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Costa-Ribeiro A, Lamas A, Mora A, Prado M, Garrido-Maestu A. Moving towards on-site detection of Shiga toxin-producing Escherichia coli in ready-to-eat leafy greens. Curr Res Food Sci 2024; 8:100716. [PMID: 38511154 PMCID: PMC10950744 DOI: 10.1016/j.crfs.2024.100716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Rapid identification of Shiga toxin-producing Escherichia coli, or STEC, is of utmost importance to assure the innocuousness of the foodstuffs. STEC have been implicated in outbreaks associated with different types of foods however, among them, ready-to-eat (RTE) vegetables are particularly problematic as they are consumed raw, and are rich in compounds that inhibit DNA-based detection methods such as qPCR. In the present study a novel method based on Loop-mediated isothermal amplification (LAMP) to overcome the limitations associated with current molecular methods for the detection of STEC in RTE vegetables targeting stx1 and stx2 genes. In this sense, LAMP demonstrated to be more robust against inhibitory substances in food. In this study, a comprehensive enrichment protocol was combined with four inexpensive DNA extraction protocols. The one based on silica purification enhanced the performance of the method, therefore it was selected for its implementation in the final method. Additionally, three different detection chemistries were compared, namely real-time fluorescence detection, and two end-point colorimetric strategies, one based on the addition of SYBR Green, and the other based on a commercial colorimetric master mix. After optimization, all three chemistries demonstrated suitable for the detection of STEC in spiked RTE salad samples, as it was possible to reach a LOD50 of 0.9, 1.4, and 7.0 CFU/25 g for the real-time, SYBR and CC LAMP assays respectively. All the performance parameters reached values higher than 90 %, when compared to a reference method based on multiplex qPCR. More specifically, the analytical sensitivity was 100, 90.0 and 100 % for real-time, SYBR and CC LAMP respectively, the specificity 100 % for all three assays, and accuracy 100, 96 and 100 %. Finally, a high degree of concordance was also obtained (1, 0.92 and 1 respectively). Considering the current technological advances, the method reported, using any of the three detection strategies, demonstrated suitable for their implementation in decentralized settings, with low equipment resources.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Laboratory of Microbiology and Technology of Marine Products (MicroTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello, 6, 36208, Vigo, Spain
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Costa-Ribeiro A, Lamas A, Prado M, Garrido-Maestu A. Evaluation of the Novel mTA10 Selective Broth, MSB, for the Co-Enrichment and Detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in Ready-to-Eat Salad Samples. Foods 2023; 13:63. [PMID: 38201091 PMCID: PMC10778508 DOI: 10.3390/foods13010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Multiplex assays implementing DNA-based methods have been demonstrated as suitable alternatives to culture-based microbiological methods; however, in most cases, they still require a suitable enrichment step. Finding suitable enrichment conditions for different bacteria may result in challenges. In the present study, a novel selective broth named MSB (mTA10 selective broth) was formulated for the simultaneous recovery of Salmonella spp., E. coli O157:H7 and L. monocytogenes. Attention was paid to ensure the optimal enrichment of L. monocytogenes as its enrichment is more challenging. To this end, cellobiose was added to increase the growth of L. monocytogenes, and sodium pyruvate was also added to improve the recovery of stressed bacteria. Four selective agents were added, namely nalidixic acid, sodium cholate, lithium chloride and potassium tellurite, to control the growth of interfering microorganisms. It was concluded that the novel broth was suitable for the simultaneous enrichment of the target pathogens, allowing them to reach concentrations higher than 7 log CFU/mL for each bacterium in pure culture. Furthermore, all heavily contaminated ready-to-eat salad samples reached concentrations higher than 5 log CFU/g. Finally, after 24 h of enrichment of spiked salad, it was possible to detect concentrations below 10 CFU/25 g.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (A.C.-R.); (M.P.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (A.C.-R.); (M.P.)
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (A.C.-R.); (M.P.)
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da Silva EC, de Oliveira CD, Ribeiro LFM, Casas MRT, Pereira JG, Possebon FS, Junior JPA. Salmonella detection with LAMP and qPCR and identification of serovars of interest by multiplex qPCR in poultry carcasses. Braz J Microbiol 2023; 54:2173-2182. [PMID: 37582950 PMCID: PMC10484893 DOI: 10.1007/s42770-023-01095-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023] Open
Abstract
Salmonella is present in the poultry production chain and is a major challenge in terms of food safety and animal health. The early Salmonella detection is one of the main tools to control and prevent the transmission of this pathogen. Microbiological isolation and serotyping to identify and differentiate Salmonella serovars are laborious processes, time-consuming, and expensive. Therefore, molecular diagnostic methods can be rapid and efficient alternatives to the detection of this pathogen. Thus, the aim herein was to standardize and evaluate the use of loop-mediated isothermal amplification (LAMP) in comparison with real-time PCR (qPCR) for detection of Salmonella associated with a multiplex qPCR for simultaneous identification and differentiation of S. Enteritidis, S. Typhimurium, S. Pullorum, and S. Gallinarum. The LAMP, qPCR, and multiplex qPCR assays were comparable in specificity. The three techniques were evaluated for specificity for 16 different serovars of Salmonella and for 37 strains of the serovars of interest. The limit of detection and the efficiency of the LAMP, qPCR, and multiplex qPCR reactions were determined. The techniques were applied to 33 samples of chicken carcasses and compared to the results of conventional microbiology for validation. As results, LAMP was specific in the detection of different Salmonella serovars but presented lower limit of detection ranging from 101 to 104 CFU/reaction. In comparison, qPCR could detect less cells (100 to 102 CFU/reaction), reaching equal specificity and better repeatability in the assays. The qPCR multiplexing for identification of the different serovars also showed good specificity, with the detection threshold between entre 101 and 102 CFU/reaction. The results obtained in the analyses on poultry carcasses suggested a correspondence between the results obtained in molecular methods and in conventional microbiology. Thus, the proposed assays are promising for the diagnosis of Salmonella in poultry carcasses, already proved to be faster and more efficient than conventional diagnostics techniques, being of great interest for poultry production, animal, and public health.
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Affiliation(s)
- Evelyn Cristine da Silva
- Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias Avenue, Botucatu, SP, 18607-440, Brazil.
| | - Catarina Demarchi de Oliveira
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - Lucas Franco Miranda Ribeiro
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - Monique Ribeiro Tiba Casas
- Bacteriology Division, Adolfo Lutz Institute (IAL), Doutor Arnaldo Avenue, São Paulo, SP, 01246-000, Brazil
| | - Juliano Gonçalves Pereira
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - Fábio Sossai Possebon
- Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias Avenue, Botucatu, SP, 18607-440, Brazil
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - João Pessoa Araújo Junior
- Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias Avenue, Botucatu, SP, 18607-440, Brazil
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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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Domesle KJ, Young SR, McDonald RC, Ge B. Versatility of a Salmonella Loop-Mediated Isothermal Amplification Assay Using Multiple Platforms and Master Mixes in Animal Food Matrices. J AOAC Int 2022; 105:1503-1515. [DOI: 10.1093/jaoacint/qsac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Background
Improvement in Salmonella detection methods greatly enhances the efficiency of various food testing programs. A Salmonella loop-mediated isothermal amplification (LAMP) assay has been validated in animal food through multi-laboratory validation.
Objective
The study aimed to demonstrate the versatility of this molecular assay while expanding it to multiple platforms and various reagent choices for use in animal food testing.
Methods
Following the U.S. Food and Drug Administration (FDA)’s Guidelines for the Validation of Analytical Methods for the Detection of Microbial Pathogens in Foods and Feeds, we examined the inclusivity, exclusivity, and LOD of the assay using two platforms (7500 Fast and Genie II) and three LAMP master mixes (GspSSD, GspSSD2.0, and WarmStart) in seven animal food matrixes (dry cat food, dry dog food, cattle feed, dairy feed, horse feed, poultry feed, and swine feed). The FDA’s Bacteriological Analytical Manual (BAM) Salmonella culture method was the reference method.
Results
Inclusivity and exclusivity data were consistent among all six platform and master mix combinations with a few exceptions. Comparable LODs were observed down to the single-cell level (WarmStart was 10-fold less sensitive). Performance was similar to the BAM method for detecting fractional positive results in seven animal food matrixes. Nonetheless, LAMP time to positive results and annealing/melting temperature differed among master mixes and platforms.
Conclusion
The Salmonella LAMP assay was successfully validated in two platforms and three master mixes, making it a flexible tool for use by the FDA’s field laboratories in regulatory testing of animal food and for adoption by other food testing programs.
Highlights
We demonstrated the LAMP assay’s versatility on two platforms and three master mixes for the rapid and reliable screening of Salmonella in seven animal food matrixes. GspSSD2.0 was the fastest master mix (time to positive results as early as 3.5 min) while Genie II had several attractive features from a user perspective.
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Affiliation(s)
- Kelly J Domesle
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology , 8401 Muirkirk Rd , Laurel, MD 20708, USA
| | - Shenia R Young
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology , 8401 Muirkirk Rd , Laurel, MD 20708, USA
| | - Ryan C McDonald
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology , 8401 Muirkirk Rd , Laurel, MD 20708, USA
| | - Beilei Ge
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Division of Animal and Food Microbiology , 8401 Muirkirk Rd , Laurel, MD 20708, USA
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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Azinheiro S, Roumani F, Carvalho J, Prado M, Garrido-Maestu A. Suitability of the MinION long read sequencer for semi-targeted detection of foodborne pathogens. Anal Chim Acta 2021; 1184:339051. [PMID: 34625270 DOI: 10.1016/j.aca.2021.339051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
Abstract
Foodborne pathogens are still a significant source of morbidity and mortality worldwide. In addition to this the current methodologies to track these microorganisms cannot cope with the current intensive production systems, thus novel methods are of outmost importance. DNA-based methods have already demonstrated suitable to address this issue, but most of them are targeted methods such as real-time PCR (qPCR), meaning that one will only find what is looking for, thus taking the risk of missing relevant pathogens in a given sample. To overcome this limitation we have developed an easy-to-implement methodology which enables the detection of several pathogens simultaneously by using long-read Next Generation Sequencing (NGS) with MinION. The method was named "semi-targeted" due to the combination of a non-targeted detection method, NGS, with the usage of selective media in order to partially eliminate non-pathogenic interfering bacteria. To this end, we included an enrichment step for the recovery of different pathogens, namely Salmonella Enteritidis and Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7, after DNA extraction and library preparation, the samples were analyzed with MinION implementing the low-cost Flongle Flow Cells. The methodology was successfully evaluated in spiked milk samples with an excellent agreement with the results obtained by qPCR and culture-based methods. The method can provide accurate results after only 2 h of sequencing. Sample multiplexing, along with the lower cost of the Flongle Flow Cells and the reduced price of the MinION platform, make the assay cost-effective that is of importance for the food industry. Starting the method with a classical microbiological approach, the enrichment, the method is easy to implement in testing laboratories, it provides flexibility in terms of potential pathogens to be detected, and the positive results can be easily confirmed following culture-based, or other type, of confirmation procedures.
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Affiliation(s)
- Sarah Azinheiro
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Foteini Roumani
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Joana Carvalho
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Marta Prado
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal.
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Hu X, Xu H, Zhang Y, Lu X, Yang Q, Zhang W. Saltatory rolling circle amplification (SRCA) for sensitive visual detection of horsemeat adulteration in beef products. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03720-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Roumani F, Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Loop-mediated isothermal amplification combined with immunomagnetic separation and propidium monoazide for the specific detection of viable Listeria monocytogenes in milk products, with an internal amplification control. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Artavia G, Cortés-Herrera C, Granados-Chinchilla F. Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis. Foods 2021; 10:1081. [PMID: 34068197 PMCID: PMC8152966 DOI: 10.3390/foods10051081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/13/2021] [Accepted: 03/19/2021] [Indexed: 12/28/2022] Open
Abstract
This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.
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Affiliation(s)
- Graciela Artavia
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Carolina Cortés-Herrera
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
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Wang F, Wu X, Xu D, Chen L, Ji L. Identification of Chicken-Derived Ingredients as Adulterants Using Loop-Mediated Isothermal Amplification. J Food Prot 2020; 83:1175-1180. [PMID: 32084666 DOI: 10.4315/jfp-19-542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/21/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Meat adulteration has recently become an issue of increasing public concern. In addition to posing a health risk to consumers with metabolic disorders or allergies, meat adulteration has triggered many economic and religious problems. Chicken meat is a common adulterant in nonchicken products because of its low cost and ready availability. A loop-mediated isothermal amplification assay coupled with a lateral flow dipstick was developed to identify chicken in nonchicken products. We optimized the amplification time and temperature to obtain the best result. This assay is performed at a constant temperature in a water bath and can be completed in 1 h. No precision instruments or equipment are needed. With a one-step reaction and easy operation, the testing cost is low. This method is highly sensitive and specific and is a valuable method for identifying chicken in nonchicken products to meets the requirements of on-site inspection and detection. HIGHLIGHTS
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Affiliation(s)
- Feng Wang
- Huzou Center Blood Station, 412 Fenghuang Road, Huzhou, Zhejiang 313000, People's Republic of China
| | - Xiaofang Wu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, People's Republic of China
| | - Deshun Xu
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, People's Republic of China
| | - Liping Chen
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, People's Republic of China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang 313000, People's Republic of China
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Sange MD, Becker A, Hassan AA, Bülte M, Ganter M, Siebert U, Abdulmawjood A. Development and validation of a loop-mediated isothermal amplification assay-a rapid and sensitive detection tool for Mycobacterium avium subsp. paratuberculosis in small ruminants. J Appl Microbiol 2019; 127:47-58. [PMID: 31002199 DOI: 10.1111/jam.14284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/09/2019] [Accepted: 04/14/2019] [Indexed: 12/22/2022]
Abstract
AIMS The aim of this study was to design an assay for the identification of Mycobacterium avium subsp. paratuberculosis (MAP) to be used in faeces and milk samples of small ruminants with a loop-mediated isothermal amplification (LAMP) system, as a time-saving and user-friendly method in contrast to real-time PCR. METHODS AND RESULTS For the detection of MAP in milk and faeces of small ruminants, we developed a set of primers, specific for the target gene ISMap02. The analytical sensitivity of LAMP, when targeting ISMap02, showed a DNA detection limit of 10 fg μl-1 . After performing spiking experiments with two MAP reference strains, DSM 44133 and ATCC 19698T , the limit of detection, using the LAMP protocol described herein were 3·8 MAP CFU per ml milk and 12·5 MAP CFU per gram faeces. All LAMP results during the establishment of the assay were compared to those of the real-time PCR results. An internal amplification control was incorporated into the assay to exclude false-negative results produced and had no significant negative impact on the analytical sensitivity. Validation of the assay was confirmed by testing field samples of faeces and revising the results with real-time PCR. CONCLUSION Our study conducted the first MAP detection system with a LAMP targeting ISMap02. Due to the positive results we encourage the use of LAMP in combination with ISMap02, when detecting MAP in faeces samples, as an alternative to targeting other genes as f57 or IS900. Further research on MAP detection in different matrices like raw milk, tissue or sperm with this system is recommended. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides new achievements in MAP diagnostic. Especially small ruminants do not show signs of diarrhoea until the terminal stage of the illness. The greatest task in fighting MAP is to rule out animals, which shed MAP with faeces and milk before showing symptoms of Johne's disease. Worldwide there is a need to eradicate animals, which are low MAP shedders to stop the illness spreading in animal holdings. MAP detection with LAMP is time saving, easy to use, does not need expensive equipment, as, for example, PCR kits and can be used without access to laboratories. The target gene ISMap02 was shown to be a specific insertion element for MAP and is a reliable aim in future MAP detection studies.
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Affiliation(s)
- M D Sange
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - A Becker
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - A A Hassan
- Institute of Food Science, Faculty of Veterinary Medicine of the Justus-Liebig-University Gießen, Gießen, Germany
| | - M Bülte
- Institute of Food Science, Faculty of Veterinary Medicine of the Justus-Liebig-University Gießen, Gießen, Germany
| | - M Ganter
- Clinic for Swine, Small Ruminants and Forensic Medicine, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - U Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - A Abdulmawjood
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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13
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Rapid and sensitive detection of viable Listeria monocytogenes in food products by a filtration-based protocol and qPCR. Food Microbiol 2018. [DOI: 10.1016/j.fm.2018.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Yang Q, Domesle KJ, Ge B. Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions. Foodborne Pathog Dis 2018; 15:309-331. [PMID: 29902082 PMCID: PMC6004089 DOI: 10.1089/fpd.2018.2445] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed.
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Affiliation(s)
- Qianru Yang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
| | - Kelly J Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
| | - Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine , U.S. Food and Drug Administration, Laurel, Maryland
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15
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Highly sensitive detection of gluten-containing cereals in food samples by real-time Loop-mediated isothermal AMPlification (qLAMP) and real-time polymerase chain reaction (qPCR). Food Chem 2018; 246:156-163. [DOI: 10.1016/j.foodchem.2017.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 11/18/2022]
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16
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Garrido-Maestu A, Azinheiro S, Carvalho J, Fuciños P, Prado M. Development and evaluation of loop-mediated isothermal amplification, and Recombinase Polymerase Amplification methodologies, for the detection of Listeria monocytogenes in ready-to-eat food samples. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Siala M, Barbana A, Smaoui S, Hachicha S, Marouane C, Kammoun S, Gdoura R, Messadi-Akrout F. Screening and Detecting Salmonella in Different Food Matrices in Southern Tunisia Using a Combined Enrichment/Real-Time PCR Method: Correlation with Conventional Culture Method. Front Microbiol 2017; 8:2416. [PMID: 29270157 PMCID: PMC5725475 DOI: 10.3389/fmicb.2017.02416] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/22/2017] [Indexed: 11/13/2022] Open
Abstract
A combined enrichment/ newly developed invA TaqMan® real-time PCR (qPCR) method as a screening assay to detect Salmonella spp. in 500 naturally food matrices is evaluated. DNA template for qPCR was extracted from an overnight pre-enriched sample in buffered peptone water using lysis–guanidine isothiocyanate method. Heterologous internal amplification control (IAC) was incorporated during qPCR assays and co-amplified with the invA gene of the target pathogen. InvA qPCR exhibited 100% specificity when testing 94 Salmonella strains (inclusivity) and 32 non-Salmonella strains (exclusivity). The qPCR showed a consistent detection of two copies of the invA gene/PCR reaction, a good intra- and inter-run reproducibility with a good PCR efficiency (89.6%). QPCR was sensitive and showed Salmonella detection at 8.5 × 100 CFU mL-1 of artificially spiked poultry meat -BWP solution in less than 40 cycles. When analyzing 500 different food matrices and comparing the results with the ISO 6579:2002 conventional culture method, the sensitivity and specificity were 100 and 76.6%, respectively. QPCR showed Salmonella spp. DNA in raw poultry meat 27/45 (60%), milk 31/93 (33.3%), raw red meat 5/13 (38.5%), and fish 11/46 (23.9%) samples. The prevalence of Salmonella spp. in cakes, dairy, cooked meals, charcuterie products using qPCR was 11/14 (26.8%), 5/22 (22.7%), 32/150 (21.3%), and 5/20 (25%), respectively, compared to 0% as demonstrated by culture. S. Anatum was the most common serovar found associated with red meat compared to S. kentucky isolated from fish and poultry meat. In conclusion, our study is the first to use a combined enrichment/invA qPCR method as a screening assay to detect Salmonella DNA in different types of commercialized food in Southern Tunisia. QPCR results indicate that Salmonella contamination is common in milk and in other types of food samples.
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Affiliation(s)
- Mariam Siala
- Department of Biology, Preparatory Institute for Engineering Studies of Sfax, University of Sfax, Sfax, Tunisia.,Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Amina Barbana
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Salma Smaoui
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Salma Hachicha
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Chema Marouane
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Sana Kammoun
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Radhouane Gdoura
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Férièle Messadi-Akrout
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
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18
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Domesle KJ, Yang Q, Hammack TS, Ge B. Validation of a Salmonella loop-mediated isothermal amplification assay in animal food. Int J Food Microbiol 2017; 264:63-76. [PMID: 29121500 DOI: 10.1016/j.ijfoodmicro.2017.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has emerged as a promising alternative to PCR for pathogen detection in food testing and clinical diagnostics. This study aimed to validate a Salmonella LAMP method run on both turbidimetry (LAMP I) and fluorescence (LAMP II) platforms in representative animal food commodities. The U.S. Food and Drug Administration (FDA)'s culture-based Bacteriological Analytical Manual (BAM) method was used as the reference method and a real-time quantitative PCR (qPCR) assay was also performed. The method comparison study followed the FDA's microbiological methods validation guidelines, which align well with those from the AOAC International and ISO. Both LAMP assays were 100% specific among 300 strains (247 Salmonella of 185 serovars and 53 non-Salmonella) tested. The detection limits ranged from 1.3 to 28 cells for six Salmonella strains of various serovars. Six commodities consisting of four animal feed items (cattle feed, chicken feed, horse feed, and swine feed) and two pet food items (dry cat food and dry dog food) all yielded satisfactory results. Compared to the BAM method, the relative levels of detection (RLODs) for LAMP I ranged from 0.317 to 1 with a combined value of 0.610, while those for LAMP II ranged from 0.394 to 1.152 with a combined value of 0.783, which all fell within the acceptability limit (2.5) for an unpaired study. This also suggests that LAMP was more sensitive than the BAM method at detecting low-level Salmonella contamination in animal food and results were available 3days sooner. The performance of LAMP on both platforms was comparable to that of qPCR but notably faster, particularly LAMP II. Given the importance of Salmonella in animal food safety, the LAMP assays validated in this study holds great promise as a rapid, reliable, and robust method for routine screening of Salmonella in these commodities.
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Affiliation(s)
- Kelly J Domesle
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, MD 20708, USA
| | - Qianru Yang
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, MD 20708, USA
| | - Thomas S Hammack
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740, USA
| | - Beilei Ge
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, MD 20708, USA.
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Garrido-Maestu A, Fuciños P, Azinheiro S, Carvalho J, Prado M. Systematic loop-mediated isothermal amplification assays for rapid detection and characterization of Salmonella spp., Enteritidis and Typhimurium in food samples. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Wang Z, Yang Q, Zhang Y, Meng Z, Ma X, Zhang W. Saltatory Rolling Circle Amplification (SRCA): a Novel Nucleic Acid Isothermal Amplification Technique Applied for Rapid Detection of Shigella Spp. in Vegetable Salad. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1021-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Shi Y, Feng Y, Xu C, Xu Z, Cheng D, Lu Y. Loop-Mediated Isothermal Amplification Assays for the Rapid Identification of Duck-Derived Ingredients in Adulterated Meat. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-016-0767-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Validation of a Loop-Mediated Amplification/ISO 6579-Based Method for Analysing Soya Meal for the Presence of Salmonella enterica. FOOD ANAL METHOD 2016. [DOI: 10.1007/s12161-016-0602-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Zhou D, Wang C, Li Z, Chen Y, Gao S, Guo J, Lu W, Su Y, Xu L, Que Y. Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay. FRONTIERS IN PLANT SCIENCE 2016; 7:279. [PMID: 27014303 PMCID: PMC4782128 DOI: 10.3389/fpls.2016.00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg(2+), 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of AgricultureFuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of AgricultureFuzhou, China
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