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Chen Y, Zhu Y, Du J, Peng C, Wang X, Wu J, Zhou Q, Chen H, Xu J. A new simplified sequence-dependent loop-mediated isothermal amplification (LAMP) detection method. Anal Bioanal Chem 2024; 416:4143-4152. [PMID: 38777877 DOI: 10.1007/s00216-024-05340-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Fluorescence dye-based loop-mediated isothermal amplification (LAMP) is a sensitive nucleic acid detection method, but is limited to single-plex detection and may yield non-specific signals. In this study, we propose a bifunctional probe-based real-time LAMP amplification method for single-plexed or multiplexed detection. The bifunctional probe is derived by modifying the 5' end of the fluorophore and an internal quencher on one of the LAMP primers; therefore, it can simultaneously be involved in the LAMP process and signal amplification. The fluorescence intensity undergoes a cumulative exponential increase during the incorporation of the bifunctional probe into double-stranded DNA amplicons. The bifunctional probe-based LAMP method is simplified and cost-effective, as the primer design and experimental operations align entirely with the ordinary LAMP. Different from other current probe-based methods, this method does not require additional enzymes, sequences, or special probe structures. Also, it is 10 min faster than several other probe-based LAMP methods. The bifunctional probe-based LAMP method allows the simultaneous detection of the target Vibrio parahaemolyticus DNA and the internal amplification control in a one-pot reaction, demonstrating its potential for multiplexed detection.
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311215, China
| | - Yuanyuan Zhu
- College of Biosystems Engineering and Food Science & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311215, China
| | - Jungang Du
- College of Biosystems Engineering and Food Science & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311215, China
| | - Cheng Peng
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311215, China.
| | - Qingli Zhou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, People's Republic of China.
| | - Huan Chen
- Hangzhou Digital-Micro Biotech Co., Ltd., Hangzhou, 311215, China
| | - Junfeng Xu
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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Azinheiro S, Roumani F, Costa-Ribeiro A, Prado M, Garrido-Maestu A. Application of MinION sequencing as a tool for the rapid detection and characterization of Listeria monocytogenes in smoked salmon. Front Microbiol 2022; 13:931810. [PMID: 36033887 PMCID: PMC9399719 DOI: 10.3389/fmicb.2022.931810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial pathogens may be present in different types of foods, and hence the development of novel methods to assure consumers' safeness is of great interest. Molecular methods are known to provide sensitive and rapid results; however, they are typically targeted approaches. In recent years, the advent of non-targeted approaches based on next-generation sequencing (NGS) has emerged as a rational way to proceed. This technology allows for the detection of several pathogens simultaneously. Furthermore, with the same set of data, it is possible to characterize the microorganisms in terms of serotype, virulence, and/ or resistance genes, among other molecular features. In the current study, a novel method for the detection of Listeria monocytogenes based on the "quasimetagenomics" approach was developed. Different enrichment media and immunomagnetic separation (IMS) strategies were compared to determine the best approach in terms of L. monocytogenes sequences generated from smoked salmon samples. Finally, the data generated were analyzed with a user-friendly workflow that simultaneously provided the species identification, serotype, and antimicrobial resistance genes. The new method was thoroughly evaluated against a culture-based approach, using smoked salmon inoculated with L. monocytogenes as the matrix of choice. The sequencing method reached a very low limit of detection (LOD50, 1.2 CFU/ 25 g) along with high diagnostic sensitivity and specificity (100%), and a perfect correlation with the culture-based method (Cohen's k = 1.00). Overall, the proposed method overcomes all the major limitations reported for the implementation of NGS as a routine food testing technology and paves the way for future developments taking its advantage into consideration.
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Affiliation(s)
- Sarah Azinheiro
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
- Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, Lugo, Spain
| | - Foteini Roumani
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
- Department of Analytical Chemistry, Nutrition and Food Science, Faculty of Veterinary Science, University of Santiago de Compostela, Lugo, Spain
| | - Ana Costa-Ribeiro
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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Zhang Y, Wang H, Shang K, Wang X, Xu P. Reliable detection of Listeria monocytogenes by a portable paper-based multi-biocatalyst platform integrating three biomarkers: Gene hly, acetoin, and listeriolysin O protein. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2021.115975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Rip D, Gouws PA. PCR-Restriction Fragment Length Polymorphism and Pulsed-Field Gel Electrophoresis Characterization of Listeria monocytogenes Isolates from Ready-to-Eat Foods, the Food Processing Environment, and Clinical Samples in South Africa. J Food Prot 2020; 83:518-533. [PMID: 32073615 DOI: 10.4315/0362-028x.jfp-19-301] [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: 06/29/2019] [Accepted: 11/06/2019] [Indexed: 11/11/2022]
Abstract
ABSTRACT Listeria monocytogenes is a ubiquitous, intracellular foodborne pathogen that is responsible for invasive listeriosis. The ability of L. monocytogenes to cause disease has some correlation with the serotypes of a specific lineage group, making the identification of lineage groups important for epidemiological analysis. The development of typing methods to link the strains of L. monocytogenes to an outbreak of listeriosis would help minimize the spread of the disease. The aim of this study was to design a PCR-restriction fragment length polymorphism (RFLP) method to differentiate between the lineage groups of L. monocytogenes. PCR-amplified fragments of the hly gene for 12 serotypes of L. monocytogenes were sequenced, aligned, and analyzed with the BioEdit program, and single nucleotide polymorphisms (SNPs) within regions of this gene were identified. Because of the difficulty in acquiring a serotype 4ab reference strain, this serotype was not included in this study. We tested the specificity and accuracy of the PCR-RFLP method on these L. monocytogenes reference strains and validated the method with 172 L. monocytogenes strains recovered from humans, food, and the food processing environment in 2000 to 2002 and 2008 to 2010 from regions within South Africa. PCR-RFLP analysis applied in this study placed L. monocytogenes serotypes into one of three lineage groups based on the sequence differences and SNPs within each lineage group. The SNPs were conserved in a region where RFLP analysis could be applied for a distinction between L. monocytogenes lineage groups. HIGHLIGHTS
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Affiliation(s)
- Diane Rip
- Food Microbiology Research Group, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Pieter A Gouws
- Food Microbiology Research Group, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
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Yushina Y, Makhova A, Zayko E, Bataeva D. Loop-mediated isothermal amplification (LAMP) for rapid detection of L. monocytogenes in meat. POTRAVINARSTVO 2019. [DOI: 10.5219/1165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is a continued need to develop improved rapid methods for detection of foodborne pathogens. Rapid and sensitive methods for enumeration of Listeria monocytogenes are important for microbiological food safety testing purpose. The aim of this project was to evaluate a commercial loop-mediated isothermal amplification (LAMP) based system with bioluminescence, named as 3M™ Molecular Detection Assay (MDA), was validated for the detection of L. monocytogenes in food products with a standard GOST 32031-2012 method as reference. The results of this study revealed that a commercial LAMP-based method performed equally effective compared with method, showing from 94% to 100% specificity and sensitivity, respectively. The LAMP-based method was shown to be rapid and reliable detection technique for L. monocytogenes present at low numbers (10 CFU.g-1) on raw meat and meat products and can be applicable in meat industry. Thus, compared with the microbiological method based GOST 32031-2012, the LAMP assay is a relatively rapid and highly sensitive method for detecting L. monocytogenes and will facilitate the surveillance for contamination of L. monocytogenes in food. The 3M MDS result and culture-based detection (GOST 32031-2012) did not differ significantly (p >0.05) regarding the number of positive samples.
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Wachiralurpan S, Sriyapai T, Areekit S, Sriyapai P, Augkarawaritsawong S, Santiwatanakul S, Chansiri K. Rapid Colorimetric Assay for Detection of Listeria monocytogenes in Food Samples Using LAMP Formation of DNA Concatemers and Gold Nanoparticle-DNA Probe Complex. Front Chem 2018; 6:90. [PMID: 29670874 PMCID: PMC5893898 DOI: 10.3389/fchem.2018.00090] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 03/14/2018] [Indexed: 11/17/2022] Open
Abstract
Listeria monocytogenes is a major foodborne pathogen of global health concern. Herein, the rapid diagnosis of L. monocytogenes has been achieved using loop-mediated isothermal amplification (LAMP) based on the phosphatidylcholine-phospholipase C gene (plcB). Colorimetric detection was then performed through the formation of DNA concatemers and a gold nanoparticle/DNA probe complex (GNP/DNA probe). The overall detection process was accomplished within approximately 1 h with no need for complicated equipment. The limits of detection for L. monocytogenes in the forms of purified genomic DNA and pure culture were 800 fg and 2.82 CFU mL−1, respectively. No cross reactions were observed from closely related bacteria species. The LAMP-GNP/DNA probe assay was applied to the detection of 200 raw chicken meat samples and compared to routine standard methods. The data revealed that the specificity, sensitivity, and accuracy were 100, 90.20, and 97.50%, respectively. The present assay was 100% in conformity with LAMP-agarose gel electrophoresis assay. Five samples that were negative by both assays appeared to have the pathogen at below the level of detection. The assay can be applied as a rapid direct screening method for L. monocytogenes.
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Affiliation(s)
- Sirirat Wachiralurpan
- Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
| | - Thayat Sriyapai
- Faculty of Environmental Culture and Ecotourism, Srinakharinwirot University, Bangkok, Thailand
| | - Supatra Areekit
- Innovative Learning Center, Srinakharinwirot University, Bangkok, Thailand
| | - Pichapak Sriyapai
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
| | | | - Somchai Santiwatanakul
- Department of Pathology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
| | - Kosum Chansiri
- Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
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Wachiralurpan S, Sriyapai T, Areekit S, Kaewphinit T, Sriyapai P, Santiwatanakul S, Chansiri K. Development of a Rapid Screening Test for Listeria monocytogenes in Raw Chicken Meat Using Loop-Mediated Isothermal Amplification (LAMP) and Lateral Flow Dipstick (LFD). FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0949-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Tao T, Chen Q, Bie X, Lu F, Lu Z. Investigation on prevalence of Listeria spp. and Listeria monocytogenes in animal-derived foods by multiplex PCR assay targeting novel genes. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.09.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Välimaa AL, Tilsala-Timisjärvi A, Virtanen E. Rapid detection and identification methods for Listeria monocytogenes in the food chain – A review. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.02.037] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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A new multiplex real-time PCR developed method for Salmonella spp. and Listeria monocytogenes detection in food and environmental samples. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.06.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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MARTINON A, WILKINSON M. SELECTION OF OPTIMAL PRIMER SETS FOR USE IN A DUPLEX SYBR GREEN-BASED, REAL-TIME POLYMERASE CHAIN REACTION PROTOCOL FOR THE DETECTION OF LISTERIA MONOCYTOGENES AND STAPHYLOCCOCUS AUREUS IN FOODS. J Food Saf 2011. [DOI: 10.1111/j.1745-4565.2011.00301.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cloning and Characterisation of a Δ-prfA Listeria monocytogenes Strain Containing an Artificial Single Copy Genomic Internal Amplification Control (IAC) for Use as Internal Sample Process Control (ISPC). FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9212-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Wang Z, Miu T, Xu H, Duan N, Ding X, Li S. Sensitive immunoassay of Listeria monocytogenes with highly fluorescent bioconjugated silica nanoparticles probe. J Microbiol Methods 2010; 83:179-84. [DOI: 10.1016/j.mimet.2010.08.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Revised: 08/13/2010] [Accepted: 08/17/2010] [Indexed: 11/24/2022]
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Chai Y, Tian D, Wang W, Cui H. A novel electrochemiluminescence strategy for ultrasensitive DNA assay using luminol functionalized gold nanoparticles multi-labeling and amplification of gold nanoparticles and biotin-streptavidin system. Chem Commun (Camb) 2010; 46:7560-2. [PMID: 20852765 DOI: 10.1039/c0cc02356f] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Luminol functionalized gold nanoparticles were used as labels for electrochemiluminescence signal amplification and an ultrasensitive, highly selective, convenient, low cost DNA detection strategy was developed.
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Affiliation(s)
- Ying Chai
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
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