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Niu Q, Su X, Lian L, Huang J, Xue S, Zhou W, Zhao H, Lu X, Cui S, Chen J, Yang B. Developing Qualitative Plasmid DNA Reference Materials to Detect Mechanisms of Quinolone and Fluoroquinolone Resistance in Foodborne Pathogens. Foods 2022; 11:154. [PMID: 35053887 PMCID: PMC8775000 DOI: 10.3390/foods11020154] [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: 12/03/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to develop homogeneous and stable plasmid DNA reference materials for detecting the mechanisms of resistance to quinolones and fluoroquinolones in foodborne pathogens. The DNA fragments of 11 target genes associated with quinolone and fluoroquinolone resistance were artificially synthesized, inserted into plasmid vectors, and transferred into recipient cells. PCR and sequencing of DNA were performed to assess the genetic stability of the target DNA in recombinant Escherichia coli DH5α cells during subculturing for 15 generations. The limit of detection (LOD) of the target DNA was determined using PCR and real-time qualitative PCR (qPCR). The homogeneity and storage stability of plasmid DNA reference materials were evaluated in terms of plasmid DNA quantity, PCR-measured gene expression, and qPCR threshold cycle. All 11 target DNAs were successfully synthesized and inserted into vectors to obtain recombinant plasmids. No nucleotide mutations were identified in the target DNA being stably inherited and detectable in the corresponding plasmids during subculturing of recombinant strains. When the target DNA was assessed using PCR and qPCR, the LOD was ≤1.77 × 105 and 3.26 × 104 copies/μL, respectively. Further, when the reference materials were stored at 37 °C for 13 days, 4 °C for 90 days, and -20 °C for 300 days, each target DNA was detectable by PCR, and no mutations were found. Although the threshold cycle values of qPCR varied with storage time, they were above the LOD, and no significant differences were found in the quantity of each plasmid DNA at different timepoints. Further, the homogeneity and stability of the materials were highly consistent with the requirements of standard reference materials. To summarize, considering that our plasmid DNA reference materials conformed to standard requirements, they can be used to detect the mechanisms of quinolone and fluoroquinolone resistance in foodborne pathogens.
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Affiliation(s)
- Qinya Niu
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (Q.N.); (X.S.); (L.L.); (J.H.); (S.X.)
| | - Xiumin Su
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (Q.N.); (X.S.); (L.L.); (J.H.); (S.X.)
| | - Luxin Lian
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (Q.N.); (X.S.); (L.L.); (J.H.); (S.X.)
| | - Jinling Huang
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (Q.N.); (X.S.); (L.L.); (J.H.); (S.X.)
| | - Shutong Xue
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (Q.N.); (X.S.); (L.L.); (J.H.); (S.X.)
| | - Wei Zhou
- Hebei Food Inspection and Research Institute, Hebei Food Safety Key Laboratory, Shijiazhuang 050091, China;
| | - Hongyang Zhao
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (H.Z.); (X.L.)
| | - Xing’an Lu
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China; (H.Z.); (X.L.)
| | - Shenghui Cui
- National Institutes for Food and Drug Control, Beijing 100050, China;
| | - Jia Chen
- College of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China;
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (Q.N.); (X.S.); (L.L.); (J.H.); (S.X.)
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A New Reference Plasmid “pGMT27” Provides an Efficient Transgenic Detection Method for Flue-Cured Tobacco. J FOOD QUALITY 2021. [DOI: 10.1155/2021/3220013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Owing to the economic value of its foliage, tobacco (Nicotiana tabacum) is cultivated all across the world. For the detection of genetically modified (GM) tobacco, there is a lack of universal standard material which ultimately limits the detection methods because the accuracy and comparability of the results cannot be ensured. Here, we prepared a reference plasmid “pGMT27” for the detection of GM tobacco, which was 18,296 bp in length harboring two of the tobacco endogenous and seven exogenous genes. By using qualitative PCR test for the nine genes, 10 copies were used for plasmid sensitivity. In the quantitative real-time PCR (qPCR) assays with pGMT27 as a calibrator, the reaction efficiencies for P-35S and NR were 101.427% and 98.036%, respectively, whereas the limit of detection (LOD) and limit of quantification (LOQ) were 5 copies and 10 copies per reaction. For standard deviation (SD) and relative standard deviation (RSD) of the Ct values, the repeatability values were from 0.04 to 0.42 and from 0.18% to 1.29%, respectively; and the reproducibility values were from 0.04 to 0.39 and from 0.18% to 1.14%, respectively. For the unknown sample test, the average conversion factor (Cf) was 0.39, and the accuracy bias was from −15.55% to 1.93%; for precision, the SD values ranged from 0.02 to 0.62, while RSD values were from 1.34% to 10.6%. We concluded that using the pGMT27 plasmid as a calibrator provided a highly efficient transgenic detection method for flue-cured tobacco.
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Venturelli GL, da Silva KJ, Treml D, Navas PB, Vargas MO, Bischoff JL, de Faria JC, Arisi ACM. New plasmid calibrators for geminivirus-resistant (EMB-PV051-1 event) common bean (Phaseolus vulgaris L.) quantitation using simplex and duplex qPCR. FOOD BIOSCI 2018. [DOI: 10.1016/j.fbio.2018.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Salisu IB, Shahid AA, Yaqoob A, Ali Q, Bajwa KS, Rao AQ, Husnain T. Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review. FRONTIERS IN PLANT SCIENCE 2017; 8:1670. [PMID: 29085378 PMCID: PMC5650622 DOI: 10.3389/fpls.2017.01670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/11/2017] [Indexed: 06/01/2023]
Abstract
As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1) DNA and (2) proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction) and enzyme-linked immunosorbent assay (ELISA) were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA) are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.
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Affiliation(s)
- Ibrahim B. Salisu
- Department of Animal Science, Faculty of Agriculture, Federal University Dutse, Jigawa, Nigeria
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad A. Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Amina Yaqoob
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Kamran S. Bajwa
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Q. Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Kim JH, Park SB, Roh HJ, Shin MK, Moon GI, Hong JH, Kim HY. Event-specific qualitative and quantitative detection of five genetically modified rice events using a single standard reference molecule. Food Chem 2017; 226:187-192. [PMID: 28254011 DOI: 10.1016/j.foodchem.2017.01.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 01/03/2017] [Accepted: 01/13/2017] [Indexed: 11/17/2022]
Abstract
One novel standard reference plasmid, namely pUC-RICE5, was constructed as a positive control and calibrator for event-specific qualitative and quantitative detection of genetically modified (GM) rice (Bt63, Kemingdao1, Kefeng6, Kefeng8, and LLRice62). pUC-RICE5 contained fragments of a rice-specific endogenous reference gene (sucrose phosphate synthase) as well as the five GM rice events. An existing qualitative PCR assay approach was modified using pUC-RICE5 to create a quantitative method with limits of detection correlating to approximately 1-10 copies of rice haploid genomes. In this quantitative PCR assay, the square regression coefficients ranged from 0.993 to 1.000. The standard deviation and relative standard deviation values for repeatability ranged from 0.02 to 0.22 and 0.10% to 0.67%, respectively. The Ministry of Food and Drug Safety (Korea) validated the method and the results suggest it could be used routinely to identify five GM rice events.
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Affiliation(s)
- Jae-Hwan Kim
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Saet-Byul Park
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyo-Jeong Roh
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Min-Ki Shin
- Food Safety Risk Assessment Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Republic of Korea
| | - Gui-Im Moon
- Food Safety Risk Assessment Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Republic of Korea
| | - Jin-Hwan Hong
- Food Safety Risk Assessment Division, National Institute of Food and Drug Safety Evaluation, Cheongju 28159, Republic of Korea
| | - Hae-Yeong Kim
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea.
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Liang W, Xu L, Sui Z, Li Y, Li L, Wen Y, Li C, Ren S, Liu G. Quantification of plasmid DNA reference materials for Shiga toxin-producing Escherichia coli based on UV, HR-ICP-MS and digital PCR. Chem Cent J 2016; 10:55. [PMID: 27621755 PMCID: PMC5018943 DOI: 10.1186/s13065-016-0201-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 09/01/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The accuracy and metrology traceability of DNA quantification is becoming a critical theme in many fields, including diagnosis, forensic analysis, microorganism detection etc. Thus the research of DNA reference materials (RMs) and consistency of DNA quantification methods has attracted considerable research interest. RESULTS In this work, we developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively. Comprehensive investigation of the plasmid RMs was performed for their sequence, purity, homogeneity and stability, and then the concentration was quantified by three different methods: ultraviolet spectrophotometer (UV), high resolution inductively coupled plasma mass spectrometry (HR-ICP-MS) and digital PCR. As a routinely applied method for DNA analysis, UV was utilized for the quantification (OD260) and purity analysis for the plasmids. HR-ICP-MS quantified the plasmid DNA through analysing the phosphorus in DNA molecules. Digital PCR distributed the DNA samples onto a microarray chip containing thousands of reaction chambers, and quantified the DNA copy numbers by analysing the number of positive signals without any calibration curves needed. CONCLUSIONS Based on the high purification of the DNA reference materials and the optimization of dPCR analysis, we successfully achieved good consistency between UV, HR-ICP-MS and dPCR, with relative deviations lower than 10 %. We then performed the co-quantification of 3 DNA RMs with three different methods together, and the uncertainties of their concentration were evaluated. Finally, the certified values and expanded uncertainties for 3 DNA RMs (pFliC, pStx1 and pStx2) were (1.60 ± 0.10) × 10(10) copies/μL, (1.53 ± 0.10) × 10(10) copies/μL and (1.70 ± 0.11) × 10(10) copies/μL respectively.Graphical abstractWe developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively, and the quantification of three different methods (UV, dPCR, ICP) was studied.
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Affiliation(s)
- Wen Liang
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Li Xu
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Zhiwei Sui
- Division of Medical and Biological Measurement, National Institute of Metrology, No.18, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100013 People’s Republic of China
| | - Yan Li
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Lanying Li
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Yanli Wen
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Chunhua Li
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Shuzhen Ren
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
| | - Gang Liu
- Laboratory of Biometrology, Shanghai Institute of Measurement and Testing Technology, 1500 Zhang Heng Road, Shanghai, 201203 People’s Republic of China
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Kim JH, Park SB, Roh HJ, Park S, Shin MK, Moon GI, Hong JH, Kim HY. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid. Food Chem 2015; 176:1-6. [DOI: 10.1016/j.foodchem.2014.12.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/13/2014] [Accepted: 12/13/2014] [Indexed: 10/24/2022]
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Treml D, Venturelli GL, Brod FCA, Faria JC, Arisi ACM. Development of an event-specific hydrolysis probe quantitative real-time polymerase chain reaction assay for Embrapa 5.1 genetically modified common bean (Phaseolus vulgaris). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11994-12000. [PMID: 25437743 DOI: 10.1021/jf503928m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A genetically modified (GM) common bean event, namely Embrapa 5.1, resistant to the bean golden mosaic virus (BGMV), was approved for commercialization in Brazil. Brazilian regulation for genetically modified organism (GMO) labeling requires that any food containing more than 1% GMO be labeled. The event-specific polymerase chain reaction (PCR) method has been the primary trend for GMO identification and quantitation because of its high specificity based on the flanking sequence. This work reports the development of an event-specific assay, named FGM, for Embrapa 5.1 detection and quantitation by use of SYBR Green or hydrolysis probe. The FGM assay specificity was tested for Embrapa 2.3 event (a noncommercial GM common bean also resistant to BGMV), 46 non-GM common bean varieties, and other crop species including maize, GM maize, soybean, and GM soybean. The FGM assay showed high specificity to detect the Embrapa 5.1 event. Standard curves for the FGM assay presented a mean efficiency of 95% and a limit of detection (LOD) of 100 genome copies in the presence of background DNA. The primers and probe developed are suitable for the detection and quantitation of Embrapa 5.1.
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Affiliation(s)
- Diana Treml
- Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina , Rod. Admar Gonzaga 1346, 88034-001 Florianópolis, Santa Catarina, Brazil
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Milavec M, Dobnik D, Yang L, Zhang D, Gruden K, Zel J. GMO quantification: valuable experience and insights for the future. Anal Bioanal Chem 2014; 406:6485-97. [PMID: 25182968 DOI: 10.1007/s00216-014-8077-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia,
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Venturelli GL, Brod FCA, Rossi GB, Zimmermann NF, Oliveira JP, Faria JC, Arisi ACM. A Specific Endogenous Reference for Genetically Modified Common Bean (Phaseolus vulgaris L.) DNA Quantification by Real-Time PCR Targeting Lectin Gene. Mol Biotechnol 2014; 56:1060-8. [DOI: 10.1007/s12033-014-9786-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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