semi-quantify using colorimetric precipitates (gold-nanoparticle probe; AuNP-probe) and fluorescence (SYBR safe dye and distance-based paper device; dPAD) in one-step loop-mediated isothermal amplification (LAMP) assay. The sensitivities and specificities of 3 detection methods were equivalent and had reliable performances achieving as high as 95.5%. Detection limits were 102 parasites/mL (0.0147 ng/µL) which were 10 times more sensitive than other related studies. To empower leishmaniasis surveillance as well as prevention and control, this dPAD combined with SYBR safe and gold nanoparticle probe LAMP assay is reliably fast, simple, inexpensive and practical for field diagnostics to point-of-care settings in resource-limited areas which can be set up in all levels of healthcare facilities, especially in low to middle income countries.
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Lin HY, Yen SC, Tsai SK, Shen F, Lin JHY, Lin HJ. Combining Direct PCR Technology and Capillary Electrophoresis for an Easy-to-Operate and Highly Sensitive Infectious Disease Detection System for Shrimp. Life (Basel) 2022; 12:life12020276. [PMID: 35207563 PMCID: PMC8879573 DOI: 10.3390/life12020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
Infectious diseases are considered the greatest threat to the modern high-density shrimp aquaculture industry. Specificity, rapidity, and sensitivity of molecular diagnostic methods for the detection of asymptomatic infected shrimp allows preventive measures to be taken before disease outbreaks. Routine molecular detection of pathogens in infected shrimp can be made easier with the use of a direct polymerase chain reaction (PCR). In this study, four direct PCR reagent brands were tested, and results showed that the detection signal of direct PCR in hepatopancreatic tissue was more severely affected. In addition, portable capillary electrophoresis was applied to improve sensitivity and specificity, resulting in a pathogen detection limit of 25 copies/PCR-reaction. Juvenile shrimp from five different aquaculture ponds were tested for white spot syndrome virus infection, and the results were consistent with the Organization for Animal Health’s certified standard method. Furthermore, this methodology could be used to examine single post larvae shrimp. The overall detection time was reduced by more than 58.2%. Therefore, the combination of direct PCR and capillary electrophoresis for on-site examination is valuable and has potential as a suitable tool for diagnostic, epidemiological, and pathological studies of shrimp aquaculture.
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Affiliation(s)
- Hung-Yun Lin
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Shao-Chieh Yen
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan;
- BiOptic Inc., New Taipei City 23141, Taiwan;
| | | | - Fan Shen
- Giant Bio Technology Inc., New Taipei City 22101, Taiwan;
| | - John Han-You Lin
- School of Veterinary Medicine, National Taiwan University, Taipei, 10617, Taiwan
- Correspondence: (J.H.-Y.L.); (H.-J.L.)
| | - Han-Jia Lin
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Correspondence: (J.H.-Y.L.); (H.-J.L.)
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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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Li C, Lin N, Feng Z, Lin M, Guan B, Chen K, Liang W, Wang Q, Li M, You Y, Chen Q. CRISPR/Cas12a Based Rapid Molecular Detection of Acute Hepatopancreatic Necrosis Disease in Shrimp. Front Vet Sci 2022; 8:819681. [PMID: 35146019 PMCID: PMC8821903 DOI: 10.3389/fvets.2021.819681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/29/2021] [Indexed: 12/26/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND), formerly called early mortality syndrome (EMS), causes high mortality in cultured penaeid shrimp, particularly Penaeus vannamei and Penaeus monodon. AHPND is mainly caused by Vibrio species carrying the pVA1 plasmid encoding the virulence genes Photorhabdus insect-related (pir) pirVPA and pirVPB. We developed a new molecular assay that combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a technology (RPA-CRISPR/Cas12a) to detect pirVPA and pirVPB, with a fluorescent signal result. The fluorescence RPA-CRISPR/Cas12a assay had a detection limit of 20 copies/μL for pirVPA and pirVPB. To improve usability and visualize RPA-CRISPR/Cas12a assay results, a lateral flow strip readout was added. With the lateral flow strip, the RPA-CRISPR/Cas12a assay had a lower limit of detection of 200 copies/μL (0.3 fmol/L). The lateral flow assay can be completed in 2 h and showed no cross-reactivity with pathogens causing other shrimp diseases. In a field test of 60 shrimp samples, the RPA-CRISPR/Cas12a lateral flow assay showed 92.5% positive predictive agreement and 100% negative predictive agreement. As the new RPA-CRISPR/Cas12a assay is rapid, specific, and does not require complicated experimental equipment, it may have important field applications for detecting AHPND in farmed shrimp.
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Affiliation(s)
- Chenglong Li
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Nan Lin
- Fujian Provincial Fisheries Technology Extension Center, Fuzhou, China
| | - Zhihua Feng
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Minhua Lin
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Biyun Guan
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Kunsen Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Wangwang Liang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Qiaohuang Wang
- Fujian Provincial Fisheries Technology Extension Center, Fuzhou, China
| | - Miaomiao Li
- Fujian Provincial Fisheries Technology Extension Center, Fuzhou, China
| | - Yu You
- Fujian Provincial Fisheries Technology Extension Center, Fuzhou, China
- *Correspondence: Yu You
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
- Qi Chen
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Wang P, Ma C, Liao L, Yu J, Yi L, Qiao Y, Liu X, Gao S, Shen H, Lu Q. Simultaneous visual diagnosis of acute hepatopancreatic necrosis disease and Enterocytozoon hepatopenaei infection in shrimp with duplex recombinase polymerase amplification. JOURNAL OF FISH DISEASES 2021; 44:1753-1763. [PMID: 34237791 DOI: 10.1111/jfd.13492] [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: 05/08/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Shrimp is a globally popular seafood. Shrimp farming has been challenged by various infectious diseases that lead to significant economic losses. The prevention of two important shrimp infectious diseases, the acute hepatopancreatic necrosis disease (AHPND) and the Enterocytozoon hepatopenaei (EHP) infection, is highly dependent on early and accurate diagnostic. On-site monitoring of the two diseases in shrimp farming facilities demands point-of-care-testing (POCT) type of diagnostic assays. This study established a duplex recombinase polymerase amplification (RPA) and lateral flow dipstick (LFD) combined assay that could simultaneously diagnose the two diseases. The optimized RPA-LFD assay could finish the diagnostic in 35 min with good specificity, and the sensitivity reached 101 and 102 gene copies per reaction for EHP and AHPND, respectively, which were at the same level as the currently available molecular diagnostic assays. Test results of clinical samples showed 100% agreement of this assay with the industrial standard nested polymerase chain reaction (PCR) assays, and samples with both diseases were simultaneously identified. Because of the isothermal 37℃ amplification and the visual reading of the signal on dipsticks, the dependence on equipment is minimal. This duplex RPA-LFD assay is well suited for simultaneous POCT diagnostic of the two important shrimp infectious diseases. Moreover, the principle can be applied to multiplex POCT diagnostic of other infectious diseases in aquaculture.
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Affiliation(s)
- Pei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Lei Liao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Junwei Yu
- Ustar Biotechnologies (Hangzhou) Ltd, Zhejiang, China
| | - Longyu Yi
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Qiao
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Xin Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Biomedical Engineering, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
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13
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Kampeera J, Dangtip S, Suvannakad R, Khumwan P, Senapin S, Kiatpathomchai W. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with colorimetric gold nanoparticle (AuNP) probe assay for visual detection of tilapia lake virus (TiLV) in Nile and red hybrid tilapia. JOURNAL OF FISH DISEASES 2021; 44:1595-1607. [PMID: 34170523 DOI: 10.1111/jfd.13482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/11/2021] [Indexed: 05/23/2023]
Abstract
Tilapia is one of the major aquaculture species with a global economic significance. Despite a high scale of production worldwide, mortality in many tilapia cultures has recently become a problem concerned with not only intensive farming but also the prevalence of infectious pathogens. Tilapia lake virus (TiLV) has emerged as a serious single-stranded RNA disease agent that thus far has continued to cause a number of incidences across the continents. Conventional PCR-based molecular detection techniques, despite having high sensitivity for TiLV, are not best suited for the onsite identification of infected fish mainly due to their requirement of laboratory resources and extended assay turnaround time. To address this practical limitation, we have developed a novel colorimetric assay based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) and gold nanoparticle (AuNP)-labelled oligonucleotide reporter probe targeting the viral genomic segment 9 that enables the assay to be completed within an hour. This technique has been shown to be compatible with a rapid nucleic extraction method that does not demand centrifugation steps or any benchtop laboratory equipment. When validated with field-acquired tilapia samples, our RT-LAMP-AuNP assay exhibited a near-perfect agreement with the semi-nested RT-PCR assay recommended by OIE with Cohen's κ coefficient of .869, yet requiring significantly less time to perform.
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Affiliation(s)
- Jantana Kampeera
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Sirintip Dangtip
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Rapheephat Suvannakad
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Pakapreud Khumwan
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Saengchan Senapin
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok, Thailand
- Fish and Shrimp Molecular Biology and Biotechnology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Nueng, Khlong Luang, Thailand
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14
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Yang X, Dong Y, Ma C, Qiao Y, Jiang G, Chen S, Dong J, Shen H, Gao S. Establishment of a visualized isothermal nucleic acid amplification method for on-site diagnosis of acute hepatopancreatic necrosis disease in shrimp farm. JOURNAL OF FISH DISEASES 2021; 44:1293-1303. [PMID: 34041767 DOI: 10.1111/jfd.13388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is a significant deadly infectious disease in the shrimp farming industry, causing serious economic losses globally every year. Because of the rapid progress speed, lack of effective treatment and high mortality rate of AHPND, monitoring with frequent diagnostic tests is vital for a successful prevention. The conventional histopathological diagnosis fell far short of the requirement for efficient monitoring, and the polymerase chain reaction (PCR)-based molecular diagnostic methods that rely on sophisticated thermocycler and trained personnel are hardly applicable in the field. Combining the recombinase polymerase amplification (RPA) and the lateral flow strips (LFSs), a diagnostic method suitable for on-site everyday monitoring of AHPND has been established in this study. This RPA-LFS method targeted the binary toxic photorhabdus insect-related genes PirA and PirB on a virulence plasmid of the AHPND-causative Vibrio parahaemolyticus strains. The diagnostic test was completed within 30 min at 37°C and showed good specificity and good sensitivity of 20 fg DNA of the AHPND shrimp or one colony-forming unit of the causative bacterium per reaction, which was better than the administration-approved standard AP4 assay. Crude templates from sample boiling could be directly used. Tests of clinical samples showed 100% consistency of this method with the standard AP4 assay. This RPA-LFS method can be a good choice for on-site diagnosis of AHPND with quick response time, easy procedure and low demand for resources, and should have significant value for the control of spreading of this dangerous disease in farmed shrimp.
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Affiliation(s)
- Xiaohan Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
- College of Life Science and Technology, Hua Zhong University of Science and Technology, Wuhan, China
| | - Yu Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Chao Ma
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Yi Qiao
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Ge Jiang
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Shiqi Chen
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
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15
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Ruang-Areerate T, Sukphattanaudomchoke C, Thita T, Leelayoova S, Piyaraj P, Mungthin M, Suwannin P, Polpanich D, Tangchaikeeree T, Jangpatarapongsa K, Choowongkomon K, Siripattanapipong S. Development of loop-mediated isothermal amplification (LAMP) assay using SYBR safe and gold-nanoparticle probe for detection of Leishmania in HIV patients. Sci Rep 2021; 11:12152. [PMID: 34108543 PMCID: PMC8190085 DOI: 10.1038/s41598-021-91540-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/26/2021] [Indexed: 12/04/2022] Open
Abstract
Asymptomatic leishmaniasis cases have continuously increased, especially among patients with HIV who are at risk to develop further symptoms of cutaneous and visceral leishmaniasis. Thus, early diagnosis using a simple, sensitive and reliable diagnostic assay is important because populations at risk mostly reside in rural communities where laboratory equipment is limited. In this study, the highly sensitive and selective determination of Leishmania infection in asymptomatic HIV patients was achieved using dual indicators (SYBR safe and gold-nanoparticle probe; AuNP-probe) in one-step LAMP method based on basic instruments. The assay can be simply evaluated under the naked eye due to clear interpretation of fluorescent emission of LAMP-SYBR safe dye-complex and colorimetric precipitate of specific AuNP-probes. The sensitivities and specificities of fluorescent SYBR safe dye and AuNP-probe indicators were equal, which were as high as 94.1 and 97.1%, respectively. Additionally, detection limits were 102 parasites/mL (0.0147 ng/µL), ten times more sensitivity than other related studies. To empower leishmaniasis surveillance, this inexpensive one-step SYBR safe and AuNP-LAMP assay is reliably fast and simple for field diagnostics to point-of-care settings, which can be set up in all levels of health care facilities including resource limited areas, especially in low to middle income countries.
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Affiliation(s)
- Toon Ruang-Areerate
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand.
| | | | - Thanyapit Thita
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Phunlerd Piyaraj
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, 10400, Thailand
| | - Patcharapan Suwannin
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Duangporn Polpanich
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Tienrat Tangchaikeeree
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Kulachart Jangpatarapongsa
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
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16
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Heat-enhancing aggregation of gold nanoparticles combined with loop-mediated isothermal amplification (HAG-LAMP) for Plasmodium falciparum detection. J Pharm Biomed Anal 2021; 203:114178. [PMID: 34082143 DOI: 10.1016/j.jpba.2021.114178] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Malaria infection represents a major public health and economic issue that leads to morbidity and mortality globally. A highly effective and uncomplicated detection tool is required for malaria control in geographical hotspots of transmission. We developed a simple and more sensitive novel approach for the detection of the 18S rRNA gene of Plasmodium falciparum based on loop-mediated isothermal amplification (LAMP) and visualization using colorimetric, streptavidin-functionalized gold nanoparticles (SA-GNPs). Two loop primers of LAMP were biotinylated to produce biotin-containing products during amplification. After the addition of SA-GNPs, clusters of avidin-biotin complexes were established in the LAMP structure. While the positive reactions remained wine red, the negative reactions became colorless with partial aggregations induced by hydrochloric acid (HCl) under heat enhancement (60 °C). All steps of the assay were completed within 50 min, its detection limit was 1 parasite/μL, and it was highly specific for P. falciparum. This effortless detection system with high sensitivity and specificity could provide an alternative choice for malaria diagnostics in resource-limited regions.
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17
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Sensitivity Validation of EWOD Devices for Diagnosis of Early Mortality Syndrome (EMS) in Shrimp Using Colorimetric LAMP-XO Technique. SENSORS 2021; 21:s21093126. [PMID: 33946302 PMCID: PMC8124682 DOI: 10.3390/s21093126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022]
Abstract
Electrowetting-on-dielectric (EWOD) is a microfluidic technology used for manipulating liquid droplets at microliter to nanoliter scale. EWOD has the ability to facilitate the accurate manipulation of liquid droplets, i.e., transporting, dispensing, splitting, and mixing. In this work, EWOD fabrication with suitable and affordable materials is proposed for creating EWOD lab-on-a-chip platforms. The EWOD platforms are applied for the diagnosis of early mortality syndrome (EMS) in shrimp by utilizing the colorimetric loop-mediated isothermal amplification method with pH-sensitive xylenol orange (LAMP-XO) diagnosis technique. The qualitative sensitivity is observed by comparing the limit of detection (LOD) while performing the LAMP-XO diagnosis test on the proposed lab-on-a-chip EWOD platform, alongside standard LAMP laboratory tests. The comparison results confirm the reliability of EMS diagnosis on the EWOD platform with qualitative sensitivity for detecting the EMS DNA plasmid concentration at 102 copies in a similar manner to the common LAMP diagnosis tests.
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18
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Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load. Sci Rep 2021; 11:9026. [PMID: 33907239 PMCID: PMC8079700 DOI: 10.1038/s41598-021-88506-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
The use of RT-LAMP (reverse transcriptase—loop mediated isothermal amplification) has been considered as a promising point-of-care method to diagnose COVID-19. In this manuscript we show that the RT-LAMP reaction has a sensitivity of only 200 RNA virus copies, with a color change from pink to yellow occurring in 100% of the 62 clinical samples tested positive by RT-qPCR. We also demonstrated that this reaction is 100% specific for SARS-CoV-2 after testing 57 clinical samples infected with dozens of different respiratory viruses and 74 individuals without any viral infection. Although the majority of manuscripts recently published using this technique describe only the presence of two-color states (pink = negative and yellow = positive), we verified by naked-eye and absorbance measurements that there is an evident third color cluster (orange), in general related to positive samples with low viral loads, but which cannot be defined as positive or negative by the naked eye. Orange colors should be repeated or tested by RT-qPCR to avoid a false diagnostic. RT-LAMP is therefore very reliable for samples with a RT-qPCR Ct < 30 being as sensitive and specific as a RT-qPCR test. All reactions were performed in 30 min at 65 °C. The use of reaction time longer than 30 min is also not recommended since nonspecific amplifications may cause false positives.
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19
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Cassedy A, Parle-McDermott A, O’Kennedy R. Virus Detection: A Review of the Current and Emerging Molecular and Immunological Methods. Front Mol Biosci 2021; 8:637559. [PMID: 33959631 PMCID: PMC8093571 DOI: 10.3389/fmolb.2021.637559] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Viruses are ubiquitous in the environment. While many impart no deleterious effects on their hosts, several are major pathogens. This risk of pathogenicity, alongside the fact that many viruses can rapidly mutate highlights the need for suitable, rapid diagnostic measures. This review provides a critical analysis of widely used methods and examines their advantages and limitations. Currently, nucleic-acid detection and immunoassay methods are among the most popular means for quickly identifying viral infection directly from source. Nucleic acid-based detection generally offers high sensitivity, but can be time-consuming, costly, and require trained staff. The use of isothermal-based amplification systems for detection could aid in the reduction of results turnaround and equipment-associated costs, making them appealing for point-of-use applications, or when high volume/fast turnaround testing is required. Alternatively, immunoassays offer robustness and reduced costs. Furthermore, some immunoassay formats, such as those using lateral-flow technology, can generate results very rapidly. However, immunoassays typically cannot achieve comparable sensitivity to nucleic acid-based detection methods. Alongside these methods, the application of next-generation sequencing can provide highly specific results. In addition, the ability to sequence large numbers of viral genomes would provide researchers with enhanced information and assist in tracing infections.
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Affiliation(s)
- A. Cassedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | | | - R. O’Kennedy
- School of Biotechnology, Dublin City University, Dublin, Ireland
- Hamad Bin Khalifa University, Doha, Qatar
- Qatar Foundation, Doha, Qatar
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20
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Golabi M, Flodrops M, Grasland B, Vinayaka AC, Quyen TL, Nguyen T, Bang DD, Wolff A. Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid and On-Site Detection of Avian Influenza Virus. Front Cell Infect Microbiol 2021; 11:652048. [PMID: 33954120 PMCID: PMC8092359 DOI: 10.3389/fcimb.2021.652048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 12/03/2022] Open
Abstract
Avian influenza virus (AIV) outbreaks occur frequently worldwide, causing a potential public health risk and great economic losses to poultry industries. Considering the high mutation rate and frequent genetic reassortment between segments in the genome of AIVs, emerging new strains are a real threat that may infect and spread through the human population, causing a pandemic. Therefore, rapid AIV diagnostic tests are essential tools for surveillance and assessing virus spreading. Real-time reverse transcription PCR (rRT-PCR), targeting the matrix gene, is the main official standard test for AIV detection, but the method requires well-equipped laboratories. Reverse transcription Loop-Mediated Isothermal Amplification (RT-LAMP) has been reported as a rapid method and an alternative to PCR in pathogen detection. The high mutation rate in the AIV genome increases the risk of false negative in nucleic acid amplification methods for detection, such as PCR and LAMP, due to possible mismatched priming. In this study, we analyzed 800 matrix gene sequences of newly isolated AIV in the EU and designed a highly efficient LAMP primer set that covers all AIV subtypes. The designed LAMP primer set was optimized in real-time RT-LAMP (rRT-LAMP) assay. The rRT-LAMP assay detected AIV samples belonging to nine various subtypes with the specificity and sensitivity comparable to the official standard rRT-PCR assay. Further, a two-color visual detection RT-LAMP assay protocol was adapted with the aim to develop on-site diagnostic tests. The on-site testing successfully detected spiked AIV in birds oropharyngeal and cloacal swabs samples at a concentration as low as 100.8 EID50 per reaction within 30 minutes including sample preparation. The results revealed a potential of this newly developed rRT-LAMP assay to detect AIV in complex samples using a simple heat treatment step without the need for RNA extraction.
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Affiliation(s)
- Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Marion Flodrops
- Laboratory of Ploufragan-Plouzané-Niort, Unit of Avian and Rabbit Virology, Immunology and Parasitology, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Beatrice Grasland
- Laboratory of Ploufragan-Plouzané-Niort, Unit of Avian and Rabbit Virology, Immunology and Parasitology, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Aaydha C Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Than Linh Quyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Trieu Nguyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Ploufragan-Plouzané-Niort, Unit of Avian and Rabbit Virology, Immunology and Parasitology, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan, France
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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21
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Mai HN, Aranguren Caro LF, Cruz-Flores R, Dhar AK. Development of a Recombinase Polymerase Amplification (RPA) assay for acute hepatopancreatic necrosis disease (AHPND) detection in Pacific white shrimp (Penaeus vannamei). Mol Cell Probes 2021; 57:101710. [PMID: 33722662 DOI: 10.1016/j.mcp.2021.101710] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is currently the most important bacterial disease of shrimp that has caused enormous losses to the shrimp industry worldwide. The causative agent of AHPND are Vibrio spp. Carrying plasmids containing the pirA and pirB genes which encode binary toxins, PirAB. Currently, AHPND is mostly diagnosed by PCR-based platforms which require the use of sophisticated laboratory instrumentation and are not suitable for a point-of-care diagnostics. Therefore, the availability of an alternative method based on isothermal amplification would be suitable for AHPND detection outside a laboratory setting and extremely useful at a pond side location. Isothermal amplification is based on the nucleic acid amplification at a single temperature and does not require the use of a thermal cycler. In this study, we developed an isothermal Recombinase Polymerase Amplification (RPA) assay for AHPND detection targeting both pirA and pirB genes, simultaneously and evaluated the specificity and sensitivity of the assay. The assay could detect AHPND without any cross-reaction with other microbial pathogens and Specific Pathogen Free (SPF) shrimp. The limit of detection of the assay was 5 copies of pirAB genes. To evaluate the reliability of the assay in detecting AHPND, DNA from Penaeus vannamei shrimp displaying acute and chronic infection were analyzed by the RPA assay and the results were compared with SYBR Green real-time PCR assay. While there was a 100% conformity between the two assay while detecting acute phase infection, RPA appeared to be more sensitive in detecting chronic phase infection. The data suggest that RPA assay described here would be a reliable method in detecting AHPND outside a standard laboratory setting.
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Affiliation(s)
- Hung Nam Mai
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Luis F Aranguren Caro
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Roberto Cruz-Flores
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA.
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22
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Sivakumar R, Dinh VP, Lee NY. Ultraviolet-induced in situ gold nanoparticles for point-of-care testing of infectious diseases in loop-mediated isothermal amplification. LAB ON A CHIP 2021; 21:700-709. [PMID: 33554994 DOI: 10.1039/d1lc00019e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The present study investigated ultraviolet-induced in situ gold nanoparticles (AuNPs) coupled with loop-mediated isothermal amplification (LAMP) for the point-of-care testing (POCT) of two major infectious pathogens, namely, Coronavirus (COVID-19) and Enterococcus faecium (E. faecium spp.). In the process, gold ions in a gold chloride (HAuCl4) solution were reduced using trisodium citrate (Na3Ct), a reducing agent, and upon UV illumination, red-colored AuNPs were produced in the presence of LAMP amplicons. The nitrogenous bases of the target deoxyribonucleic acid (DNA) acted as a physical support for capturing gold ions dissolved in the sample. The high affinity of gold with the nitrogenous bases enabled facile detection within 10 min, and the detection limit of COVID-19 plasmid DNA was as low as 42 fg μL-1. To ensure POCT, we designed a portable device that contained arrays of reagent chambers and detection chambers. In the portable device, colorimetric reagents such as HAuCl4 and Na3Ct were contained in the reagent chambers; these reagents were subsequently transferred to the detection chambers where LAMP amplicons were present and thus allowed convenient sample delivery and multiplex detection. Owing to the high sensitivity of the in situ AuNPs, simplicity of portable device fabrication, and rapid colorimetric detection, we strongly believe that the fabricated portable device could serve as a kit for rapid POCT for instantaneous detection of infectious diseases, and could be readily usable at the bedside.
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Affiliation(s)
- Rajamanickam Sivakumar
- Department of Industrial Environmental Engineering, College of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea
| | - Vu Phong Dinh
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, Korea.
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23
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Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
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Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Yu LH, Teh CSJ, Yap KP, Thong KL. Diagnostic approaches and contribution of next-generation sequencing technologies in genomic investigation of Vibrio parahaemolyticus that caused acute hepatopancreatic necrosis disease (AHPND). AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2020; 28:2547-2559. [PMID: 33013008 PMCID: PMC7519849 DOI: 10.1007/s10499-020-00610-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
A unique strain of Vibrio parahaemolyticus (designated as VPAHPND) causes acute hepatopancreatic necrosis disease (AHPND), a deadly bacterial disease associated with mass mortality in cultured shrimps since 2009. AHPND is responsible for severe economic losses worldwide, causing multimillion-dollar loss annually. Because of the rapid and high mortality rates in shrimps, substantial research has been carried out to develop rapid detection techniques. Also, recent technological advances such as the next-generation sequencing (NGS) have made it possible to elucidate relevant information about a pathogen in a single assay. This review summarizes the current research pertaining to VPAHPND, focusing on diagnosis and contribution of NGS technologies in the genomic studies of AHPND.
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Affiliation(s)
- Lean Huat Yu
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Cindy Shuan Ju Teh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kien Pong Yap
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Nanocat Research Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Chaijarasphong T, Munkongwongsiri N, Stentiford GD, Aldama-Cano DJ, Thansa K, Flegel TW, Sritunyalucksana K, Itsathitphaisarn O. The shrimp microsporidian Enterocytozoon hepatopenaei (EHP): Biology, pathology, diagnostics and control. J Invertebr Pathol 2020; 186:107458. [PMID: 32882232 DOI: 10.1016/j.jip.2020.107458] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 07/12/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022]
Abstract
Disease is a major limiting factor in the global production of cultivated shrimp. The microsporidian parasite Enterocytozoon hepatopenaei (EHP) was formally characterized in 2009 as a rare infection of the black tiger shrimp Penaeus monodon. It remained relatively unstudied until mid-2010, after which infection with EHP became increasingly common in the Pacific whiteleg shrimp Penaeus vannamei, by then the most common shrimp species farmed in Asia. EHP infects the hepatopancreas of its host, causing hepatopancreatic microsporidiosis (HPM), a condition that has been associated with slow growth of the host in aquaculture settings. Unlike other infectious disease agents that have caused economic losses in global shrimp aquaculture, EHP has proven more challenging because too little is still known about its environmental reservoirs and modes of transmission during the industrial shrimp production process. This review summarizes our current knowledge of the EHP life cycle and the molecular strategies that it employs as an obligate intracellular parasite. It also provides an analysis of available and new methodologies for diagnosis since most of the current literature on EHP focuses on that topic. We summarize current knowledge of EHP infection and transmission dynamics and currently recommended, practical control measures that are being applied to limit its negative impact on shrimp cultivation. We also point out the major gaps in knowledge that urgently need to be bridged in order to improve control measures.
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Affiliation(s)
- Thawatchai Chaijarasphong
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand; Department of Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand
| | - Natthinee Munkongwongsiri
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd., Bangkok 10400, Thailand
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK; Centre for Sustainable Aquaculture Futures, University of Exeter, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Diva J Aldama-Cano
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand; Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd., Bangkok 10400, Thailand
| | - Kwanta Thansa
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd., Bangkok 10400, Thailand
| | - Timothy W Flegel
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand; National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park (TSP), Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kallaya Sritunyalucksana
- Aquatic Animal Health Research Team (AQHT), Integrative Aquaculture Biotechnology, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd., Bangkok 10400, Thailand
| | - Ornchuma Itsathitphaisarn
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok 10400, Thailand.
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26
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de Guia ACM, Fernando SID, Medina NP, Eugenio PJG, Pilare R, Velasco RR, Domingo CYJ, Monserate JJ, Quiazon KMA. Gold nanoparticle-based detection of pirAvp toxin gene causing acute hepatopancreatic necrosis disease (AHPND). SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-3073-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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27
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In vitro disinfection efficacy and clinical protective effects of common disinfectants against acute hepatopancreatic necrosis disease (AHPND)-causing Vibrio isolates in Pacific white shrimp Penaeus vannamei. J Microbiol 2020; 58:675-686. [PMID: 32720097 DOI: 10.1007/s12275-020-9537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 06/04/2020] [Accepted: 06/16/2020] [Indexed: 10/23/2022]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is one of the most significant bacterial diseases in global shrimp culture, causing severe economic losses. In the present study, we carried out in vitro antimicrobial tests to investigate the disinfection efficacy of 14 common disinfectants toward different AHPND-causing Vibrio spp., including eight isolates of V. parahaemolyticus, four isolates of V. campbellii, and one isolate of V. owensii. Polyhexamethylene biguanidine hydrochloride (PHMB) was revealed to possess the strongest inhibitory activity. Through analyzing and evaluating the results of antimicrobial tests and acute toxicity test, we selected PHMB and hydrogen peroxide (H2O2) for further clinical protection test. Clinical manifestations indicated that both PHMB (2 mg/L and 4 mg/L) and H2O2 (12 mg/L) could effectively protect juvenile Penaeus vannamei from the infection of V. parahaemolyticus isolate Vp362 at 106 CFU/ml, and the survival rate was over 80%. When the bacterial concentration was reduced to 105 CFU/ml, 104 CFU/ml, and 103 CFU/ml, the survival rate after treated by 1 mg/L PHMB was 64.44%, 93.33%, and 100%, respectively. According to the results, PHMB and H2O2 showed a lower toxicity while a better protection activity, particularly against a lower concentration of the pathogens. Therefore, these two disinfectants are proved to be promising disinfectants that can be applied to prevent and control AHPND in shrimp culture. Moreover, the methods of this study also provided valuable information for the prevention of other important bacterial diseases and suggested a reliable means for screening potential drugs in aquaculture.
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Ağel HE, Sağcan H, Ceyhan I, Durmaz R. Optimization of isothermal amplification method for Mycobacteriumtuberculosisdetection and visualization method for fieldwork. Turk J Med Sci 2020; 50:1069-1075. [PMID: 32151124 PMCID: PMC7379476 DOI: 10.3906/sag-1910-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/08/2020] [Indexed: 11/23/2022] Open
Abstract
Background/aim Tuberculosis is still one of the most contagious diseases around the world. Key factors of tuberculosis control are rapid diagnostic, efficient treatment, and prevention of contamination by surveillance and monitoring. However, culture is the gold standard method for laboratory diagnosis of tuberculosis; the results are several weeks to obtain. In order to prevent contamination of tuberculosis, diagnosis must be made in short time and treatment should be started as soon as possible. The aim of this study is to optimize the loop-mediated isothermal amplification (LAMP) method, which provides a much faster and more sensitive result than the polymerase chain reaction (PCR) method and allows the replication of target nucleic acid sequences under isothermal conditions without the need for laboratory infrastructure. Materials and methods Sputum samples were homogenized with 5% trypsin solution in CaCl2 to obtain DNA. DNA was purified using QIAGEN QIAamp DNA mini kit. LAMP primers were design using Primer explorer V5 program according to IS6110 gene of Mycobacterium tuberculosis. NEB Bst 3.0 DNA polymerase kit was used for LAMP reactions. Besides, LAMP reactions were compared with TaqMan based RT-PCR method using NEB’s Taq polymerase kit. Finally, for visualization of LAMP products, lateral flow dipsticks that produced by Milenia Biotec, colorimetric 2X LAMP master mix that produced by NEB and 2% w/v agarose gel electrophoresis methods were used. Results Optimum amplification temperature for LAMP was found to be 71.4 °C. The detection limit of the method was 102 CFU/mL and sensitivity was determined 100% compared to five different Mycobacterium species. Conclusion The current study indicated that the LAMP-LFD and colorimetric LAMP protocol optimized with sputum samples can be reliable used as a rapid, sensitive and specific assay in the diagnosis of tuberculosis in the field.
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Affiliation(s)
- Hatice Esra Ağel
- Materials Institute, TÜBİTAK Marmara Research Center, Kocaeli, Turkey
| | - Hasan Sağcan
- Department of Medical Laboratory Techniques, Vocational School of Health Services, İstanbul Medipol University, İstanbul, Turkey
| | - Ismail Ceyhan
- Department of Medical Microbiology, Atatürk Chest Diseases and Chest Surgery Training and Research Hospital, Ankara, Turkey
| | - Riza Durmaz
- Department of Medical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University, Ankara, Turkey
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29
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Advances in anti-breast cancer drugs and the application of nano-drug delivery systems in breast cancer therapy. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2020.101662] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Srimongkol G, Ditmangklo B, Choopara I, Thaniyavarn J, Dean D, Kokpol S, Vilaivan T, Somboonna N. Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products. Sci Rep 2020; 10:7768. [PMID: 32385390 PMCID: PMC7211006 DOI: 10.1038/s41598-020-64710-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 01/20/2023] Open
Abstract
Staphylococcus aureus strains carrying enterotoxin A gene (sea) causes food poisoning and cannot be distinguished from non-pathogenic strains by the culture method. Here, we developed a rapid, specific and sensitive visual detection of sea using loop-mediated isothermal amplification (LAMP) combined with nanogold probe (AuNP) or styryl dye (STR). LAMP-AuNP and LAMP-STR can detect as low as 9.7 fg (3.2 sea copies) and 7.2 sea copies, respectively, which were lower than PCR (97 fg or 32 sea copies). The excellent performance of these new assays was demonstrated in food samples using crude DNA lysates. While the culture method detected 104 CFU/g in ground pork and 10 CFU/mL in milk in 5-7 days, LAMP-AuNP could detect down to 10 CFU/g for both samples in 27 minutes. Analyzing 80 pork and milk samples revealed that the LAMP-AuNP showed 100% sensitivity, 97-100% specificity and 97.5-100% accuracy, which were superior to the culture method, and comparable to PCR but without requirement of a thermal cycler. Furthermore, our LAMP-AuNP detect sea at a range below the food safety control (<100 CFU/g). The LAMP-STR quantitated sea in 10-1,000 CFU (7.2-720 copies). Our crude DNA lysis combined with LAMP-AuNP/STR present effective point-of-care detection and facilitate appropriate control strategies.
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Affiliation(s)
- Grittaya Srimongkol
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jiraporn Thaniyavarn
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Sirirat Kokpol
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Yu J, Xie J, Cao Y, Kang R, Lin Y, Wei Y, Liao D, Li X, Ye Y, Pan M, Xiao L, Ye J. A modified loop-mediated isothermal amplification method for detecting avian infectious laryngotracheitis virus. Anim Biotechnol 2020; 32:766-773. [PMID: 32324091 DOI: 10.1080/10495398.2020.1755676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This study was aimed to establish a highly specific and sensitive loop-mediated isothermal amplification (LAMP) method for diagnosing avian infectious laryngotracheitis (AILT). DNA was extracted from isolated infectious laryngotracheitis virus (ILTV) strains and control samples, followed by PCR using three sets of six specific primers. The detection efficiency of the LAMP assay was evaluated by the turbidity and calcein methods. The sensitivity of LAMP was then assessed using a concentration gradient followed by a specificity analysis. Furthermore, the detection efficiency of LAMP and PCR was compared. Finally, a clinical test was performed to evaluate the value of the LAMP assay. The optimal temperature for the LAMP reaction was 66 °C. Meanwhile, the primers selected for the LAMP assay were highly specific for the target virus. The sensitivity of the turbidity and calcein methods for LAMP was consistent. The minimum detection concentration of LAMP was 0.06 pg/μL, which was 100-fold higher than that of PCR. Furthermore, the results from clinical samples showed that the LAMP method could identify AILT from many samples. The newly designed LAMP assay was an effective method for AILT detection at an optimal temperature of 66 °C with a minimum detection concentration of 0.06 pg/µL.
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Affiliation(s)
- Jifeng Yu
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Jing Xie
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Ye Cao
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Runmin Kang
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yi Lin
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yong Wei
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Dangjin Liao
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xingyu Li
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yonggang Ye
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Meng Pan
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Lu Xiao
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Jianqiang Ye
- Key Laboratory of Animal Genetics and Breeding of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
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32
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Teixeira A, Paris JL, Roumani F, Diéguez L, Prado M, Espiña B, Abalde-Cela S, Garrido-Maestu A, Rodriguez-Lorenzo L. Multifuntional Gold Nanoparticles for the SERS Detection of Pathogens Combined with a LAMP-in-Microdroplets Approach. MATERIALS (BASEL, SWITZERLAND) 2020; 13:ma13081934. [PMID: 32325992 DOI: 10.1021/acsanm.9b01223] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 05/25/2023]
Abstract
We developed a droplet-based optofluidic system for the detection of foodborne pathogens. Specifically, the loop-mediated isothermal amplification (LAMP) technique was combined with surface-enhanced Raman scattering (SERS), which offers an excellent method for DNA ultradetection. However, the direct SERS detection of DNA compromises the simplicity of data interpretation due to the variability of its SERS fingerprints. Therefore, we designed an indirect SERS detection method using multifunctional gold nanoparticles (AuNPs) based on the formation of pyrophosphate generated during the DNA amplification by LAMP. Towards this goal, we prepared multifunctional AuNPs involving three components with key roles: (1) thiolated poly(ethylene glycol) as stabilizing agent, (2) 1-naphthalenethiol as Raman reporter, and (3) glutathione as a bioinspired chelating agent of magnesium (II) ions. Thus, the variation in the SERS signal of 1-naphthalenethiol was controlled by the aggregation of AuNPs triggered by the complexation of pyrophosphate and glutathione with free magnesium ions. Using this strategy, we detected Listeria monocytogenes, not only in buffer, but also in a food matrix (i.e., ultra-high temperaturemilk) enabled by the massive production of hotspots as a result of the self-assemblies that enhanced the SERS signal. This allowed the development of a microdroplet-LAMP-SERS platform with isothermal amplification and real-time identification capabilities.
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Affiliation(s)
- Alexandra Teixeira
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Juan L Paris
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Foteini Roumani
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Lorena Diéguez
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Marta Prado
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Begoña Espiña
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Sara Abalde-Cela
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
| | - Laura Rodriguez-Lorenzo
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal
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Teixeira A, Paris JL, Roumani F, Diéguez L, Prado M, Espiña B, Abalde-Cela S, Garrido-Maestu A, Rodriguez-Lorenzo L. Multifuntional Gold Nanoparticles for the SERS Detection of Pathogens Combined with a LAMP-in-Microdroplets Approach. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E1934. [PMID: 32325992 PMCID: PMC7215531 DOI: 10.3390/ma13081934] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/31/2022]
Abstract
We developed a droplet-based optofluidic system for the detection of foodborne pathogens. Specifically, the loop-mediated isothermal amplification (LAMP) technique was combined with surface-enhanced Raman scattering (SERS), which offers an excellent method for DNA ultradetection. However, the direct SERS detection of DNA compromises the simplicity of data interpretation due to the variability of its SERS fingerprints. Therefore, we designed an indirect SERS detection method using multifunctional gold nanoparticles (AuNPs) based on the formation of pyrophosphate generated during the DNA amplification by LAMP. Towards this goal, we prepared multifunctional AuNPs involving three components with key roles: (1) thiolated poly(ethylene glycol) as stabilizing agent, (2) 1-naphthalenethiol as Raman reporter, and (3) glutathione as a bioinspired chelating agent of magnesium (II) ions. Thus, the variation in the SERS signal of 1-naphthalenethiol was controlled by the aggregation of AuNPs triggered by the complexation of pyrophosphate and glutathione with free magnesium ions. Using this strategy, we detected Listeria monocytogenes, not only in buffer, but also in a food matrix (i.e., ultra-high temperaturemilk) enabled by the massive production of hotspots as a result of the self-assemblies that enhanced the SERS signal. This allowed the development of a microdroplet-LAMP-SERS platform with isothermal amplification and real-time identification capabilities.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Laura Rodriguez-Lorenzo
- International Iberian Nanotechnology Laboratory (INL), Avda Mestre José Veiga, 4715-310 Braga, Portugal; (A.T.); (J.L.P.); (F.R.); (L.D.); (M.P.); (B.E.); (S.A.-C.); (A.G.-M.)
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Wangman P, Chaivisuthangkura P, Taengchaiyaphum S, Pengsuk C, Sithigorngul P, Longyant S. Development of a rapid immunochromatographic strip test for the detection of Vibrio parahaemolyticus toxin B that cause acute hepatopancreatic necrosis disease. JOURNAL OF FISH DISEASES 2020; 43:207-214. [PMID: 31752048 DOI: 10.1111/jfd.13115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Here, two monoclonal antibodies (MAbs) specific to different epitopes on ToxB, a toxin produced by Vibrio parahaemolyticus that causes acute hepatopancreatic necrosis disease (VPAHPND ), were employed to develop a rapid strip test. One MAb was conjugated to colloidal gold to bind to ToxB at the application pad, and another MAb was used to capture colloidal gold MAb-protein complexes at the test line (T) on the nitrocellulose strip. To validate test performance, a downstream control line (C) of goat anti-mouse immunoglobulin G antibody was used to capture the free colloidal gold conjugate MAb. The sample in the application buffer could be applied directly to the application well, and the test result was obtained within 15 min. The sensitivity of the kit is approximately 6.25 µg/ml of toxin, which was equivalent to the toxin produced by approximately 107 cfu/ml of bacteria. This kit is convenient and easy to use since it can be used to identify VPAHPND directly using a single colony of bacteria grown on agar culture plates. Because of its high specificity and simplicity, as well as not being reliant on sophisticated equipment or specialized skills, this strip test could be used by farmers for surveillance for ToxB-producing bacteria.
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Affiliation(s)
- Pradit Wangman
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Parin Chaivisuthangkura
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Suparat Taengchaiyaphum
- Aquatic Animal Health Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Bangkok, Thailand
| | - Chalinan Pengsuk
- Faculty of Agricultural Product Innovation and Technology, Srinakharinwirot University, Nakhon Nayok, Thailand
| | - Paisarn Sithigorngul
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Siwaporn Longyant
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
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35
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Santos HM, Tsai CY, Maquiling KRA, Tayo LL, Mariatulqabtiah AR, Lee CW, Chuang KP. Diagnosis and potential treatments for acute hepatopancreatic necrosis disease (AHPND): a review. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2020; 28:169-185. [PMID: 32834683 PMCID: PMC7223513 DOI: 10.1007/s10499-019-00451-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/04/2019] [Indexed: 05/05/2023]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) or formerly known as early mortality syndrome (EMS) is an emerging disease that has caused significant economic losses to the aquaculture industry. The primary causative agent of AHPND is Vibrio parahaemolyticus, a Gram-negative rod-shaped bacterium that has gained plasmids encoding the fatal binary toxins Pir A/Pir B that cause rapid death of the infected shrimp. In this review, the current research studies and information about AHPND in shrimps have been presented. Molecular diagnostic tools and potential treatments regarding AHPND were also included. This review also includes relevant findings which may serve as guidelines that can help for further investigation and studies on AHPND or other shrimp diseases.
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Affiliation(s)
- Harvey M. Santos
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
| | - Ching-Yi Tsai
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
| | - Kenth Roger A. Maquiling
- School of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, 1002 Intramuros, Manila Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, 1002 Intramuros, Manila Philippines
| | - Abdul R. Mariatulqabtiah
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Chi-Wen Lee
- Department of Post-Baccalaureate Veterinary Medicine, Asia University, Taichung, 41354 Taiwan
| | - Kuo Pin Chuang
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
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Point-of-care rapid detection of Vibrio parahaemolyticus in seafood using loop-mediated isothermal amplification and graphene-based screen-printed electrochemical sensor. Biosens Bioelectron 2019; 132:271-278. [DOI: 10.1016/j.bios.2019.02.060] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/18/2022]
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Anupama KP, Chakraborty A, Karunasagar I, Karunasagar I, Maiti B. Loop-mediated isothermal amplification assay as a point-of-care diagnostic tool for Vibrio parahaemolyticus: recent developments and improvements. Expert Rev Mol Diagn 2019; 19:229-239. [PMID: 30657706 DOI: 10.1080/14737159.2019.1571913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION A number of DNA-based diagnostic tools have been developed for the detection of Vibrio parahaemolyticus in seafood. However, the loop-mediated isothermal amplification (LAMP) has distinct advantages with regards to its simplicity, speed and the ease of performing without any need for sophisticated equipment. Over the last decade, LAMP has emerged as a potential tool for the detection of V. parahaemolyticus. Area covered: The literature search was restricted to LAMP assay and its variants for the detection of V. parahaemolyticus. The focus in this review is to enlist the various techniques that have been developed using the principle of the LAMP towards improved simplicity, sensitivity and specificity of the assay. Expert commentary: LAMP assay and its variants are significantly faster and require minimum accessories compared to other DNA based molecular techniques such as PCR and their types. Despite the availability of several versions, LAMP-based diagnostics is not the first choice for the detection of V. parahaemolyticus in the seafood sector. Our recommendation would be to explore the possibilities of developing cost-effective LAMP kits and implementing these kits as point-of-care diagnostic tools for rapid and sensitive detection of pathogenic V. parahaemolyticus.
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Affiliation(s)
- Karanth Padyana Anupama
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India
| | - Anirban Chakraborty
- b Division of Molecular Genetics and Cancer , Nitte University Centre for Science Education and Research , Mangaluru , India
| | - Iddya Karunasagar
- c NITTE (Deemed to be University), University Enclave , Mangaluru, Medical Sciences Complex , India
| | - Indrani Karunasagar
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India.,c NITTE (Deemed to be University), University Enclave , Mangaluru, Medical Sciences Complex , India
| | - Biswajit Maiti
- a Division of Infectious Diseases , Nitte University Centre for Science Education and Research , Mangaluru , India
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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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Zhou Y, Xiao J, Ma X, Wang Q, Zhang Y. An effective established biosensor of bifunctional probes-labeled AuNPs combined with LAMP for detection of fish pathogen Streptococcus iniae. Appl Microbiol Biotechnol 2018; 102:5299-5308. [DOI: 10.1007/s00253-018-9016-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/07/2018] [Accepted: 04/10/2018] [Indexed: 12/20/2022]
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Highly sensitive detection of gluten-containing cereals in food samples by real-time Loop-mediated isothermal AMPlification (qLAMP) and real-time polymerase chain reaction (qPCR). Food Chem 2018; 246:156-163. [DOI: 10.1016/j.foodchem.2017.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 11/18/2022]
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Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Evaluation of Different Genetic Targets for Salmonella enterica Serovar Enteriditis and Typhimurium, Using Loop-Mediated Isothermal AMPlification for Detection in Food Samples. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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Arunrut N, Kiatpathomchai W, Ananchaipattana C. Multiplex PCR assay and lyophilization for detection of Salmonella spp., Staphylococcus aureus and Bacillus cereus in pork products. Food Sci Biotechnol 2018; 27:867-875. [PMID: 30263813 DOI: 10.1007/s10068-017-0286-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/27/2017] [Accepted: 12/02/2017] [Indexed: 10/18/2022] Open
Abstract
Multiplex PCR (m-PCR) has the potential for more rapid detection of pathogens compared to simple PCR through the simultaneous amplification of multiple gene targets using several sets of specific primers. Here, we developed an m-PCR assay which combined dry reagent mixtures for ready-to-use simultaneous detection of Salmonella spp., Bacillus cereus, and Staphylococcus aureus. The assay did not show cross-reactivity with several common bacterial pathogens and the detection limit was 103 CFU/mL for mixed genomic DNA in pure culture. Lyophilized m-PCR reagents are stable for 2 months stored at 4 °C and for 1 month stored at 25 °C. Detection sensitivities of both dry and fresh mixes were able to simultaneously detect 10 CFU/mL of each pathogen in artificially inoculated samples after enrichment for 6 and 12 h. Results demonstrated that this method is both sensitive and specific and can be used for rapid detection and differentiation of foodborne diseases.
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Affiliation(s)
- Narong Arunrut
- 1Department of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, 39 Muh1, Thanyaburi, Pathum Thani Thailand.,2Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Neung, Khlong Luang, Pathum Thani Thailand
| | - Wansika Kiatpathomchai
- 2Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Neung, Khlong Luang, Pathum Thani Thailand
| | - Chiraporn Ananchaipattana
- 1Department of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, 39 Muh1, Thanyaburi, Pathum Thani Thailand
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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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Rapid diagnosis of Vibrio owensii responsible for shrimp acute hepatopancreatic necrosis disease with isothermal recombinase polymerase amplification assay. Mol Cell Probes 2017; 33:4-7. [PMID: 28179103 DOI: 10.1016/j.mcp.2017.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/03/2017] [Accepted: 02/03/2017] [Indexed: 11/24/2022]
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Lee SH, Baek YH, Kim YH, Choi YK, Song MS, Ahn JY. One-Pot Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting MERS-CoV. Front Microbiol 2017; 7:2166. [PMID: 28119682 PMCID: PMC5220095 DOI: 10.3389/fmicb.2016.02166] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/23/2016] [Indexed: 01/09/2023] Open
Abstract
Due to the limitation of rapid development of specific antiviral drug or vaccine for novel emerging viruses, an accurate and rapid diagnosis is a key to manage the virus spread. We developed an efficient and rapid method with high specificity for the Middle East Respiratory Syndrome coronavirus (MERS-CoV), based on one-pot reverse transcription loop-mediated isothermal amplification (one-pot RT-LAMP). A set of six LAMP primers [F3, B3, FIP, BIP, LF (Loop-F), and LB (Loop-B)] were designed using the sequence of nucleocapsid (N) gene with optimized RT-LAMP enzyme conditions: 100 U M-MLV RTase and 4 U Bst polymerase, implying that the reaction was able to detect four infectious viral genome copies of MERS-CoV within a 60 min reaction time period. Significantly, EvaGreen dye has better signal read-out properties in one-pot RT-LAMP reaction and is more compatible with DNA polymerase than SYBR green I. Isothermally amplified specific N genes were further evaluated using field-deployable microchamber devices, leading to the specific identification of as few as 0.4 infectious viral genome copies, with no cross-reaction to the other acute respiratory disease viruses, including influenza type A (H1N1 and H3N2), type B, human coronavirus 229E, and human metapneumovirus. This sensitive, specific and feasible method provides a large-scale technical support in emergencies, and is also applied as a sample-to-detection module in Point of Care Testing devices.
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Affiliation(s)
- Se Hee Lee
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
| | - Yun Hee Baek
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
| | - Young-Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
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