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Alfahl Z, Biggins S, Higgins O, Chueiri A, Smith TJ, Morris D, O'Dwyer J, Hynds PD, Burke LP, O’Connor L. A rapid on-site loop-mediated isothermal amplification technology as an early warning system for the detection of Shiga toxin-producing Escherichia coli in water. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001485. [PMID: 39109421 PMCID: PMC11304963 DOI: 10.1099/mic.0.001485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
Shiga toxin-producing Escherichia coli (STEC) is an important waterborne pathogen capable of causing serious gastrointestinal infections with potentially fatal complications, including haemolytic-uremic syndrome. All STEC serogroups harbour genes that encode at least one Shiga toxin (stx1 and/or stx2), which constitute the primary virulence factors of STEC. Loop-mediated isothermal amplification (LAMP) enables rapid real-time pathogen detection with a high degree of specificity and sensitivity. The aim of this study was to develop and validate an on-site portable diagnostics workstation employing LAMP technology to permit rapid real-time STEC detection in environmental water samples. Water samples (n=28) were collected from groundwater wells (n=13), rivers (n=12), a turlough (n=2) and an agricultural drain (n=1) from the Corrib catchment in Galway. Water samples (100 ml) were passed through a 0.22 µm filter, and buffer was added to elute captured cells. Following filtration, eluates were tested directly using LAMP assays targeting stx1, stx2 and E. coli phoA genes. The portable diagnostics workstation was used in field studies to demonstrate the on-site testing capabilities of the instrument. Real-time PCR assays targeting stx1 and stx2 genes were used to confirm the results. The limit of detection for stx1, stx2 and phoA LAMP assays were 2, 2 and 6 copies, respectively. Overall, stx1, stx2 and phoA genes were detected by LAMP in 15/28 (53.6 %), 9/28 (32.2 %) and 24/28 (85.7 %) samples, respectively. For confirmation, the LAMP results for stx1 and stx2 correlated perfectly (100 %) with those obtained using PCR. The portable diagnostics workstation exhibited high sensitivity throughout the on-site operation, and the average time from sample collection to final result was 40 min. We describe a simple, transferable and efficient diagnostic technology for on-site molecular analysis of various water sources. This method allows on-site testing of drinking water, enabling evidence-based decision-making by public health and water management authorities.
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Affiliation(s)
- Zina Alfahl
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Sean Biggins
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
- Molecular Diagnostics Research Group, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Owen Higgins
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
- Molecular Diagnostics Research Group, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Alexandra Chueiri
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
- Molecular Diagnostics Research Group, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Terry J. Smith
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
- Molecular Diagnostics Research Group, College of Science and Engineering, University of Galway, Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Jean O'Dwyer
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Irish Centre for Research in Applied Geosciences (iCRAG), University College Dublin, Dublin, Ireland
| | - Paul D. Hynds
- Irish Centre for Research in Applied Geosciences (iCRAG), University College Dublin, Dublin, Ireland
- Environmental Sustainability and Health Institute, Technological University Dublin, Dublin, Ireland
| | - Liam P. Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Louise O’Connor
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
- Molecular Diagnostics Research Group, College of Science and Engineering, University of Galway, Galway, Ireland
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Priya GB, Agrawal RK, Milton AAP, Mishra M, Mendiratta SK, Singh BR, Kumar D, Gandham RK, Dubal ZB, Rajkhowa S, Luke A, Patil G. Rapid and visual detection of Shiga-toxigenic Escherichia coli (STEC) in carabeef meat harnessing loop-mediated isothermal amplification (LAMP). Braz J Microbiol 2024; 55:1723-1733. [PMID: 38639846 PMCID: PMC11153427 DOI: 10.1007/s42770-024-01335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Shiga toxigenic E. coli are important foodborne zoonotic pathogens. The present study was envisaged to standardize loop-mediated isothermal amplification assays targeting stx1 and stx2 genes for rapid and visual detection of STEC and compare its sensitivity with PCR. The study also assessed the effect of short enrichment on the detection limit of LAMP and PCR. The developed LAMP assays were found to be highly specific. Analytical sensitivity of LAMP was 94 fg/µLand 25.8 fg/µL for stx-1 and stx-2 while LOD of 5 CFU/g of carabeef was measured after 6-12 h enrichment. The study highlights the importance of short (6-12 h) enrichment for improving the sensitivity of LAMP. The entire detection protocol could be performed within 9 h yielding results on the same day. The developed LAMP assays proved to be a handy and cost-effective alternative for screening STEC contamination in meat.
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Affiliation(s)
- Govindarajan Bhuvana Priya
- College of Agriculture, Central Agricultural University, Imphal, Manipur, India
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ravi Kant Agrawal
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
| | | | - Madhu Mishra
- Division of Bacteriology & Mycology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sanjod Kumar Mendiratta
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Bhoj Raj Singh
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Zunjar Baburao Dubal
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | | | - Ashish Luke
- Division of Livestock Products Technology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Girish Patil
- ICAR-NRC on Meat, Post Box 19, Boduppal Post, Chengicherla, Hyderabad, 500092, India
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Zhang W, Qu H, Wu X, Shi J, Wang X. Rapid, sensitive, and user-friendly detection of Pseudomonas aeruginosa using the RPA/CRISPR/Cas12a system. BMC Infect Dis 2024; 24:458. [PMID: 38689239 PMCID: PMC11061930 DOI: 10.1186/s12879-024-09348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Pseudomonas aeruginosa (P. aeruginosa) is a life-threatening bacterium known for its rapid development of antibiotic resistance, posing significant challenges in clinical treatment, biosecurity, food safety, and environmental monitoring. Early and accurate identification of P. aeruginosa is crucial for effective intervention. METHODS The lasB gene of P. aeruginosa was selected as the target for the detection. RPA primers for recombinase polymerase amplification (RPA) and crRNA for CRISPR/Cas12a detection were meticulously designed to target specific regions within the lasB gene. The specificity of the RPA/CRISPR/Cas12a detection platform was assessed using 15 strains. The detection limit of RPA/CRISPR/Cas12a detection platform was determined by utilizing a pseudo-dilution series of the P. aeruginosa DNA. The practical applicability of the RPA/CRISPR/Cas12a detection platform was validated by comparing it with qPCR on 150 samples (35 processed meat product samples, 55 cold seasoned vegetable dishes, 60 bottled water samples). RESULTS The RPA/CRISPR/Cas12a detection platform demonstrates high specificity, with no cross-reactivity with non-P. aeruginosa strains. This assay exhibits remarkable sensitivity, with a limit of detection (LOD) of 100 copies/µL for fluorescence assay and 101 copies/µL for the LFTS method. Furthermore, the performance of the RPA/CRISPR/Cas12a detection platform is comparable to that of the well-established qPCR method, while offering advantages such as shorter reaction time, simplified operation, and reduced equipment requirements. CONCLUSIONS The RPA/CRISPR/Cas12a detection platform presents a straightforward, accurate, and sensitive approach for early P. aeruginosa detection and holds great promise for diverse applications requiring rapid and reliable identification.
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Affiliation(s)
- Wenjing Zhang
- Medical college, Henan University of Chinese Medicine, No.156, Jinshui East Road, Zhengzhou, 450046, Henan, China.
| | - Hai Qu
- Autobio Diagnostics Co., Ltd., No.199, 15th Ave, Zhengzhou, 450016, Henan, China
| | - Xin Wu
- Medical college, Henan University of Chinese Medicine, No.156, Jinshui East Road, Zhengzhou, 450046, Henan, China
| | - Jingjing Shi
- Pharmacy College, Henan University of Chinese Medicine, No.156, Jinshui East Road, Zhengzhou, 450046, Henan, China
| | - Xinling Wang
- Pharmacy College, Henan University of Chinese Medicine, No.156, Jinshui East Road, Zhengzhou, 450046, Henan, China.
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Jena S, Gaur D, Dubey NC, Tripathi BP. Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases. Int J Biol Macromol 2023:125089. [PMID: 37245760 DOI: 10.1016/j.ijbiomac.2023.125089] [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: 02/11/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.
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Affiliation(s)
- Saikrushna Jena
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Divya Gaur
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Nidhi C Dubey
- Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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Isothermal Recombinase Polymerase Amplification (RPA) of E. coli gDNA in Commercially Fabricated PCB-Based Microfluidic Platforms. MICROMACHINES 2021; 12:mi12111387. [PMID: 34832799 PMCID: PMC8619769 DOI: 10.3390/mi12111387] [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: 10/10/2021] [Revised: 11/04/2021] [Accepted: 11/10/2021] [Indexed: 12/04/2022]
Abstract
Printed circuit board (PCB) technology has been recently proposed as a convenient platform for seamlessly integrating electronics and microfluidics in the same substrate, thus facilitating the introduction of integrated and low-cost microfluidic devices to the market, thanks to the inherent upscaling potential of the PCB industry. Herein, a microfluidic chip, encompassing on PCB both a meandering microchannel and microheaters to accommodate recombinase polymerase amplification (RPA), is designed and commercially fabricated for the first time on PCB. The developed microchip is validated for RPA-based amplification of two E. coli target genes compared to a conventional thermocycler. The RPA performance of the PCB microchip was found to be well-comparable to that of a thermocycler yet with a remarkably lower power consumption (0.6 W). This microchip is intended for seamless integration with biosensors in the same PCB substrate for the development of a point-of-care (POC) molecular diagnostics platform.
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Lenkowski M, Nijakowski K, Kaczmarek M, Surdacka A. The Loop-Mediated Isothermal Amplification Technique in Periodontal Diagnostics: A Systematic Review. J Clin Med 2021; 10:1189. [PMID: 33809163 PMCID: PMC8000232 DOI: 10.3390/jcm10061189] [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: 01/26/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/26/2022] Open
Abstract
The course of periodontal disease is affected by many factors; however, the most significant are the dysbiotic microflora, showing different pathogenicity levels. Rapid colonization in the subgingival environment can radically change the clinical state of the periodontium. This systematic review aims to present an innovative technique of loop-mediated isothermal amplification for rapid panel identification of bacteria in periodontal diseases. The decisive advantage of the loop-mediated isothermal amplification (LAMP) technique in relation to molecular methods based on the identification of nucleic acids (such as polymerase chain reaction (PCR or qPCR) is the ability to determine more pathogens simultaneously, as well as with higher sensitivity. In comparison with classical microbiological seeding techniques, the use of the LAMP method shortens a few days waiting time to a few minutes, reducing the time necessary to identify the species and determine the number of microorganisms. The LAMP technology requires only a small hardware base; hence it is possible to use it in outpatient settings. The developed technique provides the possibility of almost immediate assessment of periodontal status and, above all, risk assessment of complications during the treatment (uncontrolled spread of inflammation), which can certainly be of key importance in clinical work.
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Affiliation(s)
- Marcin Lenkowski
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Kacper Nijakowski
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
| | - Anna Surdacka
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland
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Das D, Namboodiri S. Selection of a suitable paper membrane for Loop Mediated Isothermal DNA amplification reaction (LAMP) in a point-of-care diagnostic kit – Experimental and CFD analysis. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Kim S, Kim S. Bacterial pathogen detection by conventional culture‐based and recent alternative (polymerase chain reaction, isothermal amplification, enzyme linked immunosorbent assay, bacteriophage amplification, and gold nanoparticle aggregation) methods in food samples: A review. J Food Saf 2020. [DOI: 10.1111/jfs.12870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sang‐Oh Kim
- Department of Plant and Food Sciences Sangmyung University Cheonan Republic of Korea
| | - Sang‐Soon Kim
- Department of Food Engineering Dankook University Cheonan Republic of Korea
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Single-Cell-Based Digital PCR Detection and Association of Shiga Toxin-Producing Escherichia coli Serogroups and Major Virulence Genes. J Clin Microbiol 2020; 58:JCM.01684-19. [PMID: 31896667 DOI: 10.1128/jcm.01684-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/13/2019] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli serogroups O157, O26, O45, O103, O111, O121, and O145, when carrying major virulence genes, the Shiga toxin genes stx 1 and stx 2 and the intimin gene eae, are important foodborne pathogens. They are referred to as the "top 7" Shiga toxin-producing E. coli (STEC) serogroups and were declared by the USDA as adulterants to human health. Since top 7 serogroup-positive cattle feces and ground beef can also contain nonadulterant E. coli strains, regular PCR cannot confirm whether the virulence genes are carried by adulterant or nonadulterant E. coli serogroups. Thus, traditional gold-standard STEC detection requires bacterial isolation and characterization, which are not compatible with high-throughput settings and often take a week to obtain a definitive result. In this study, we demonstrated that the partition-based multichannel digital PCR (dPCR) system can be used to detect and associate the E. coli serogroup-specific gene with major virulence genes and developed a single-cell-based dPCR approach for rapid (within 1 day) and accurate detection and confirmation of major STEC serogroups in high-throughput settings. Major virulence genes carried by each of the top 7 STEC serogroups were detected by dPCR with appropriately diluted intact bacterial cells from pure cultures, culture-spiked cattle feces, and culture-spiked ground beef. Furthermore, from 100 randomly collected, naturally shed cattle fecal samples, 3 O103 strains carrying eae and 2 O45 strains carrying stx 1 were identified by this dPCR assay and verified by the traditional isolation method. This novel and rapid dPCR assay is a culture-independent, high-throughput, accurate, and sensitive method for STEC detection and confirmation.
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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Reduced False Positives and Improved Reporting of Loop-Mediated Isothermal Amplification using Quenched Fluorescent Primers. Sci Rep 2019; 9:7400. [PMID: 31089184 PMCID: PMC6517417 DOI: 10.1038/s41598-019-43817-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 11/08/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as an alternative to PCR based methods. There are numerous reported techniques to detect the LAMP amplification including turbidity, bioluminescence and intercalating fluorescent dyes. In this report we show that quenched fluorescent labels on various LAMP primers can be used to quantify and detect target DNA molecules down to single copy numbers. By selecting different fluorophores, this method can be simply multiplexed. Moreover this highly specific LAMP detection technique can reduce the incidence of false positives originating from mispriming events. Attribution of these events to particular primers will help inform and improve LAMP primer design.
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Kogovšek P, Ambrožič-Avguštin J, Dovč A, Dreo T, Hristov H, Krapež U, Ravnikar M, Slavec B, Lotrič M, Žel J, Zorman Rojs O. Loop-mediated isothermal amplification: rapid molecular detection of virulence genes associated with avian pathogenic Escherichia coli in poultry. Poult Sci 2019; 98:1500-1510. [PMID: 30476321 PMCID: PMC6377436 DOI: 10.3382/ps/pey516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/18/2018] [Indexed: 11/20/2022] Open
Abstract
Infections with pathogenic Escherichia coli can lead to different animal- and human-associated diseases. E. coli infections are common in intensive poultry farming, and important economic losses can be expected during infections with avian pathogenic E. coli (APEC) strains followed by colibacillosis. Loop-mediated isothermal amplification (LAMP) assays were developed for rapid detection of 3 APEC-associated virulence genes: sitA, traT, and ompT. All 3 LAMP assays are shown to be specific, repeatable, and reproducible. High sensitivities of the assays are shown, where as few as 1,000 bacterial cells/mL can be detected in different matrices. On-site applicability of this LAMP method is demonstrated through testing of different sample types, from animal swabs and tissues, and from environmental samples collected from 6 commercial poultry farms. All 3 virulence genes were detected at high rates (above 85%) in samples from layer and broiler chickens with clinical signs and, interestingly, high prevalence of those genes was detected also in samples collected from clinically healthy broiler flock (above 75%) while lower prevalence was observed in remaining 3 clinically healthy chicken flocks (less than 75%). Importantly, these virulence genes were detected in almost all of the air samples from 11 randomly selected poultry houses, indicating air as an important route of E. coli spread. Three LAMP assays that target APEC-associated virulence genes are shown to be sensitive and robust and are therefore applicable for rapid on-site testing of various sample types, from animal swabs to air. This on-site LAMP testing protocol offers rapid diagnostics, with results obtained in <35 min, and it can be applied to other important microorganisms to allow the required prompt measures to be taken.
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Affiliation(s)
| | | | - Alenka Dovč
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tanja Dreo
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Hristo Hristov
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Uroš Krapež
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, 1000 Ljubljana, Slovenia.,Wine Research Centre, University of Nova Gorica, 5000 Nova Gorica, Slovenia
| | - Brigita Slavec
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | | - Jana Žel
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Olga Zorman Rojs
- Veterinary Faculty, Institute for Poultry, Birds, Small Mammals and Reptiles, University of Ljubljana, 1000 Ljubljana, Slovenia
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Wong YP, Othman S, Lau YL, Radu S, Chee HY. Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms. J Appl Microbiol 2018; 124:626-643. [PMID: 29165905 PMCID: PMC7167136 DOI: 10.1111/jam.13647] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022]
Abstract
Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.
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Affiliation(s)
- Y-P Wong
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - S Othman
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Y-L Lau
- Department of Parasitology, Faculty of Medicine, Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - S Radu
- Centre of Excellence for Food Safety Research (FOSREC), Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - H-Y Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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