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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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Abdelfattah MM, Osman AM, Elnagar MA, Ibrahim MF, Albert M, M Talal M, Abdel Fattah NF, Loutfy SA, Helwa R. In-house protocol: spin-based viral RNA purification. AMB Express 2022; 12:70. [PMID: 35680770 PMCID: PMC9181933 DOI: 10.1186/s13568-022-01413-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/29/2022] [Indexed: 12/01/2022] Open
Abstract
A worldwide shortage of molecular biology consumables is in surge. This includes filter tips, nucleic acid purification kits, polymerases, reverse-transcriptase, and different types of reagents which are included in viral diagnostic kits. In developing countries, the problem is even worse, since there is few capital enterprise to adopt this kind of industry. So, our aim is to develop a suitable, functional, comparable to commercial ones, and affordable in-house protocol to purify viral RNA. We sought some published and commercial RNA purification solutions to set-up an in-house protocol for viral RNA extraction. Solution was prepared accordingly. Also, LPA (linearized polyacrylamide) carrier was evaluated. The whole setting of in-house solutions with addition of LPA carrier was compared to QIAamp viral RNA minikit solutions. Our results showed that linearized polyacrylamide (LPA) carrier in homemade solutions is comparable to poly A carrier which is used in the most commercial kit. In addition, the whole setting of RNA purification solutions did achieve the purpose of viral RNA purification. Also, the result was confirmed using sputum of a Sars-Cov2 infected patient. Our experiments did end up with an affordable homemade solutions for viral RNA purification.
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Affiliation(s)
- Mahmoud M Abdelfattah
- Molecular Cancer Biology Group, Zoology Department, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | - Ahmed M Osman
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mohamed A Elnagar
- Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed F Ibrahim
- Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Magdy Albert
- Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Maya M Talal
- Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nasra F Abdel Fattah
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Reham Helwa
- Molecular Cancer Biology Group, Zoology Department, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt.
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