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Wu R, Meng B, Corredig M, Griffiths MW. Rapid Detection of Hepatitis A Virus in Foods Using a Bioluminescent Assay in Real-Time (BART) and Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Technology. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:144-157. [PMID: 36640204 PMCID: PMC9839959 DOI: 10.1007/s12560-022-09548-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/30/2022] [Indexed: 06/13/2023]
Abstract
Foodborne hepatitis A infections have been considered as a major threat for public health worldwide. Increased incidences of hepatitis A virus (HAV) infection has been associated with growing global trade of food products. Rapid and sensitive detection of HAV in foods is very essential for investigating the outbreaks. Real-time RT-PCR has been most widely used for the detection of HAV by far. However, the technology relies on fluorescence determination of the amplicon and requires sophisticated, high-cost instruments and trained personnel, limiting its use in low resource settings. In this study, a robust, affordable, and simple assay, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in combination with a bioluminescence-based determination of amplification in real-time (BART), was developed for the detection of HAV in different food matrices, including green onion, strawberry, mussel, and milk. The efficiencies of a one-step RT-LAMP-BART and a two-step RT-LAMP-BART were investigated for the detection of HAV in different food matrices and was compared with that of real-time RT-PCR. The sensitivity of the RT-LAMP-BART assay was significantly affected by Mg2+ concentration (P < 0.05), in addition to primer quality. The optimal Mg2+ concentration was 2 mM for one-step RT-LAMP-BART and 4 mM for two-step RT-LAMP-BART. Compared with cartridge-purified primers, HPLC-purified primers could greatly improve the sensitivity of the RT-LAMP-BART assay (P < 0.05). For detecting HAV in different food matrices, the performance of two-step RT-LAMP-BART was comparable with that of real-time RT-PCR and was better than that of one-step RT-LAMP-BART. The detection limit of the two-step RT-LAMP-BART for HAV in green onion, strawberry, mussel, and milk was 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, 8.3 × 100 PFU/5 g, and 8.3 × 100 PFU/40 mL, respectively. The developed RT-LAMP-BART was an effective, simple, sensitive, and robust method for foodborne HAV detection.
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Affiliation(s)
- Ruiqin Wu
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Milena Corredig
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mansel W Griffiths
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada
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2
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Microfluidic chip and isothermal amplification technologies for the detection of pathogenic nucleic acid. J Biol Eng 2022; 16:33. [PMID: 36457138 PMCID: PMC9714395 DOI: 10.1186/s13036-022-00312-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
The frequency of outbreaks of newly emerging infectious diseases has increased in recent years. The coronavirus disease 2019 (COVID-19) outbreak in late 2019 has caused a global pandemic, seriously endangering human health and social stability. Rapid detection of infectious disease pathogens is a key prerequisite for the early screening of cases and the reduction in transmission risk. Fluorescence quantitative polymerase chain reaction (qPCR) is currently the most commonly used pathogen detection method, but this method has high requirements in terms of operating staff, instrumentation, venues, and so forth. As a result, its application in the settings such as poorly conditioned communities and grassroots has been limited, and the detection needs of the first-line field cannot be met. The development of point-of-care testing (POCT) technology is of great practical significance for preventing and controlling infectious diseases. Isothermal amplification technology has advantages such as mild reaction conditions and low instrument dependence. It has a promising prospect in the development of POCT, combined with the advantages of high integration and portability of microfluidic chip technology. This study summarized the principles of several representative isothermal amplification techniques, as well as their advantages and disadvantages. Particularly, it reviewed the research progress on microfluidic chip-based recombinase polymerase isothermal amplification technology and highlighted future prospects.
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Lahrich S, Laghrib F, Farahi A, Bakasse M, Saqrane S, El Mhammedi MA. Review on the contamination of wastewater by COVID-19 virus: Impact and treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:142325. [PMID: 33182015 PMCID: PMC7481832 DOI: 10.1016/j.scitotenv.2020.142325] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 04/14/2023]
Abstract
Emerging viruses are a major public health problem. Most zoonotic pathogens originate in wildlife, including human immunodeficiency virus (HIV), influenza, Ebola, and coronavirus. Severe acute respiratory syndrome (SARS) is a viral respiratory illness caused by a coronavirus called SARS-associated coronavirus (SARS-CoV). Viruses are charged colloidal particles that have the ability to adsorb on surfaces depending on pH. Their sorptive interaction with solid particles has important implications for their behavior in aquatic environments, soils, sewage sludge, and other solid materials and their removal or concentration by water treatment processes. Current state of knowledge on the potential of wastewater surveillance to understand the COVID-19 pandemic is reviewed. This study also identified wastewater irrigation systems with a higher risk of COVID-19 transmission. Emphasis was placed on methodologies for the detection and quantification of SARS-CoV-2 in wastewater.
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Affiliation(s)
- S Lahrich
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco
| | - F Laghrib
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco
| | - A Farahi
- Ibn Zohr University, Team of Catalysis and Environment, Faculty of Sciences, BP 8106 Cité Dakhla, Agadir, Morocco
| | - M Bakasse
- Chouaib Doukkali University, Faculty of Sciences, Laboratory of Organic Bioorganic Chemistry and Environment, El Jadida, Morocco
| | - S Saqrane
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco
| | - M A El Mhammedi
- Sultan Moulay Slimane University of Beni Mellal, Laboratory of Chemistry, Modeling and Environmental Sciences, Polydisciplinary Faculty, 25 000 Khouribga, Morocco.
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A simple, sensitive and non-enzymatic signal amplification strategy driven by seesaw gate. Anal Chim Acta 2020; 1108:160-166. [DOI: 10.1016/j.aca.2020.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/13/2020] [Accepted: 02/11/2020] [Indexed: 11/22/2022]
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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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Reed AJ, Connelly RP, Williams A, Tran M, Shim BS, Choe H, Gerasimova YV. Label-Free Pathogen Detection by a Deoxyribozyme Cascade with Visual Signal Readout. SENSORS AND ACTUATORS. B, CHEMICAL 2019; 282:945-951. [PMID: 31462856 PMCID: PMC6713451 DOI: 10.1016/j.snb.2018.11.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A colorimetric nucleic acid based test for label-free pathogen detection has been developed and used for the detection of the Zika virus. The test relies on nucleic acid sequence-based amplification (NASBA) of a viral RNA followed by interrogation of the amplicon by a cascade of deoxyribozymes constituting a visual split deoxyribozyme (vsDz) probe. The probe consists of a split phosphodiesterase deoxyribozyme, which forms its catalytic core upon binding to a specific amplicon fragment. The catalytically active complex recognizes and cleaves an inhibited peroxidase-like deoxyribozyme (PDz), thereby activating it. Active PDz catalyzes hydrogen peroxide-mediated oxidation of a colorless substrate into a colored product, thereby generating a visible signal. Viral RNA (106 copies/mL or higher) triggers intense color within 2 hr. The test selectively differentiates between Zika and closely related dengue and West Nile viruses. The reported technology combines isothermal amplification and visual detection and therefore represents a basis for the future development of a cost-efficient and instrument-free method for point-of-care nucleic acid analysis.
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Affiliation(s)
- Adam J. Reed
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Ryan P. Connelly
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Allison Williams
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Maithi Tran
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Byoung-Shik Shim
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yulia V. Gerasimova
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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8
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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9
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Mayboroda O, Katakis I, O'Sullivan CK. Multiplexed isothermal nucleic acid amplification. Anal Biochem 2018; 545:20-30. [PMID: 29353064 DOI: 10.1016/j.ab.2018.01.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
Multiplexed isothermal amplification and detection of nucleic acid sequences and biomarkers is of increasing importance in diverse areas including advanced diagnostics, food quality control and environmental monitoring. Whilst there are several very elegant isothermal amplification approaches, multiplexed amplification remains a challenge, requiring careful experimental design and optimisation, from judicious primer design in order to avoid the formation of primer dimers and non-specific amplification, applied temperature as well as the ratio and concentration of primers. In this review, we describe the various approaches that have been reported to date for multiplexed isothermal amplification, for both "one-pot" multiplexing as well as parallelised multiplexing using loop-mediated isothermal amplification, strand-displacement amplification, helicase-dependent amplification, rolling circle amplification, nucleic acid sequence-based amplification, with a particular focus on recombinase polymerase amplification.
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Affiliation(s)
- Olena Mayboroda
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ioanis Katakis
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
| | - Ciara K O'Sullivan
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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10
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Mo QH, Wang HB, Tan H, Wu BM, Feng ZL, Wang Q, Lin JC, Yang Z. Comparative detection of rotavirus RNA by conventional RT-PCR, TaqMan RT-PCR and real-time nucleic acid sequence-based amplification. J Virol Methods 2015; 213:1-4. [DOI: 10.1016/j.jviromet.2014.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/18/2014] [Indexed: 12/01/2022]
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11
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Li J, Macdonald J. Advances in isothermal amplification: novel strategies inspired by biological processes. Biosens Bioelectron 2015; 64:196-211. [DOI: 10.1016/j.bios.2014.08.069] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 01/02/2023]
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12
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Rapid and simultaneous detection of three major diarrhea-causing viruses by multiplex real-time nucleic acid sequence-based amplification. Arch Virol 2015; 160:719-25. [DOI: 10.1007/s00705-014-2328-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
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Abstract
Viruses are common causes of foodborne outbreaks. Viral diseases have low fatality rates but transmission to humans via food is important due to the high probability of consuming fecally contaminated food or water because of poor food handling. Because of the low infectious doses of some foodborne viruses, there is a need for standardization and the development of new sensitive methods for detecting viruses. The focus is on molecular and non-molecular approaches, and emerging methods for the detection of foodborne viruses. The detection of noroviruses, hepatitis A and E viruses, rotaviruses and adenoviruses will be discussed. The chapter will conclude with insights into future research directions.
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14
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Hryniszyn A, Skonieczna M, Wiszniowski J. Methods for Detection of Viruses in Water and Wastewater. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aim.2013.35060] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Wang J, Morabito K, Tang JX, Tripathi A. Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization. BIOMICROFLUIDICS 2013; 7:44107. [PMID: 24404041 PMCID: PMC3745474 DOI: 10.1063/1.4816943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/16/2013] [Indexed: 05/06/2023]
Abstract
The separation of target nucleic acid sequences from biological samples has emerged as a significant process in today's diagnostics and detection strategies. In addition to the possible clinical applications, the fundamental understanding of target and sequence specific hybridization on surface modified magnetic beads is of high value. In this paper, we describe a novel microfluidic platform that utilizes a mobile magnetic field in static microfluidic channels, where single stranded DNA (ssDNA) molecules are isolated via nucleic acid hybridization. We first established efficient isolation of biotinylated capture probe (BP) using streptavidin-coated magnetic beads. Subsequently, we investigated the hybridization of target ssDNA with BP bound to beads and explained these hybridization kinetics using a dual-species kinetic model. The number of hybridized target ssDNA molecules was determined to be about 6.5 times less than that of BP on the bead surface, due to steric hindrance effects. The hybridization of target ssDNA with non-complementary BP bound to bead was also examined, and non-specific hybridization was found to be insignificant. Finally, we demonstrated highly efficient capture and isolation of target ssDNA in the presence of non-target ssDNA, where as low as 1% target ssDNA can be detected from mixture. The microfluidic method described in this paper is significantly relevant and is broadly applicable, especially towards point-of-care biological diagnostic platforms that require binding and separation of known target biomolecules, such as RNA, ssDNA, or protein.
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Affiliation(s)
- Jingjing Wang
- Center for Biomedical Engineering, School of Engineering and Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, USA
| | - Kenneth Morabito
- Center for Biomedical Engineering, School of Engineering and Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, USA
| | - Jay X Tang
- Department of Physics, Brown University, Providence, Rhode Island 02912, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering and Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, USA
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Mattison K, Harlow J, Morton V, Cook A, Pollari F, Bidawid S, Farber JM. Enteric viruses in ready-to-eat packaged leafy greens. Emerg Infect Dis 2011; 16:1815-7; discussion 1817. [PMID: 21029560 PMCID: PMC3311121 DOI: 10.3201/eid1611.100877] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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17
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Hu X, Hu C, Peng T, Zhou X, Qu J. Plasmon-induced inactivation of enteric pathogenic microorganisms with Ag-AgI/Al2O3 under visible-light irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:7058-62. [PMID: 20734989 DOI: 10.1021/es1012577] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The plasmon-induced photocatalytic inactivation of enteric pathogenic microorganisms in water using Ag-AgI/Al(2)O(3) under visible-light irradiation was investigated. The catalyst was found to be highly effective at killing Shigella dysenteriae (S. dysenteriae), Escherichia coli (E. coli), and human rotavirus type 2 Wa (HRV-Wa). Its bactericidal efficiency was significantly enhanced by HCO(3)(-) and SO(4)(2-) ions, which are common in water, while phosphate had a slightly positive effect on the disinfection. Meanwhile, more inactivation of E. coli was observed at neutral and alkaline pH than at acid pH in Ag-AgI/Al(2)O(3) suspension. Furthermore, the effects of inorganic anions and pH on the transfer of plasmon-induced charges were investigated using cyclic voltammetry analyses. Two electron-transfer processes occurred, from bacteria to Ag nanoparticles (NPs) and from inorganic anions to Ag NPs to form anionic radicals. These inorganic anions including OH(-) in water not only enhanced electron transfer from plasmon-excited Ag NPs to AgI and from E. coli to Ag NPs, but their anionic radicals also increased bactericidal efficiency due to their absorbability by cells. The plasmon-induced electron holes (h(+)) on Ag NPs, O(2)(•-), and anionic radicals were involved in the reaction. The enhanced electron transfer is more crucial than the electrostatic force interaction of bacteria and catalyst for the plasmon-induced inactivation of bacteria using Ag-AgI/Al(2)O(3).
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Affiliation(s)
- Xuexiang Hu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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18
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Rotaviruses from Canadian farm samples. Arch Virol 2010; 155:1127-37. [DOI: 10.1007/s00705-010-0700-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 05/10/2010] [Indexed: 01/29/2023]
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Brassard J, Lamoureux L, Gagné MJ, Poitras É, Trottier YL, Houde A. Comparison of commercial viral genomic extraction kits for the molecular detection of foodborne viruses. Can J Microbiol 2009; 55:1016-9. [DOI: 10.1139/w09-054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
When genetic material is extracted from viruses responsible for food illnesses, two broad types of possibilities are offered: conventional methods, which are well established but usually long and exacting to perform, or commercial kits, which are faster and easy to use but much more expensive. Thus, it is important to evaluate some performance parameters such as the analytical sensitivity to be able to select the optimal technique for each situation. The principal objective of this study was to establish and compare the analytical sensitivities of three commercial genetic material extraction methods (TRIzol reagent, FTA cards, and QIAGEN kits) along with three selected viruses, adenovirus, hepatitis A virus, and rotavirus. Viral detection was carried out using a standard PCR technique for adenovirus and reverse transcription PCR for rotavirus and hepatitis A virus. The results obtained showed that with the QIAGEN kit, the sensitivity was 2 logs lower than with the two other methods for all three viruses studied. Nevertheless, despite their lower analytical sensitivities, the other two extraction methods should not be overlooked and ought to be considered when evaluating the most efficient approach suitable for a specific commodity, since food-related outbreaks may be traced to a wide variety of food types.
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Affiliation(s)
- Julie Brassard
- Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, Saint-Hyacinthe, QC J2S 8E3, Canada
- Health Canada, Quebec Region, Health Products and Food Branch, Food Directorate, 1001 St-Laurent, Longueuil, QC J4K 1C7, Canada
| | - Lisyanne Lamoureux
- Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, Saint-Hyacinthe, QC J2S 8E3, Canada
- Health Canada, Quebec Region, Health Products and Food Branch, Food Directorate, 1001 St-Laurent, Longueuil, QC J4K 1C7, Canada
| | - Marie-Josée Gagné
- Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, Saint-Hyacinthe, QC J2S 8E3, Canada
- Health Canada, Quebec Region, Health Products and Food Branch, Food Directorate, 1001 St-Laurent, Longueuil, QC J4K 1C7, Canada
| | - Élyse Poitras
- Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, Saint-Hyacinthe, QC J2S 8E3, Canada
- Health Canada, Quebec Region, Health Products and Food Branch, Food Directorate, 1001 St-Laurent, Longueuil, QC J4K 1C7, Canada
| | - Yvon-Louis Trottier
- Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, Saint-Hyacinthe, QC J2S 8E3, Canada
- Health Canada, Quebec Region, Health Products and Food Branch, Food Directorate, 1001 St-Laurent, Longueuil, QC J4K 1C7, Canada
| | - Alain Houde
- Agriculture and Agri-Food Canada, Food Research and Development Centre, 3600 Casavant Blvd. West, Saint-Hyacinthe, QC J2S 8E3, Canada
- Health Canada, Quebec Region, Health Products and Food Branch, Food Directorate, 1001 St-Laurent, Longueuil, QC J4K 1C7, Canada
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Saijo M, Morikawa S, Kurane I. Real-time quantitative polymerase chain reaction for virus infection diagnostics. ACTA ACUST UNITED AC 2008; 2:1155-71. [DOI: 10.1517/17530059.2.10.1155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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RODRÍGUEZ-LÁZARO DAVID, HERNÁNDEZ MARTA, D'AGOSTINO MARTIN, COOK NIGEL. APPLICATION OF NUCLEIC ACID SEQUENCE-BASED AMPLIFICATION FOR THE DETECTION OF VIABLE FOODBORNE PATHOGENS: PROGRESS AND CHALLENGES. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1745-4581.2006.00048.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Arora K, Chand S, Malhotra BD. Recent developments in bio-molecular electronics techniques for food pathogens. Anal Chim Acta 2006; 568:259-74. [PMID: 17761267 DOI: 10.1016/j.aca.2006.03.078] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 03/20/2006] [Accepted: 03/23/2006] [Indexed: 01/26/2023]
Abstract
Food borne illnesses contribute to the majority of infections caused by pathogenic microorganisms. Detection of these pathogens originating from different sources has led to increased interest of researchers. New bio-molecular techniques for food pathogen detection are being developed to improve the sensor characteristics such as sensitivity, reusability, simplicity and economic viability. Present article deals with the various methods of food pathogen detection with special emphasis on bio-molecular electronics techniques such as biosensors, microarrays, electronic nose, and nano-materials based methods.
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Affiliation(s)
- Kavita Arora
- Biomolecular Electronics and Conducting Polymer Research Group, National Physical Laboratory, K.S. Krishnan Road, New Delhi 110012, India.
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23
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Nainan OV, Xia G, Vaughan G, Margolis HS. Diagnosis of hepatitis a virus infection: a molecular approach. Clin Microbiol Rev 2006; 19:63-79. [PMID: 16418523 PMCID: PMC1360271 DOI: 10.1128/cmr.19.1.63-79.2006] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Current serologic tests provide the foundation for diagnosis of hepatitis A and hepatitis A virus (HAV) infection. Recent advances in methods to identify and characterize nucleic acid markers of viral infections have provided the foundation for the field of molecular epidemiology and increased our knowledge of the molecular biology and epidemiology of HAV. Although HAV is primarily shed in feces, there is a strong viremic phase during infection which has allowed easy access to virus isolates and the use of molecular markers to determine their genetic relatedness. Molecular epidemiologic studies have provided new information on the types and extent of HAV infection and transmission in the United States. In addition, these new diagnostic methods have provided tools for the rapid detection of food-borne HAV transmission and identification of the potential source of the food contamination.
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Affiliation(s)
- Omana V Nainan
- Centers for Disease Control and Prevention, 1600 Clifton Road, N.E., Mailstop A33, Atlanta, GA 30333, USA.
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24
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Lim DV, Simpson JM, Kearns EA, Kramer MF. Current and developing technologies for monitoring agents of bioterrorism and biowarfare. Clin Microbiol Rev 2005; 18:583-607. [PMID: 16223949 PMCID: PMC1265906 DOI: 10.1128/cmr.18.4.583-607.2005] [Citation(s) in RCA: 218] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.
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Affiliation(s)
- Daniel V Lim
- Department of Biology, Center for Biological Defense, University of South Florida, Tampa, FL 33620-5200, USA.
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Brassard J, Seyer K, Houde A, Simard C, Trottier YL. Concentration and detection of hepatitis A virus and rotavirus in spring water samples by reverse transcription-PCR. J Virol Methods 2005; 123:163-9. [PMID: 15620398 DOI: 10.1016/j.jviromet.2004.09.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Accepted: 09/27/2004] [Indexed: 11/28/2022]
Abstract
Every year, enteric viruses such as hepatitis A virus (HAV), rotaviruses, and noroviruses are responsible for viral gastro-enteritis and hepatitis reported worldwide. These viruses are mostly transmitted via the faecal-oral route, from direct contact between people, or by ingestion of contaminated food and water. Since only a few viral particles may cause disease, detection of low concentration of these viruses in food matrices is usually complex. The development of methods to concentrate viruses from food matrices is crucial in collecting data for the development of control strategies or for diagnostic purposes. In the present study, samples of bottled spring water were inoculated with known amounts of HAV (strain HM-175), and rotaviruses (strain Wa) viral particles and filtered through positively charged membranes. Elution of viruses attached to the membranes was achieved with a tryptose phosphate broth-glycine buffer. Eluates were further concentrated using Microsep 100. Finally, RNA was extracted using the Qiagen RNeasy kit followed by an evaporation step with a SpeedVac instrument. The detection limit by reverse-transcription (RT-PCR) was at least 10(-1) TCID50%/ml and at least 10(-3) TCID50%/ml for HAV and rotavirus, respectively.
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Affiliation(s)
- Julie Brassard
- Canadian Food Inspection Agency, Saint-Hyacinthe Laboratory, 3400 Casavant Blvd. West, Saint-Hyacinthe, Que., Canada J2S 8E3
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Jean J, D'Souza DH, Jaykus LA. Multiplex nucleic acid sequence-based amplification for simultaneous detection of several enteric viruses in model ready-to-eat foods. Appl Environ Microbiol 2004; 70:6603-10. [PMID: 15528524 PMCID: PMC525130 DOI: 10.1128/aem.70.11.6603-6610.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Accepted: 06/25/2004] [Indexed: 11/20/2022] Open
Abstract
Human enteric viruses are currently recognized as one of the most important causes of food-borne disease. Implication of enteric viruses in food-borne outbreaks can be difficult to confirm due to the inadequacy of the detection methods available. In this study, a nucleic acid sequence-based amplification (NASBA) method was developed in a multiplex format for the specific, simultaneous, and rapid detection of epidemiologically relevant human enteric viruses. Three previously reported primer sets were used in a single reaction for the amplification of RNA target fragments of 474, 371, and 165 nucleotides for the detection of hepatitis A virus and genogroup I and genogroup II noroviruses, respectively. Amplicons were detected by agarose gel electrophoresis and confirmed by electrochemiluminescence and Northern hybridization. Endpoint detection sensitivity for the multiplex NASBA assay was approximately 10(-1) reverse transcription-PCR-detectable units (or PFU, as appropriate) per reaction. When representative ready-to-eat foods (deli sliced turkey and lettuce) were inoculated with various concentrations of each virus and processed for virus detection with the multiplex NASBA method, all three human enteric viruses were simultaneously detected at initial inoculum levels of 10(0) to 10(2) reverse transcription-PCR-detectable units (or PFU)/9 cm2 in both food commodities. The multiplex NASBA system provides rapid and simultaneous detection of clinically relevant food-borne viruses in a single reaction tube and may be a promising alternative to reverse transcription-PCR for the detection of viral contamination of foods.
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Affiliation(s)
- Julie Jean
- Food Science Department, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, USA.
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27
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D'Souza DH, Jaykus LA. Nucleic acid sequence based amplification for the rapid and sensitive detection of Salmonella enterica from foods. J Appl Microbiol 2004; 95:1343-50. [PMID: 14633009 DOI: 10.1046/j.1365-2672.2003.02106.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS The purpose of this study was to apply nucleic acid sequence-based amplification (NASBA) for the detection of Salmonella enterica serovar Enteritidis (S. Enteritidis) in representative foods. METHODS AND RESULTS A previously reported primer and probe set based on mRNA sequences of the dnaK gene of Salmonella were used in this study. To test for possible food matrix inhibition and assay detection limits, 25-g samples of representative food commodities (fresh meats, poultry, fish, ready-to-eat salads and bakery products) were pre-enriched with and without S. Enteritidis inoculation. The NucliSens(R) Basic Kit, supplemented with enzymes from various other commercial sources, was used for RNA isolation, NASBA amplification and electrochemiluminescent (ECL) detection. The end point detection limit of the NASBA-ECL assay was equivalent to 101 CFU of S. Enteritidis per amplification reaction. When the assay was tested on noncontaminated foods, none of the food matrices produced false-positive results. Some of the food matrices inhibited the NASBA-ECL reaction unless the associated RNA was diluted 10-fold prior to amplification. CONCLUSIONS For all food items tested, positive ECL signals were achieved after 18 h of pre-enrichment and subsequent NASBA at initial inoculum levels of 102 and 101 CFU per 25 g food sample. SIGNIFICANCE AND IMPACT OF THE STUDY This rapid, semi-automated detection method has potential for use in the food, agricultural and public health sectors.
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Affiliation(s)
- D H D'Souza
- Department of Food Science, North Carolina State University, Raleigh, NC, USA.
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Burke M, O'Sullivan PJ, Soini AE, Berney H, Papkovsky DB. Evaluation of the phosphorescent palladium(II)-coproporphyrin labels in separation-free hybridization assays. Anal Biochem 2003; 320:273-80. [PMID: 12927834 DOI: 10.1016/s0003-2697(03)00383-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Palladium(II)-coproporphyrin label and a set of corresponding monofunctional labeling reagents with different linker arms were evaluated for labeling of oligonucleotides and subsequent use in hybridization assays. The properties of resulting oligonucleotide probes including phosphorescence spectra, quantum yields, lifetimes, and labeling yields were examined as functions of the label and oligonucleotide structures. Upon hybridization with complementary sequences bearing dabcyl, QSY-7, and rhodamine green dyes, the probes displayed strong quenching due to close proximity effects. Intensity and lifetime changes of the phosphorescence, distance, and temperature dependences were investigated in detail. The potential of the new label and probes for sensitive and separation-free hybridization assays was discussed.
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Affiliation(s)
- Martina Burke
- Biochemistry Department/ABCRF, University College Cork, Lee Maltings, Cork, Ireland
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Cook N. The use of NASBA for the detection of microbial pathogens in food and environmental samples. J Microbiol Methods 2003; 53:165-74. [PMID: 12654488 DOI: 10.1016/s0167-7012(03)00022-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The isothermal amplification method nucleic acid sequence-based amplification (NASBA), which amplifies RNA, has been reported as useful for the detection of microbial pathogens in food and environmental samples. Methods have been published for Campylobacter spp., Listeria monocytogenes and Salmonella enterica ser. Enteritidis in various foods and for Cryptosporidium parvum in water. Both 16S rRNA and various mRNAs have been used as target molecules for detection; the latter may have advantages in allowing specific detection of viable cells. Most of the methods to detect pathogens in foods have employed enrichment in nutrient medium prior to NASBA, as this can ensure sensitivity of detection and encourage the detection of only viable target cells. Although a relatively recent method, NASBA has the potential for adoption as a diagnostic tool for environmental pathogens.
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Affiliation(s)
- Nigel Cook
- DEFRA Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK.
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