1
|
Mück F, Scotti F, Mauvisseau Q, Thorbek BLG, Wangensteen H, de Boer HJ. Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight. Front Pharmacol 2024; 15:1353434. [PMID: 38375033 PMCID: PMC10875096 DOI: 10.3389/fphar.2024.1353434] [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: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
Collapse
Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, United Kingdom
| | | | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | | |
Collapse
|
2
|
Mück F, Scotti F, Mauvisseau Q, Raclariu-Manolică AC, Schrøder-Nielsen A, Wangensteen H, de Boer HJ. Complementary authentication of Chinese herbal products to treat endometriosis using DNA metabarcoding and HPTLC shows a high level of variability. Front Pharmacol 2023; 14:1305410. [PMID: 38116075 PMCID: PMC10728824 DOI: 10.3389/fphar.2023.1305410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Traditional Chinese Medicine (TCM) is popular for the treatment of endometriosis, a complex gynecological disease that affects 10% of women globally. The growing market for TCMs has yielded a significant incentive for product adulteration, and although emerging technologies show promise to improve their quality control, many challenges remain. We tested the authenticity of two traditional Chinese herbal formulae used in women's healthcare for the treatment of endometriosis, known as Gui Zhi Fu Ling Wan (FL) and Ge Xia Zhu Yu Tang (GX). Dual-locus DNA metabarcoding analysis coupled with high-performance thin-layer chromatography (HPTLC) were used to authenticate 19 FL and six GX commercial herbal products, as well as three ad hoc prepared artificial mixtures. HPTLC was able to detect most of the expected ingredients via comparative component analysis. DNA metabarcoding was able to detect an unexpected species diversity in the products, including 38 unexpected taxa. Chromatography has a resolution for all species indirectly through the identification of marker compounds for the different species ingredients. Metabarcoding on the other hand yields an overview of species diversity in each sample, but interpretation of the results can be challenging. Detected species might not be present in quantities that matter, and without validated quantification, some detected species can be hard to interpret. Comparative analysis of the two analytical approaches also reveals that DNA for species might be absent or too fragmented to amplify as the relevant chemical marker compounds can be detected but no amplicons are assigned to the same species. Our study emphasizes that integrating DNA metabarcoding with phytochemical analysis brings valuable data for the comprehensive authentication of Traditional Chinese Medicines ensuring their quality and safe use.
Collapse
Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom
| | | | - Ancuţa Cristina Raclariu-Manolică
- Natural History Museum, University of Oslo, Oslo, Norway
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamț, Romania
| | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | | |
Collapse
|
3
|
Lievens A, Paracchini V, Garlant L, Pietretti D, Maquet A, Ulberth F. Detection and Quantification of Botanical Impurities in Commercial Oregano ( Origanum vulgare) Using Metabarcoding and Digital PCR. Foods 2023; 12:2998. [PMID: 37627997 PMCID: PMC10453138 DOI: 10.3390/foods12162998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
DNA technology for food authentication is already well established, and with the advent of Next Generation Sequencing (NGS) and, more specifically, metabarcoding, compositional analysis of food at the molecular level has rapidly gained popularity. This has led to several reports in the media about the presence of foreign, non-declared species in several food commodities. As herbs and spices are attractive targets for fraudulent manipulation, a combination of digital PCR and metabarcoding by NGS was employed to check the purity of 285 oregano samples taken from the European market. By using novel primers and analytical approaches, it was possible to detect and quantify both adulterants and contaminants in these samples. The results highlight the high potential of NGS for compositional analysis, although its quantitative information (read count percentages) is unreliable, and other techniques are therefore needed to complement the sequencing information for assessing authenticity ('true to the name') of food ingredients.
Collapse
Affiliation(s)
- Antoon Lievens
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | | | - Linda Garlant
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | - Danilo Pietretti
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | - Alain Maquet
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| | - Franz Ulberth
- European Commission, Joint Research Centre (JRC), B-2440 Geel, Belgium
| |
Collapse
|
4
|
IoT-based food traceability system: Architecture, technologies, applications, and future trends. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
5
|
Kandil NH, Ayoub IM, El-Ahmady SH, El-Moghazy SA. Advances in the quality control of fenugreek seeds using chromatographic, spectroscopic and DNA-based techniques: A comprehensive review. PHYTOCHEMICAL ANALYSIS : PCA 2022; 33:155-169. [PMID: 34672396 DOI: 10.1002/pca.3091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Fenugreek has been used in traditional remedies since ancient times. It has a long history of use against medical ailments as an antidiabetic, anticarcinogenic, hypocholesterolemic, antioxidant, antibacterial, hypoglycemic, gastric stimulant, and anti-anorexia agent. The major active constituents include alkaloids, fibres, saponins, proteins, and amino acids. OBJECTIVES To provide a comprehensive overview of the application of chromatographic and spectroscopic methods, in addition to DNA-profiling methods to assess the quality of fenugreek. Also, to highlight the recent application of chemometrics combined with quality control methods during the last two decades. METHODOLOGY A literature search conducted from January 2000 up to December 2020 using various scientific databases (e.g., Scopus, Medline, PubMed, EBSCO, JSTOR, ScienceDirect, Google Scholar, Web of Science and Egyptian Knowledge Bank, Academic Journals, and Springer Link); general web searches were also undertaken using Google applying some related search terms. Studies involving the application of quality control analyses were classified into three categories according to the conducted analysis method including chromatographic [high-performance liquid chromatography (HPLC), high-performance thin-layer chromatography (HPTLC), and gas chromatography (GC)], spectroscopic [ultraviolet (UV), infrared (IR), and nuclear magnetic resonance (NMR)], and DNA-based markers. RESULTS This review shed the light on relevant studies covering the past two decades, presenting the application of spectroscopic and chromatographic methods and DNA profiling in the quality control of fenugreek. CONCLUSION The reviewed chromatographic and spectroscopic methods combined with chemometrics provide a powerful tool that could be applied widely for the quality control of fenugreek.
Collapse
Affiliation(s)
- Nariman H Kandil
- Department of Pharmacognosy, Faculty of Pharmacy, Badr University in Cairo, Cairo, Egypt
| | - Iriny M Ayoub
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Sherweit H El-Ahmady
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Safaa A El-Moghazy
- Department of Pharmacognosy, Faculty of Pharmacy, Badr University in Cairo, Cairo, Egypt
| |
Collapse
|
6
|
Lievens A, Paracchini V, Pietretti D, Garlant L, Maquet A, Ulberth F. DNA Accounting: Tallying Genomes to Detect Adulterated Saffron. Foods 2021; 10:2670. [PMID: 34828951 PMCID: PMC8624925 DOI: 10.3390/foods10112670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/18/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
The EU General Food Law not only aims at ensuring food safety but also to 'prevent fraudulent or deceptive practices; the adulteration of food; and any other practices which may mislead the consumer'. Especially the partial or complete, deliberate, and intentional substitution of valuable ingredients (e.g., Saffron) for less valuable ones is of concern. Due to the variety of products on the market an approach to detect food adulteration that works well for one species may not be easily applicable to another. Here we present a broadly applicable approach for the detection of substitution of biological materials based on digital PCR. By simultaneously measuring and forecasting the number of genome copies in a sample, fraud is detectable as a discrepancy between these two values. Apart from the choice of target gene, the procedure is identical across all species. It is scalable, rapid, and has a high dynamic range. We provide proof of concept by presenting the analysis of 141 samples of Saffron (Crocus sativus) from across the European market by DNA accounting and the verification of these results by NGS analysis.
Collapse
Affiliation(s)
- Antoon Lievens
- European Commission, Joint Research Centre, B-2440 Geel, Belgium; (D.P.); (L.G.); (A.M.); (F.U.)
| | | | - Danilo Pietretti
- European Commission, Joint Research Centre, B-2440 Geel, Belgium; (D.P.); (L.G.); (A.M.); (F.U.)
| | - Linda Garlant
- European Commission, Joint Research Centre, B-2440 Geel, Belgium; (D.P.); (L.G.); (A.M.); (F.U.)
| | - Alain Maquet
- European Commission, Joint Research Centre, B-2440 Geel, Belgium; (D.P.); (L.G.); (A.M.); (F.U.)
| | - Franz Ulberth
- European Commission, Joint Research Centre, B-2440 Geel, Belgium; (D.P.); (L.G.); (A.M.); (F.U.)
| |
Collapse
|
7
|
Fanelli V, Mascio I, Miazzi MM, Savoia MA, De Giovanni C, Montemurro C. Molecular Approaches to Agri-Food Traceability and Authentication: An Updated Review. Foods 2021; 10:1644. [PMID: 34359514 PMCID: PMC8306823 DOI: 10.3390/foods10071644] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/14/2022] Open
Abstract
In the last decades, the demand for molecular tools for authenticating and tracing agri-food products has significantly increased. Food safety and quality have gained an increased interest for consumers, producers, and retailers, therefore, the availability of analytical methods for the determination of food authenticity and the detection of major adulterations takes on a fundamental role. Among the different molecular approaches, some techniques such as the molecular markers-based methods are well established, while some innovative approaches such as isothermal amplification-based methods and DNA metabarcoding have only recently found application in the agri-food sector. In this review, we provide an overview of the most widely used molecular techniques for fresh and processed agri-food authentication and traceability, showing their recent advances and applications and discussing their main advantages and limitations. The application of these techniques to agri-food traceability and authentication can contribute a great deal to the reassurance of consumers in terms of transparency and food safety and may allow producers and retailers to adequately promote their products.
Collapse
Affiliation(s)
- Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Michele Antonio Savoia
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Claudio De Giovanni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (I.M.); (M.M.M.); (M.A.S.); (C.D.G.); (C.M.)
- Spin off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council of Italy (CNR), Via Amendola 122/D, 70126 Bari, Italy
| |
Collapse
|
8
|
Rouphael Y, Corrado G, Colla G, De Pascale S, Dell’Aversana E, D’Amelia LI, Fusco GM, Carillo P. Biostimulation as a Means for Optimizing Fruit Phytochemical Content and Functional Quality of Tomato Landraces of the San Marzano Area. Foods 2021; 10:foods10050926. [PMID: 33922497 PMCID: PMC8145630 DOI: 10.3390/foods10050926] [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: 03/15/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022] Open
Abstract
The effect of plant biostimulation on fruits of traditional tomato germplasm is largely unknown. We examined how a tropical plant-derived biostimulant impacts the nutritional, functional, and compositional characteristics of tomato fruits from four landraces, collected in the San Marzano (SM) tomato Protected Designation of Origin (PDO) region, by profiling primary and secondary metabolites. Biostimulation was not able to completely reshuffle the morpho-physiological and nutritional profile of the four landraces. Their distinct phytochemical profile indicated a genotype-specific tuning of the analyzed traits, which also included an improved yield and fruit quality. Biostimulation of SM1 and SM3 increased photosynthetic accumulation of carbohydrate reserves, improved mineral nutrient use efficiency and consequently, yield (+21% and 34%, respectively). Moreover, biostimulation augmented the nutraceutical properties of the SM2 landrace. Interestingly, the plant-derived product increased in all genotypes lycopene, but not polyphenol accumulation in fruits. Our results show the potential of biostimulatory applications towards optimizing the fruit quality of the acclaimed SM landraces, which is suitable to satisfy both the rising consumer demand for premium traditional tomatoes and the technological needs of the food industry.
Collapse
Affiliation(s)
- Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (Y.R.); (S.D.P.)
| | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (Y.R.); (S.D.P.)
- Correspondence: ; Tel.: +39-0812-539-294
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, University of Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy;
| | - Stefania De Pascale
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (Y.R.); (S.D.P.)
| | - Emilia Dell’Aversana
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (E.D.); (L.I.D.); (G.M.F.); (P.C.)
| | - Luisa Ida D’Amelia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (E.D.); (L.I.D.); (G.M.F.); (P.C.)
| | - Giovanna Marta Fusco
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (E.D.); (L.I.D.); (G.M.F.); (P.C.)
| | - Petronia Carillo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (E.D.); (L.I.D.); (G.M.F.); (P.C.)
| |
Collapse
|
9
|
Garai A, Chowdhury S, Sarkar B, Roy TK. Cost-effective subsidy policy for growers and biofuels-plants in closed-loop supply chain of herbs and herbal medicines: An interactive bi-objective optimization in T-environment. Appl Soft Comput 2021. [DOI: 10.1016/j.asoc.2020.106949] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
10
|
|
11
|
Stagnati L, Soffritti G, Martino M, Bortolini C, Lanubile A, Busconi M, Marocco A. Cocoa beans and liquor fingerprinting: A real case involving SSR profiling of CCN51 and “Nacional” varieties. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107392] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Development of nucleic acid isolation by non-silica-based nanoparticles and real-time PCR kit for edible vegetable oil traceability. Food Chem 2019; 300:125205. [PMID: 31330372 DOI: 10.1016/j.foodchem.2019.125205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/08/2019] [Accepted: 07/17/2019] [Indexed: 11/21/2022]
Abstract
For efficient extraction of amplifiable DNA from edible vegetable oils, we developed a novel DNA extraction approach based on the non-silica-based dipolar nanocomposites. The nanoparticle comprises a hydrophilic polymethyl methacrylate core with abundant capillaries, hydrophilic vesicles decorated with molecules having DNA affinity and a coating hydrophobic polystyrene layer. The nanoparticles are soluble in oil, adsorb the DNA from the aqueous phase and gave a high DNA recovery ratio. All DNA extracts from fully refined vegetable oil soybean, peanut, rapeseed, and cottonseed oils, including their blends, were sufficiently pure to be amplified by real-time PCR targeting the chloroplast ribulose-1,5-bisphosphate gene (rbcL), therefore, the species of origin and their ratios in mixed vegetable oils blended from two or three oil-species could be determined. These results indicate that the novel DNA isolation and real-time PCR kit is a simple, sensitive and efficient tool for the species identification and traceability in refined vegetable oils.
Collapse
|
13
|
Xing RR, Hu RR, Han JX, Deng TT, Chen Y. DNA barcoding and mini-barcoding in authenticating processed animal-derived food: A case study involving the Chinese market. Food Chem 2019; 309:125653. [PMID: 31670116 DOI: 10.1016/j.foodchem.2019.125653] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/14/2019] [Accepted: 10/05/2019] [Indexed: 11/16/2022]
Abstract
This study used DNA barcoding and DNA mini-barcoding to test a variety of animal-derived food products sold in the Chinese market for potential mislabeling. Samples (52) including meat, poultry, and fish purchased from retail and online sources were examined. Regions of cytochrome C oxidase I (COI) gene (~650 bp) and 16S rRNA (~220 bp) were used as full- and mini-barcode markers, respectively. Approximately 94% (49 of 52) of the samples generated barcode sequences. The failure rate for full COI full-barcodes was 44%, but we obtained the 16S rRNA mini-barcode from 87% of the COI-failed cases. Overall, the survey revealed that 23% (12 of 52) of animal-derived products were mislabeled and, in most cases, contain undeclared species. Thus, regulatory measures and continuous monitoring for mislabeling of animal-derived products should be conducted.
Collapse
Affiliation(s)
- Ran-Ran Xing
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Ran-Ran Hu
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jian-Xun Han
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Agriculture and Biotechnology, Zhejiang University, Zhejiang 310058, China
| | - Ting-Ting Deng
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ying Chen
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
| |
Collapse
|
14
|
Barrias S, Fernandes JR, Eiras-Dias JE, Brazão J, Martins-Lopes P. Label free DNA-based optical biosensor as a potential system for wine authenticity. Food Chem 2019; 270:299-304. [DOI: 10.1016/j.foodchem.2018.07.058] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022]
|
15
|
Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
Collapse
Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| |
Collapse
|
16
|
Verdone M, Rao R, Coppola M, Corrado G. Identification of zucchini varieties in commercial food products by DNA typing. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.07.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
17
|
Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: The Next Culture-Independent Game Changer. Front Microbiol 2017; 8:1069. [PMID: 28725217 PMCID: PMC5495826 DOI: 10.3389/fmicb.2017.01069] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/29/2017] [Indexed: 02/01/2023] Open
Abstract
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other 'omics' disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable detection techniques in clinical microbiology, food and public health laboratories. Early advances in the discipline of metagenomics, however, have indicated noteworthy challenges. Through forthcoming improvements in sequencing technology and analytical pipelines among others, we anticipate that within the next decade, detection and characterization of pathogens via metagenomics-based workflows will be implemented in routine usage in diagnostic and public health laboratories.
Collapse
Affiliation(s)
- Jessica D. Forbes
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, WinnipegMB, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, MontrealQC, Canada
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, MontrealQC, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, OttawaON, Canada
- Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, OttawaON, Canada
| | - Aleisha Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, WinnipegMB, Canada
| |
Collapse
|
18
|
Manzanares-Palenzuela CL, Martín-Clemente JP, Lobo-Castañón MJ, López-Ruiz B. Electrochemical detection of magnetically-entrapped DNA sequences from complex samples by multiplexed enzymatic labelling: Application to a transgenic food/feed quantitative survey. Talanta 2016; 164:261-267. [PMID: 28107927 DOI: 10.1016/j.talanta.2016.11.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 02/02/2023]
Abstract
Monitoring of genetically modified organisms in food and feed demands molecular techniques that deliver accurate quantitative results. Electrochemical DNA detection has been widely described in this field, yet most reports convey qualitative data and application in processed food and feed samples is limited. Herein, the applicability of an electrochemical multiplex assay for DNA quantification in complex samples is assessed. The method consists of the simultaneous magnetic entrapment via sandwich hybridisation of two DNA sequences (event-specific and taxon-specific) onto the surface of magnetic microparticles, followed by bienzymatic labelling. As proof-of-concept, we report its application in a transgenic food/feed survey where relative quantification (two-target approach) of Roundup Ready Soybean® (RRS) was performed in food and feed. Quantitative coupling to end-point PCR was performed and calibration was achieved from 22 and 243 DNA copies spanning two orders of magnitude for the event and taxon-specific sequences, respectively. We collected a total of 33 soybean-containing samples acquired in local supermarkets, four out of which were found to contain undeclared presence of genetically modified soybean. A real-time PCR method was used to verify these findings. High correlation was found between results, indicating the suitability of the proposed multiplex method for food and feed monitoring.
Collapse
Affiliation(s)
- C L Manzanares-Palenzuela
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Pz. Ramón y Cajal s/n, 28040 Madrid, Spain; Departamento de Biotecnología - Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - J P Martín-Clemente
- Departamento de Biotecnología - Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain.
| | - M J Lobo-Castañón
- Departamento de Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain.
| | - B López-Ruiz
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Pz. Ramón y Cajal s/n, 28040 Madrid, Spain.
| |
Collapse
|