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Ajene IJ, Heya H, Khamis FM. Evaluating the mitochondrial genomic diversity, global distribution and niche overlap of two invasive Phthorimaea species. Heliyon 2024; 10:e29010. [PMID: 38617910 PMCID: PMC11015427 DOI: 10.1016/j.heliyon.2024.e29010] [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: 04/25/2023] [Revised: 03/21/2024] [Accepted: 03/28/2024] [Indexed: 04/16/2024] Open
Abstract
This study sought to evaluate the genetic diversity of two invasive Phthorimaea species (Phthorimaea operculella Zeller and Phthorimaea absoluta Meyrick), and identify potential niche overlap of both species. The complete mitogenomes of P. operculella and P. absoluta were sequenced and compared. Furthermore, the diversity within the family Gelechiidae was assessed. Subsequently, two species distribution models (MaxEnt and BIOCLIM) were used to identify niche overlaps of both species globally. The complete mitogenomes of both species were similar in size and structure, with a pairwise identity of 92.3%. The models showed a niche overlap of both species and revealed areas of marginal to high suitability for both pests in countries where they have not been reported. Therefore, these results present a compelling case for a deeper genetic and ecological investigation of the Gelechiidae family for taxonomic harmonization, an early warning for surveillance, stricter phytosanitary considerations and preventive management against the spread of the pests.
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Affiliation(s)
- Inusa Jacob Ajene
- International Center of Insect Physiology and Ecology, Nairobi, Kenya
| | - Helen Heya
- Kenya Plant Health Inspectorate Service, Nairobi, Kenya
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2
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N’Tcha C, Sina H, Bourobou DN, Hoteyi SMI, Boya B, Agnimonhan R, Mavoungou JF, Adjanohoun A, Babalola OO, Baba-Moussa L. Resistance and Biofilm Production Profile of Potential Isolated from Kpètè-Kpètè Used to Produce Traditional Fermented Beer. Microorganisms 2023; 11:1939. [PMID: 37630499 PMCID: PMC10459457 DOI: 10.3390/microorganisms11081939] [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: 05/25/2023] [Revised: 07/16/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
This study aimed to characterize the pathogenicity of bacteria isolated from the starter of two traditional beers produced and consumed in Benin. After standard microbial identification, species were identified by specific biochemical tests such as catalase, coagulase, and API 20 E. Antibiotic sensitivity was tested according to the French Society of Microbiology Antibiogram Committee. The crystal violet microplate technique evaluated the biofilm production and conventional PCR was used to identify genes encoding virulence and macrolide resistance. According to our data, the traditional starter known as kpètè-kpètè that is used to produce beer is contaminated by Enterobacteriaceae and staphylococci species. Thus, 28.43% of the isolated bacteria were coagulase-negative staphylococci (CNS), and 10.93% coagulase-positive staphylococci (CPS). Six species such as Klebsiella terrigena (1.38%), Enterobacter aerogens (4.14%), Providencia rettgeri (5.51%), Chryseomonas luteola (6.89%), Serratia rubidae (15.16%), and Enterobacter cloacae (27.56%) were identified among Enterobacteriaceae. Those bacterial strains are multi-resistant to conventional antibiotics. The hight capability of produced biofilms was recorded with Enterobacter aerogens, Klebsiella terrigena (100%), Providencia rettgeri (75%), and Staphylococcus spp (60%). Enterobacter cloacae (4%) and coagulase-negative Staphylococcus (5.55%) harbor the macrolide resistance gene. For other strains, these genes were not detected. Foods contaminated with bacteria resistant to antibiotics and carrying a virulence gene could constitute a potential public health problem. There is a need to increase awareness campaigns on hygiene rules in preparing and selling these traditional beers.
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Affiliation(s)
- Christine N’Tcha
- Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin; (C.N.); (H.S.); (S.M.I.H.); (B.B.); (R.A.)
| | - Haziz Sina
- Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin; (C.N.); (H.S.); (S.M.I.H.); (B.B.); (R.A.)
| | - Dyana Ndiade Bourobou
- Institut de Recherches Agronomiques et Forestières (IRAF), BP.12978 Gros-Bouquet, Libreville B.P. 16 182, Gabon; (D.N.B.); (J.F.M.)
| | - S. M. Ismaël Hoteyi
- Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin; (C.N.); (H.S.); (S.M.I.H.); (B.B.); (R.A.)
| | - Bawa Boya
- Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin; (C.N.); (H.S.); (S.M.I.H.); (B.B.); (R.A.)
| | - Raoul Agnimonhan
- Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin; (C.N.); (H.S.); (S.M.I.H.); (B.B.); (R.A.)
| | - Jacques François Mavoungou
- Institut de Recherches Agronomiques et Forestières (IRAF), BP.12978 Gros-Bouquet, Libreville B.P. 16 182, Gabon; (D.N.B.); (J.F.M.)
| | - Adolphe Adjanohoun
- National Agronomic Research Institute of Benin, Cotonou 01 BP 884, Benin;
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Lamine Baba-Moussa
- Laboratory of Biology and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin; (C.N.); (H.S.); (S.M.I.H.); (B.B.); (R.A.)
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3
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Gopi K, Mazumder D, Crawford J, Gadd P, Tadros CV, Atanacio A, Saintilan N, Sammut J. Developing a MySQL Database for the Provenance of Black Tiger Prawns ( Penaeus monodon). Foods 2023; 12:2677. [PMID: 37509769 PMCID: PMC10379408 DOI: 10.3390/foods12142677] [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: 03/28/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
As the demand for seafood increases, so does the incidence of seafood fraud. Confirming provenance of seafood is important to combat fraudulent labelling but requires a database that contains the isotopic and elemental "fingerprints" of authentic seafood samples. Local isotopic and elemental databases can be scaled up or combined with other databases to increase the spatial and species coverage to create a larger database. This study showcases the use of isotopic and elemental fingerprints of the black tiger prawn (Penaeus monodon) to develop a database that can be used to securely store the data necessary for determining provenance. The utility of this database was tested through querying and building seven different datasets that were used to develop models to determine the provenance of P. monodon. The models built using the data retrieved from the database demonstrated that the provenance of P. monodon could be determined with >80% accuracy. As the database was developed using MySQL, it can be scaled up to include additional regions, species, or methodologies depending on the needs of the users. Combining the database with methods of determining provenance will provide regulatory bodies and the seafood industry with another provenance tool to combat fraudulent seafood labelling.
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Affiliation(s)
- Karthik Gopi
- Centre for Ecosystem Science, The School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- University Centre for Rural Health, Sydney School of Public Health, The University of Sydney, Sydney, NSW 2052, Australia
| | - Debashish Mazumder
- Centre for Ecosystem Science, The School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW 2052, Australia
| | - Jagoda Crawford
- Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW 2052, Australia
| | - Patricia Gadd
- Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW 2052, Australia
| | - Carol V Tadros
- Centre for Ecosystem Science, The School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW 2052, Australia
| | - Armand Atanacio
- Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW 2052, Australia
| | - Neil Saintilan
- School of Natural Sciences, Macquarie University, Sydney, NSW 2052, Australia
| | - Jesmond Sammut
- Centre for Ecosystem Science, The School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
- Australian Nuclear Science and Technology Organisation (ANSTO), Sydney, NSW 2052, Australia
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4
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Chatzoglou E, Tsaousi N, Apostolidis AP, Exadactylos A, Sandaltzopoulos R, Giantsis IA, Gkafas GA, Malandrakis EE, Sarantopoulou J, Tokamani M, Triantaphyllidis G, Miliou H. High-Resolution Melting (HRM) Analysis for Rapid Molecular Identification of Sparidae Species in the Greek Fish Market. Genes (Basel) 2023; 14:1255. [PMID: 37372435 DOI: 10.3390/genes14061255] [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: 05/08/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The red porgy (Pagrus pagrus) and the common dentex (Dentex dentex) are Sparidae species of high commercial value, traded in the Greek market. In some cases, fish species identification from Greek fisheries is difficult for the consumer due to the strong morphological similarities with their imported counterparts or closely related species such as Pagrus major, Pagrus caeroleustictus, Dentex gibbosus and Pagellus erythrinus, especially when specimens are frozen, filleted or cooked. Techniques based on DNA sequencing, such as COI barcoding, accurately identify species substitution incidents; however, they are time consuming and expensive. In this study, regions of mtDNA were analyzed with RFLPs, multiplex PCR and HRM in order to develop a rapid method for species identification within the Sparidae family. HRM analysis of a 113 bp region of cytb and/or a 156 bp region of 16s could discriminate raw or cooked samples of P. pagrus and D. dentex from the aforementioned closely related species and P. pagrus specimens sampled in the Mediterranean Sea when compared to those fished in the eastern Atlantic. HRM analysis exhibited high accuracy and repeatability, revealing incidents of mislabeling. Multiple samples can be analyzed within three hours, rendering this method a useful tool in fish fraud monitoring.
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Affiliation(s)
- Evanthia Chatzoglou
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Nefeli Tsaousi
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Apostolos P Apostolidis
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Athanasios Exadactylos
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
| | - Georgios A Gkafas
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Emmanouil E Malandrakis
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Joanne Sarantopoulou
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Maria Tokamani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - George Triantaphyllidis
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Helen Miliou
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
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Giantsis IA, Tokamani M, Triantaphyllidis G, Tzatzani S, Chatzinikolaou E, Toros A, Bouchorikou A, Chatzoglou E, Miliou H, Sarantopoulou J, Gkafas GA, Exadactylos A, Sandaltzopoulos R, Apostolidis AP. Development of Multiplex PCR and Melt-Curve Analysis for the Molecular Identification of Four Species of the Mullidae Family, Available in the Market. Genes (Basel) 2023; 14:genes14050960. [PMID: 37239320 DOI: 10.3390/genes14050960] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
The authentication of food products and the verification of their identity are of major importance for consumers. Food fraud through mislabeling is an illegal practice consisting of the substitution of an expensive food product by a relatively cheaper one, misleading false labelling of their origin and adulteration in processed or frozen products. This issue is particularly of high importance concerning fish and seafood, which are easily adulterated primarily due to difficult morphological identification. Fish species of the Mullidae family are considered among the most high-valued seafood products traded in Greece and Eastern Mediterranean in general, in terms of the price and demand. Specifically, the red mullet (Mullus barbatus) and the striped red mullet (Mullus surmuletus) are both indigenous in the Aegean (FAO Division 37.3.1) and the Ionian (FAO Division 37.2.2) Seas, with high levels of consumers' preferences. However, they could be easily adulterated or misidentified by the invasive Aegean Sea Lessepsian migrator goldband goatfish (Upeneus moluccensis) as well as by the imported West African goatfish (Pseudupeneus prayensis). Keeping this in mind, we designed two novel, time-saving and easy-to-apply multiplex PCR assays and one multiple Melt-Curve analysis real-time PCR for the identification of these four species. These methodologies are based on species-specific primers targeting single nucleotide polymorphisms (SNPs) detected via sequencing analysis of the mitochondrial cytochrome C oxidase subunit I (CO1) and of the cytochrome b (CYTB) genes in newly collected individuals, with additional comparison with congeneric and conspecific haplotypes obtained from the GenBank database. Both methodologies, targeting CO1 or CYTB, utilize one common and four diagnostic primers, producing amplicons of different length that are easily and reliably separated on agarose gel electrophoresis, yielding a single clear band of diagnostic size for each species or a certain Melt-Curve profile. The applicability of this cost-effective and fast methodology was tested in 328 collected specimens, including 10 cooked samples obtained from restaurants. In the vast majority (327 out of the 328) of the specimens tested, one single band was produced, in agreement with the expected products with a single exception a M. barbatus sample that was identified as M. surmuletus, the identity of which was confirmed using sequencing, indicating erroneous morphological identification. The developed methodologies are expected to contribute to the detection of commercial fraud in fish authentication.
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Affiliation(s)
- Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Maria Tokamani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - George Triantaphyllidis
- Laboratory of Applied Hydrobiology, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Stella Tzatzani
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Emmanuella Chatzinikolaou
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Athanasios Toros
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Anastasia Bouchorikou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Evanthia Chatzoglou
- Laboratory of Applied Hydrobiology, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Helen Miliou
- Laboratory of Applied Hydrobiology, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Joanne Sarantopoulou
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Georgios A Gkafas
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Athanasios Exadactylos
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Apostolos P Apostolidis
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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De Graeve M, Birse N, Hong Y, Elliott CT, Hemeryck LY, Vanhaecke L. Multivariate versus machine learning-based classification of rapid evaporative Ionisation mass spectrometry spectra towards industry based large-scale fish speciation. Food Chem 2023; 404:134632. [DOI: 10.1016/j.foodchem.2022.134632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 11/22/2022]
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Assouma FF, Sina H, Adjobimey T, Noumavo ADP, Socohou A, Boya B, Dossou AD, Akpovo L, Konmy BBS, Mavoungou JF, Adjanohoun A, Baba-Moussa L. Susceptibility and Virulence of Enterobacteriaceae Isolated from Urinary Tract Infections in Benin. Microorganisms 2023; 11:microorganisms11010213. [PMID: 36677505 PMCID: PMC9864207 DOI: 10.3390/microorganisms11010213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Enterobacteriaceae represent one of the main families of Gram-negative bacilli responsible for serious urinary tract infections (UTIs). The present study aimed to define the resistance profile and the virulence of Enterobacteriaceae strains isolated in urinary tract infections in Benin. A total of 390 urine samples were collected from patients with UTIs, and Enterobacteriaceae strains were isolated according to standard microbiology methods. The API 20E gallery was used for biochemical identification. All the isolated strains were subjected to antimicrobial susceptibility testing using the disc diffusion method. Extended-spectrum beta-lactamase (ESBL) production was investigated using a double-disc synergy test (DDST), and biofilm production was quantified using the microplate method. Multiplex PCR was used to detect uro-virulence genes, namely: PapG, IronB, Sfa, iucD, Hly, FocG, Sat, FyuA and Cnf, using commercially designed primers. More than 26% (103/390) of our samples were contaminated by Enterobacteriaceae strains at different levels. Thus, E. coli (31.07%, 32/103), Serratia marcescens (11.65%, 12/103), Klebsiella ornithinolytica (8.74%, 9/103), Serratia fonticola (7.77%, 8/103) and Enterobacter cloacae (6.80%, 7/103) were identified. Among the isolated strains, 39.81% (41/103) were biofilm-forming, while 5.83% (6/103) were ESBL-producing. Isolates were most resistant to erythromycin, cefixime, ceftriaxone and ampicillin (≥90%) followed by ciprofloxacin, gentamycin, doxycycline and levofloxacin (≥50%), and least resistant to imipenem (27.18%). In regard to virulence genes, Sfa was the most detected (28.15%), followed by IronB (22.23%), iucD (21.36%), Cnf (15.53%), PapG (9.71%), FocG (8.74%), Sat (6.79%), FyuA (5.82%) and Hyl (2.91%). These data may help improve the diagnosis of uropathogenic strains of Enterobacteriaceae, but also in designing effective strategies and measures for the prevention and management of severe, recurrent, or complicated urinary tract infections in Benin.
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Affiliation(s)
- Funkè F. Assouma
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
| | - Haziz Sina
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
- Correspondence: (H.S.); (L.B.-M.)
| | - Tomabu Adjobimey
- Laboratory of Biochemistry and Molecular Biology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
| | - Agossou Damien Pacôme Noumavo
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
- Laboratory of Microbiology and Food Technologies, Department of Plant Biology, Faculty of Science and Technology, University of Abomey-Calavi, Cotonou 04 BP 1107, Benin
| | - Akim Socohou
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
| | - Bawa Boya
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
| | | | - Lauriane Akpovo
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
| | - Basile Boni Saka Konmy
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
- Department of Microbiology, International University of Libreville, ESSASSA-Libreville Campus, Essassa BP 20411, Gabon
| | - Jacques F. Mavoungou
- Department of Microbiology, International University of Libreville, ESSASSA-Libreville Campus, Essassa BP 20411, Gabon
| | - Adolphe Adjanohoun
- National Agronomic Research Institute of Benin, Cotonou 01 BP 884, Benin
| | - Lamine Baba-Moussa
- Laboratory of Biochemistry and Molecular Typing in Microbiology, Department of Biochemistry and Cell Biology, Faculty of Science and Technology, University of Abomey-Calavi, Abomey-Calavi 05 BP 1604, Benin
- Correspondence: (H.S.); (L.B.-M.)
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Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods 2023; 12:foods12010228. [PMID: 36613444 PMCID: PMC9818732 DOI: 10.3390/foods12010228] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
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Mukherjee S, Hanak P, Jilkova D, Musilova Z, Horka P, Lerch Z, Zdenkova K, Cermakova E. Simultaneous detection and quantification of two European anglerfishes by novel genomic primer. J Food Compost Anal 2023. [DOI: 10.1016/j.jfca.2022.104992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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A systematic approach for pufferfish identification at the species level using DNA-based methods. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Socohou A, Adjobimey T, Nanoukon C, Sina H, Kakossou M, Moussé W, Adjanohoun A, Baba-Moussa L. Genetic diversity and virulence factors of Gram-negative bacilli isolated at the CHU-Z in Abomey-Calavi/So-Ava (Benin). SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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12
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Harnessing the Full Power of Chemometric-Based Analysis of Total Reflection X-ray Fluorescence Spectral Data to Boost the Identification of Seafood Provenance and Fishing Areas. Foods 2022; 11:foods11172699. [PMID: 36076884 PMCID: PMC9455438 DOI: 10.3390/foods11172699] [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: 08/09/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Provenance and traceability are crucial aspects of seafood safety, supporting managers and regulators, and allowing consumers to have clear information about the origin of the seafood products they consume. In the present study, we developed an innovative spectral approach based on total reflection X-ray fluorescence (TXRF) spectroscopy to identify the provenance of seafood and present a case study for five economically relevant marine species harvested in different areas of the Atlantic Portuguese coast: three bony fish-Merluccius merluccius, Scomber colias, and Sparus aurata; one elasmobranch-Raja clavata; one cephalopod-Octopus vulgaris. Applying a first-order Savitzky-Golay transformation to the TXRF spectra reduced the potential matrix physical effects on the light scattering of the X-ray beam while maintaining the spectral differences inherent to the chemical composition of the samples. Furthermore, a variable importance in projection partial least-squares discriminant analysis (VIP-PLS-DA), with k - 1 components (where k is the number of geographical origins of each seafood species), produced robust high-quality models of classification of samples according to their geographical origin, with several clusters well-evidenced in the dispersion plots of all species. Four of the five species displayed models with an overall classification above 80.0%, whereas the lowest classification accuracy for S. aurata was 74.2%. Notably, about 10% of the spectral features that significantly contribute to class differentiation are shared among all species. The results obtained suggest that TXRF spectra can be used for traceability purposes in seafood species (from bony and cartilaginous fishes to cephalopods) and that the presented chemometric approach has an added value for coupling with classic TXRF spectral peak deconvolution and elemental quantification, allowing characterization of the geographical origin of samples, providing a highly accurate and informative dataset in terms of food safety.
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Species-specific molecular signatures for the commercially important scombrids using mitochondrial gene analysis; a tool for fisheries management. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2022. [DOI: 10.1016/j.japb.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Characteristics of Escherichia coli Isolated from Intestinal Microbiota Children of 0–5 Years Old in the Commune of Abomey-Calavi. J Pathog 2022; 2022:6253894. [PMID: 35707744 PMCID: PMC9192313 DOI: 10.1155/2022/6253894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli is a commensal bacterium and one of the first bacteria to colonize the digestive tract of newborns after birth. It is characterized by great versatility and metabolic flexibility that allows its survival in different niches. The present study aims at analyzing the diversity of E. coli strains isolated from the intestinal microbiota of children aged from 0 to 5 years in the commune of Abomey-Calavi in Benin. For this purpose, a descriptive and analytical cross-sectional study was conducted. A total of 135 stool samples were collected from the pediatric clinic of Abomey-Calavi. Microbiological analyses were performed according to standard microbiology analytical techniques. The molecular characterization of E. coli was performed by investigating eight genes (dinB, icdA, pabB, polB, putP, trpA, trpB, and uidA) using the PCR technique. The results showed that the average loading rate on stool samples was 3.74 × 107 CFU/g for TAMF. A total of 7 species of bacteria were identified at different proportions: Staphylococcus spp (55.36%), E. coli (14.29%), Klebsiella ornithinolytica (12.5%), Serratia odorifera (5.36%), and Enterobacter aerogenes (5.36%). Interestingly, isolated E. coli presented a resistance of 100% to cefotaxime and aztreonam. In addition, resistances of 95.24% and 50% were observed against erythromycin and nalidixic acid, respectively. The molecular characterization of the isolated E. coli strains allowed us to discover another molecular variation within the isolated strains. Genes encoding the enzymes isocitrate dehydrogenase (icd) and DNA polymerase II (polB) were detected at 96.30% in the isolated E. coli strains. Moreover, the genes encoding the enzymes beta-D-glucuronidase (uidA) and DNA polymerase (dinB) were detected at 88.89% in the isolated E. coli strains. Interestingly, 81.48%, 85.19, 92.59%, and 100% of isolated E. coli strains expressed the genes encoding the enzymes tryptophan synthase subunit A (trpA), proline permease (putP), p-aminobenzoate synthase, and tryptophan synthase subunit B (trpB), respectively. The diversity of E. coli strains reflects the importance of regulatory mechanisms in the adaptation of bacteria to the gut microbiota.
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Yao L, Qu M, Jiang Y, Guo Y, Li N, Li F, Tan Z, Wang L. The development of genus-specific and species-specific real-time PCR assays for the authentication of Patagonian toothfish and Antarctic toothfish in commercial seafood products. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1674-1683. [PMID: 34453344 DOI: 10.1002/jsfa.11507] [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: 02/24/2021] [Revised: 08/05/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The substitution or mislabeling of toothfish is an issue of significant concern for seafood authorities; it also reduces the effectiveness of marine conservation and management programs for its over-exploitation and illegal trafficking, boosting the need for identification methods. RESULTS Two species-specific real-time polymerase chain reaction (PCR) assays for the identification of Patagonian toothfish (Dissostichus eleginoides) and Antarctic toothfish (Dissostichus mawsoni) and a genus-specific real-time PCR assay for Dissostichus spp. identification were developed based on fragments of the 16S rRNA and COI (cytochrome c oxidase subunit I) genes. These methods were confirmed to be rapid, simple, and sensitive (absolute sensitivity of 0.0002 ng μL-1 and relative sensitivity of 0.1 g kg-1 with good specificity). These methods can be applied to processed and commercial fish products. CONCLUSIONS These approaches can be beneficial for protecting both consumers and producers from economic fraud and might also help protect toothfish from over-exploitation as well as combat illegal, unreported, and unregulated (IUU) fisheries. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Lin Yao
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Meng Qu
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yanhua Jiang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yingying Guo
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Na Li
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Fengling Li
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhijun Tan
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Lianzhu Wang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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Giagkazoglou Z, Griffiths AM, Imsiridou A, Chatzispyrou A, Touloumis K, Hebb JL, Mylona D, Malamidou AK, Apostolidi ED, Batjakas IΕ, Gubili C. Flying under the radar: DNA barcoding ray wings in Greece detects protected species and umbrella labelling terms. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Agostinetto G, Brusati A, Sandionigi A, Chahed A, Parladori E, Balech B, Bruno A, Pescini D, Casiraghi M. ExTaxsI: an exploration tool of biodiversity molecular data. Gigascience 2022; 11:giab092. [PMID: 35077538 PMCID: PMC8848311 DOI: 10.1093/gigascience/giab092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/16/2021] [Accepted: 11/30/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area. RESULTS In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics. CONCLUSIONS ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data.
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Affiliation(s)
- Giulia Agostinetto
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Alberto Brusati
- Istituto Auxologico Italiano - IRCCS, Via Giuseppe Zucchi 18, 20095 Cusano Milanino, Italy
- Università degli Studi di Pavia, Dipartimento di Scienze del Sistema Nervoso e del Comportamento, Via Agostino Bassi 21, 27100 Pavia, Italy
| | - Anna Sandionigi
- Quantia Consulting srl, Via F. Petrarca 20, 22066 Mariano Comense, Italy
| | - Adam Chahed
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Elena Parladori
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Antonia Bruno
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
| | - Dario Pescini
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Piazza dell'Ateneo Nuovo 1, 20126 Milan, Italy
| | - Maurizio Casiraghi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Piazza della Scienza 2, 20126 Milan, Italy
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Hong Y, Kim JJ, Yu YC, Kim HS, Moon G, Park EM. Ultra-fast PCR method for the distinguishing between Miichthys miiuy and Sciaenops ocellatus. Food Sci Biotechnol 2021; 30:1225-1231. [PMID: 34603821 DOI: 10.1007/s10068-021-00954-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022] Open
Abstract
The mi-iuy croaker Miichthys miiuy has immense commercial value in the Republic of Korea. The red drum Sciaenops ocellatus is widely produced by aquaculture, although its price is approximately 25% that of M. miiuy. S. ocellatus has black spots on its tail, enabling it to be distinguished from M. miiuy based on appearance. However, identifying S. ocellatus after simple processing steps, such as skin removal and dicing, is difficult. Certain traders misrepresent and sell S. ocellatus as M. miiuy or cultured M. miiuy for illegal economical gain. Therefore, an accurate and rapid identification method is required to distinguish between M. miiuy and S. ocellatus in the field. Here, a method for rapid field identification was developed based on species-specific primers using a portable ultra-fast PCR instrument. The ultra-fast real-time PCR method can complete the entire analytical procedure, including DNA isolation, amplification, and detection, within 30 min, thus maintaining the accuracy of identifying M. miiuy and S. ocellatus products on site. Forty-nine commercial products were tested, and all samples were successfully identified. Thus, the developed method is rapid, efficient tool for ensuring consumer protection. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00954-4.
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Affiliation(s)
- Yewon Hong
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Jung Ju Kim
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Yeon-Cheol Yu
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Hyung Soo Kim
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Guiim Moon
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
| | - Eun Mi Park
- New Hazardous Substance Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Osong, 28159 Chungcheongbuk-do Korea
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Pathogenicity and Molecular Characterization of Staphylococcus aureus Strains Isolated from the Hospital Environment of CHU-Z Abomey-Calavi/Sô-Ava (Benin). BIOMED RESEARCH INTERNATIONAL 2021; 2021:6637617. [PMID: 34395621 PMCID: PMC8363449 DOI: 10.1155/2021/6637617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/15/2021] [Accepted: 07/26/2021] [Indexed: 11/18/2022]
Abstract
Staphylococcus aureus is a major human pathogen present on a third of the healthy population. The bacterium possesses an extensive arsenal of virulence factors. The pathogenicity is linked with S. aureus high plasticity and its exceptional ability to incorporate foreign genetic material. The aim of the present study was to perform molecular characterization of Staphylococcus aureus strains isolated from the clinical environment of the CHU-Z Abomey-Calavi/Sô-Ava. Isolation of Staphylococcus aureus bacterium was performed on Chapman agar. Toxin production by isolated S. aureus strains was investigated using the radial immunoprecipitation technique. A colorimetric assay was used to evaluate Staphylococcus aureus lipase (SA-Lipase) production. Finally, the expression of antibiotic resistance genes and genes encoding toxins production was investigated. Our data suggest that none of the isolated Staphylococcus aureus strains expressed the investigated toxin genes. Interestingly, SA-Lipase was produced by 14.28% of our isolated S. aureus strains. The mecA gene was present in 57.14% of the isolated strains, while PVL and TSST-1 genes were identified in 2.85 and 7.14% of S. aureus, respectively. Significant genetic diversity was observed along the hospital environment S. aureus strains. The present study reveals the level of virulence of S. aureus strains isolated in the different units of CHU-Z Abomey Calavi/Sô-Ava through the production of lipase, PVL, and epidermolysins. The molecular study has favored a genetic characterization within the isolated strains.
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Habib KA, Neogi AK, Rahman M, Oh J, Lee YH, Kim CG. DNA barcoding of brackish and marine water fishes and shellfishes of Sundarbans, the world's largest mangrove ecosystem. PLoS One 2021; 16:e0255110. [PMID: 34339426 PMCID: PMC8328341 DOI: 10.1371/journal.pone.0255110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.
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Affiliation(s)
- Kazi Ahsan Habib
- Faculty of Fisheries, Department of Fisheries Biology and Genetics, Aquaculture and Marine Science, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
- Department of Fisheries Biology and Genetics, Aquatic Bioresource Research Lab, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
- * E-mail: ,
| | - Amit Kumer Neogi
- Department of Fisheries Biology and Genetics, Aquatic Bioresource Research Lab, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Muntasir Rahman
- Department of Biological Science, Wayne State University, Detroit, Michigan, United States of America
| | - Jina Oh
- Marine Biology and Biological Oceanography Division, Korea Institute of Ocean Science and Technology (KIOST), Busan, Korea
| | - Youn-Ho Lee
- Marine Biology and Biological Oceanography Division, Korea Institute of Ocean Science and Technology (KIOST), Busan, Korea
| | - Choong-Gon Kim
- Marine Biology and Biological Oceanography Division, Korea Institute of Ocean Science and Technology (KIOST), Busan, Korea
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In-house and on-field validation of the multiplex PCR assay developed for authentication of three commercially important shrimp species. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Monteiro CS, Deconinck D, Eljasik P, Sobczak M, Derycke S, Panicz R, Kane N, Mazloomrezaei M, H Devlin R, Faria MA. A fast HRMA tool to authenticate eight salmonid species in commercial food products. Food Chem Toxicol 2021; 156:112440. [PMID: 34311008 DOI: 10.1016/j.fct.2021.112440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/30/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
Atlantic and Pacific salmon are frequently consumed species with very different economic values: farmed Atlantic salmon is cheaper than wild-caught Pacific salmons. Species replacements occur with the high valued Pacific species (Oncorhynchus keta, O. gorbuscha, O. kisutch, O. nerka and O. tshawytscha) substituted by cheaper farmed Atlantic salmon (Salmo salar) and Atlantic salmon by rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta). Here we use High-Resolution Melting Analysis (HRMA) to identify eight salmonid species. We designed primers to generate short amplicons of 72 and 116 bp from the fish barcode genes CO1 and CYTB. The time of analysis was under 70 min, after DNA extraction. Food processing of Atlantic salmon (fresh, "Bellevue", "gravadlax", frozen and smoked) did not impact the HRMA profiles allowing reliable identification. A blind test was conducted by three different institutes, showing correct species identifications irrespective of the laboratory conducting the analysis. Finally, a total of 82 retail samples from three European countries were analyzed and a low substitution rate of 1.2% was found. The developed tool provides a quick way to investigate salmon fraud and contributes to safeguard consumers.
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Affiliation(s)
- Carolina Sousa Monteiro
- LAQV-REQUIMTE, Faculty of Pharmacy, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Dumas Deconinck
- Flanders Research Institute for Agriculture, Fisheries and Food, ILVO, Aquatic Environment and Quality, Ankerstraat 1, B-8400, Oostende, Belgium; Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Ch. Deberiotstraat 32, B-3000, Leuven, Belgium
| | - Piotr Eljasik
- Department of Meat Science, Faculty of Food Science and Fisheries, West Pomeranian University of Technology Szczecin, Kazimierza Królewicza 4, 71-550, Szczecin, Poland
| | - Małgorzata Sobczak
- Department of Meat Science, Faculty of Food Science and Fisheries, West Pomeranian University of Technology Szczecin, Kazimierza Królewicza 4, 71-550, Szczecin, Poland
| | - Sofie Derycke
- Flanders Research Institute for Agriculture, Fisheries and Food, ILVO, Aquatic Environment and Quality, Ankerstraat 1, B-8400, Oostende, Belgium; Department of Biology, Ghent University, Krijgslaan 281, Building S8, 9000, Ghent, Belgium
| | - Remigiusz Panicz
- Department of Meat Science, Faculty of Food Science and Fisheries, West Pomeranian University of Technology Szczecin, Kazimierza Królewicza 4, 71-550, Szczecin, Poland
| | - Nicola Kane
- BIOREX Food Diagnostics, 9A the Technology Park, Belfast Road, Antrim, BT41 1QS, UK
| | - Mohsen Mazloomrezaei
- BIOREX Food Diagnostics, 9A the Technology Park, Belfast Road, Antrim, BT41 1QS, UK
| | - Robert H Devlin
- Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, BC, V7V 1N6, Canada
| | - Miguel A Faria
- LAQV-REQUIMTE, Faculty of Pharmacy, University of Porto, R. Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal.
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van der Zwan H, van der Sluis R. Polly Wants a Genome: The Lack of Genetic Testing for Pet Parrot Species. Genes (Basel) 2021; 12:1097. [PMID: 34356113 PMCID: PMC8307168 DOI: 10.3390/genes12071097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/04/2022] Open
Abstract
Parrots are considered the third most popular pet species, after dogs and cats, in the United States of America. Popular birds include budgerigars, lovebirds and cockatiels and are known for their plumage and vocal learning abilities. Plumage colour variation remains the main driving force behind breeder selection. Despite the birds' popularity, only two molecular genetic tests-bird sexing and pathogen screening-are commercially available to breeders. For a limited number of species, parentage verification tests are available, but are mainly used in conservation and not for breeding purposes. No plumage colour genotyping test is available for any of the species. Due to the fact that there isn't any commercial plumage genotype screening or parentage verification tests available, breeders mate close relatives to ensure recessive colour alleles are passed to the next generation. This, in turn, leads to inbreeding depression and decreased fertility, lower hatchability and smaller clutch sizes, all important traits in commercial breeding systems. This review highlights the research carried out in the field of pet parrot genomics and points out the areas where future research can make a vital contribution to understanding how parrot breeding can be improved to breed healthy, genetically diverse birds.
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Affiliation(s)
- Henriëtte van der Zwan
- Focus Area for Human Metabolomics, North-West University, Potchefstroom 2531, South Africa;
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Mohd Khair SZN, Abd Radzak SM, Mohamed Yusoff AA. The Uprising of Mitochondrial DNA Biomarker in Cancer. DISEASE MARKERS 2021; 2021:7675269. [PMID: 34326906 PMCID: PMC8302403 DOI: 10.1155/2021/7675269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/18/2022]
Abstract
Cancer is a heterogeneous group of diseases, the progression of which demands an accumulation of genetic mutations and epigenetic alterations of the human nuclear genome or possibly in the mitochondrial genome as well. Despite modern diagnostic and therapeutic approaches to battle cancer, there are still serious concerns about the increase in death from cancer globally. Recently, a growing number of researchers have extensively focused on the burgeoning area of biomarkers development research, especially in noninvasive early cancer detection. Intergenomic cross talk has triggered researchers to expand their studies from nuclear genome-based cancer researches, shifting into the mitochondria-mediated associations with carcinogenesis. Thus, it leads to the discoveries of established and potential mitochondrial biomarkers with high specificity and sensitivity. The research field of mitochondrial DNA (mtDNA) biomarkers has the great potential to confer vast benefits for cancer therapeutics and patients in the future. This review seeks to summarize the comprehensive insights of nuclear genome cancer biomarkers and their usage in clinical practices, the intergenomic cross talk researches that linked mitochondrial dysfunction to carcinogenesis, and the current progress of mitochondrial cancer biomarker studies and development.
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Affiliation(s)
- Siti Zulaikha Nashwa Mohd Khair
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Siti Muslihah Abd Radzak
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
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Bioinformatics Approach to Mitigate Mislabeling in EU Seafood Market and Protect Consumer Health. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18147497. [PMID: 34299949 PMCID: PMC8305968 DOI: 10.3390/ijerph18147497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
Fisheries products are some of the most traded commodities world-wide and the potential for fraud is a serious concern. Fish fraud represents a threat to human health and poses serious concerns due to the consumption of toxins, highly allergenic species, contaminates or zoonotic parasites, which may be present in substituted fish. The substitution of more expensive fish by cheaper species, with similar morphological characteristics but different origins, reflects the need for greater transparency and traceability upon which which the security of the entire seafood value-chain depends. Even though EU regulations have made significant progress in consumer information by stringent labelling requirements, fraud is still widespread. Many molecular techniques such as DNA barcoding provide valuable support to enhance the Common Fisheries Policy (CFP) in the protection of consumer interests by unequivocally detecting any kind of fraud. This paper aims to highlight both the engagement of EU fishery policy and the opportunity offered by new biotechnology instruments to mitigate the growing fraud in the globalized fish market and to enforce the food security system to protect consumers' health. In this paper, after a presentation of EU rules on fish labeling and a general overview on the current state of the global fish market, we discuss the public health implications and the opportunities offered by several techniques based on genetics, reporting a case study to show the efficacy of the DNA barcoding methodology in assessing fish traceability and identification, comparing different species of the Epinephelus genus, Mottled Grouper (Mycteroperca rubra) and Wreckfish (Polyprion americanus), often improperly sold with the commercial name of "grouper".
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Noh ES, Lee MN, Kim EM, Nam BH, Noh JK, Park JY, Kim KH, Kang JH. Discrimination of raw material species in mixed seafood products (surimi) using the next generation sequencing method. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2020.100786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rapid detection of fraudulence in seven commercial shrimp products by species-specific PCR assays. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Optimum DNA Extraction Methods for Edible Bird's Nest Identification Using Simple Additive Weighting Technique. FOODS (BASEL, SWITZERLAND) 2021; 10:foods10051086. [PMID: 34068860 PMCID: PMC8153580 DOI: 10.3390/foods10051086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022]
Abstract
A simple additive weighting (SAW) technique was used to determine and compare the overall performance of five DNA extraction methods from conventional (SDS method) to commercial kits (Qiagen, Wizard, and NucleoSpin) for identifying origins of edible bird’s nest (EBN) using end-point polymerase chain reaction (PCR). A hybrid method (SDS/Qiagen) which has been developed by combining the conventional SDS method with commercialised Qiagen was determined as the most suitable in terms of speed and cost-effectiveness. The determination of optimum extraction method was by the performances on efficiency and feasibility, extracted DNA concentration, purity, PCR amplifiability, handling time and safety of reagents used. The hybrid SDS/Qiagen method is less costly compared to the commercial kits and offered a more rapid alternative to the conventional SDS method with significant improvement in the yield, purity and PCR amplifiability. The developed hybrid SDS/Qiagen method provides a more practical alternative over the lengthy process using conventional method and expensive process using commercial kits. Using the simple additive weighting (SAW) technique and analysis, the Qiagen method is considered the most efficient and feasible method without consideration of cost as it yielded the purest extracted DNA and achieved the highest PCR amplifiability with the shortest turnaround time.
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Colihueque N, Espinoza R, Parraguez M. Authentication of Frozen Chilean Blue Mussel (Mytilus chilensis) Commercialized in the Town of Osorno, Southern Chile, Using PCR-RFLP Analysis. Recent Pat Food Nutr Agric 2021; 11:49-55. [PMID: 30599114 DOI: 10.2174/2212798410666181231154406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/08/2018] [Accepted: 12/17/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND DNA-based technologies are reliable authentication methods for food products, enabling the detection of fraud, non-intentional substitution and control of mislabeling. The Chilean blue mussel (Mytilus chilensis) is a seafood commercialized in Chile under different formats, including packages of frozen specimens. In this format, the valves of mussels are removed during processing, thus impeding identification of the product by the consumer due to the lack of external characters. OBJECTIVE To assess the authenticity of frozen Chilean blue mussels commercialized in southern Chile, particularly in the town of Osorno. METHODS Six commercial brands of frozen Chilean blue mussel were authenticated by the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method, based on the analysis of an 18S rDNA fragment. RESULTS Restriction patterns obtained indicate that three brands (50%) proved to be 100% authentic, given that all specimens contained in the package were Chilean blue mussels. The other three brands (50%) contained specimens of other commercial mytilids, particularly the cholga mussel (Aulacomya ater), in a variable percentage (12.5-50%). CONCLUSION This study based on the PCR-RFLP method provides evidence that Chilean blue mussels commercialized in a town located in southern Chile lack authenticity. This finding highlights the necessity for national producers to improve the production and/or packaging processes of this seafood. The authentication of commercial mussels is a matter of consumer interest and has been described in a recent patent on this issue that proposes an alternative methodology.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biologia Molecular y Citogenetica, Departamento de Ciencias Biologicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - René Espinoza
- Departamento de Acuicultura y Recursos Agroalimentarios, Universidad de Los Lagos, Osorno, Chile
| | - Margarita Parraguez
- Laboratorio de Genetica, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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Kang TS. Identification and Authentication of Commercial Mi-iuy Croaker (Miichthys miiuy) Products by Two PCR-Based Methods. J Food Prot 2021; 84:463-471. [PMID: 33003192 DOI: 10.4315/jfp-20-143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/25/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Mi-iuy croaker (Miichthys miiuy) is one of the most important ingredients of Korean cuisine and, thus, has a high economic value. However, the similar morphological traits among croaker fish belonging to family Sciaenidae are often exploited for seafood fraud. In this study, an M. miiuy-specific primer set was designed and further improved by the development of a rapid and cost-effective duplex PCR method. The specificity of M. miiuy-specific duplex PCR was tested using 22 seafood species, and no cross-reactivity was observed. The sensitivity of the PCR assay was found to be 0.1 ng/μL. For the first time, labeling compliance of 43 commercial mi-iuy croaker products was verified using both full DNA barcoding and M. miiuy-specific duplex PCR methods. For species identification, BOLDSYSTEMS and GenBank database were screened with the consensus sequences of each PCR product as a query. This identification result was further confirmed using the M. miiuy-specific duplex PCR method. The findings of this study revealed that principal species substituted were law croaker (Pseudotolithus senegallus, n = 4), bigeye croaker (Micropogonias megalops, n = 3), whitemouth croaker (Micropogonias furnieri, n = 1), and tigertoothed croaker (Otolithes ruber, n = 1). A significant percentage (21%) of mislabeling was present in commercial mi-iuy products sold on the South Korean market. HIGHLIGHTS
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Affiliation(s)
- Tae Sun Kang
- Department of Food and Nutrition, College of Health Science, Sangji University, Wonju, South Korea (ORCID: https://orcid.org/0000-0001-5939-6247)
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A R, A K, S A S, E S, N F. Character-based identification key for commercially important fishes of Pulicat lake: tool for conservation and management. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:120-125. [PMID: 33565345 DOI: 10.1080/24701394.2021.1883009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fishes are an important group of vertebrates in the animal world and make a significant contribution to global biodiversity. Fish is used as a source of food and contains many essential vitamins and fatty acids. The study of fish and their stability is important because, from year to year, fish stocks are often very important. For the conservation and management of these dwindling resources, correct identification of species is a prerequisite. Character-based methods of identification are of considerable use in this context, which classify specimens into species using classification rules that compactly describe species in terms of key diagnostic nucleotides in the gene sequences chosen. In this study, a total of 56 species of fishes distributed in Pulicat lake waters is taken as the target group. Mitochondrial CO1 sequences of each species were downloaded and modified. The species-specific diagnostic nucleotides for the selected group of species were identified using the BLOG version 2.0 software. Species-specific probes with a length range of 18-37 bp were designed on the basis of identified diagnostic nucleotide sites. The method is an effective tool for quickly and easily obtaining a significant amount of reliable information and could be used for forensic applications and conservation of fishes in Pulicat Lake.
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Affiliation(s)
- Rathipriya A
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Chennai, India
| | - Kathirvelpandian A
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Chennai, India
| | - Shanmugam S A
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Chennai, India
| | - Suresh E
- Institute of Fisheries Postgraduate Studies, TNJFU OMR Campus, Chennai, India
| | - Felix N
- Directorate of Incubation and Vocational Training in Aquaculture, ECR-Muttukadu, Chennai-603 112, India
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Martin KR, Waits LP, Parent CE. Teaching an Old Shell New Tricks: Extracting DNA from Current, Historical, and Ancient Mollusk Shells. Bioscience 2021. [DOI: 10.1093/biosci/biaa164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
The use of unconventional DNA sources has increased because the acquisition of traditional samples can be invasive, destructive, or impossible. Mollusks are one group for which novel genetic sources are crucial, but methodology remains relatively undeveloped. Many species are important ecologically and in aquaculture production. However, mollusks have the highest number of extinctions of any taxonomic group. Traditionally, mollusk shell material was used for morphological research and only recently has been used in DNA studies. In the present article, we review the studies in which shell DNA was extracted and found that effective procedures consider taxon-specific biological characteristics, environmental conditions, laboratory methods, and the study objectives. Importantly, these factors cannot be considered in isolation because of their fundamental, sometimes reciprocal, relationships and influence in the long-term preservation and recovery of shell DNA. Successful recovery of shell DNA can facilitate research on pressing ecological and evolutionary questions and inform conservation strategies to protect molluscan diversity.
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Affiliation(s)
- Kelly R Martin
- Department of Biological Sciences, and Lisette Waits is a distinguished professor of wildlife resources and is head of the Fish and Wildlife Sciences Department, University of Idaho, Moscow, Idaho, United States
| | - Lisette P Waits
- Department of Biological Sciences, and Lisette Waits is a distinguished professor of wildlife resources and is head of the Fish and Wildlife Sciences Department, University of Idaho, Moscow, Idaho, United States
| | - Christine E Parent
- Department of Biological Sciences, and Lisette Waits is a distinguished professor of wildlife resources and is head of the Fish and Wildlife Sciences Department, University of Idaho, Moscow, Idaho, United States
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Population genetic structure of Semisulcospira gottschei: simultaneous examination of mtDNA and microsatellite markers. Mol Biol Rep 2021; 48:97-104. [PMID: 33433834 DOI: 10.1007/s11033-020-05821-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/05/2020] [Indexed: 10/22/2022]
Abstract
Semisulcospira gottschei is an Asian endemic species inhabiting Korea and China. However, genetic structure analysis of the resource management of this species has not been performed. To investigate the genetic diversity among populations, microsatellites can be used to determine the geographic origins of marine and freshwater species. This study investigated the genetic structures of the Korean and Chinese populations of S. gottschei based on mitochondrial DNA (mtDNA) Cytochrome oxidase subunit I (COI) and polymorphic microsatellite loci developed from Semisulcospira coreana. Analysis of the mtDNA COI sequence revealed 43 haplotypes, which indicated no gene flow between the Korean and Chinese populations. To further elucidate the genetic structures of the Korean and Chinese populations, the population genetics of S. gottschei were analyzed using nine microsatellite markers. The genetic diversity analysis showed an average of 5.25 alleles per locus, with an average allelic richness of 4.02. Excessive homozygosity was found at all loci, which was expected to be due to the presence of null alleles at all loci. Populations of S. gottschei formed two separate clusters according to pairwise FST and AMOVA. Also, the UPGMA tree, PCA, STRUCTURE, and GeneClass indicated separation of the 11 populations into two clusters: Korea and China. These results have potential use in the management, restoration, and distinction of the origin country of populations.
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Using real time fluorescence loop-mediated isothermal amplification for rapid species authentication of Atlantic salmon (Salmo salar). J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2020.103659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Chen X, Fu M, Xu W, Huang M, Cui X, Cao M, Xiong X, Xiong X. One‐step triplex high‐resolution melting (HRM) analysis for rapid identification of Atlantic cod (
Gadus morhua
), Alaska pollock (
Gadus chalcogrammus
) and haddock (
Melanogrammus aeglefinus
). Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaoye Chen
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Mingyang Fu
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Wenjie Xu
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Manhong Huang
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Xiaowen Cui
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Min Cao
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Xiaohui Xiong
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
| | - Xiong Xiong
- College of Food Science and Light Industry Nanjing Tech University Nanjing211800China
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36
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Wallstrom MA, Morris KA, Carlson LV, Marko PB. Seafood mislabeling in Honolulu, Hawai’i. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Prida V, Sepúlveda M, Quezada-Romegialli C, Harrod C, Gomez-Uchida D, Cid B, Canales-Aguirre CB. Chilean Salmon Sushi: Genetics Reveals Product Mislabeling and a Lack of Reliable Information at the Point of Sale. Foods 2020; 9:E1699. [PMID: 33228244 PMCID: PMC7699462 DOI: 10.3390/foods9111699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Species diagnosis is essential to assess the level of mislabeling or misnamed seafood products such as sushi. In Chile, sushi typically includes salmon as the main ingredient, but species used are rarely declared on the menu. In order to identify which species are included in the Chilean sushi market, we analyzed 84 individual sushi rolls sold as "salmon" from sushi outlets in ten cities across Chile. Using a polymerase chain reaction-restriction fragment length polymorphism protocol (PCR-RFLP), we identified mislabeled and misnamed products. Atlantic salmon was the most common salmonid fish used in sushi, followed by coho salmon, rainbow trout, and Chinook salmon. We found a total of 23% and 18% of the products were mislabeled and misnamed, respectively. In 64% of cases, the salesperson selling the product could not identify the species. We also identified the use of wild-captured Chinook salmon samples from a naturalized population. Our results provide a first indication regarding species composition in Chilean sushi, a quantification of mislabeling and the level of misinformation declared by sales people to consumers. Finally, considering that Chinook salmon likely originates from a non-licensed origin and that sushi is an uncooked product, proper identification in the food production chain may have important consequences for the health of consumers.
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Affiliation(s)
- Valentina Prida
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile;
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
| | - Maritza Sepúlveda
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Playa Ancha, Valparaíso 2340000, Chile
| | - Claudio Quezada-Romegialli
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Valparaíso, Playa Ancha, Valparaíso 2340000, Chile
| | - Chris Harrod
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta 1271155, Chile
| | - Daniel Gomez-Uchida
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción 4070032, Chile
| | - Beatriz Cid
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
- Departamento de Sociología, Facultad de Ciencias Sociales, Universidad de Concepción, Concepción 4070032, Chile
| | - Cristian B. Canales-Aguirre
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile;
- Núcleo Milenio de Salmónidos Invasores (INVASAL), Concepción 4030000, Chile; (M.S.); (C.Q.-R.); (C.H.); (D.G.-U.); (B.C.)
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Tohoyessou MG, Mousse W, Sina H, Kona F, Azanghadji T, Guessennd N, Baba-Moussa F, Dadie T, Adjanohoun A, Baba-Moussa L. Toxin Production and Resistance of Staphylococcus Species Isolated from Fermented Artisanal Dairy Products in Benin. J Pathog 2020; 2020:7938149. [PMID: 33204534 PMCID: PMC7649661 DOI: 10.1155/2020/7938149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/01/2020] [Accepted: 10/13/2020] [Indexed: 11/28/2022] Open
Abstract
Staphylococcus species are considered as one of the major pathogens causing outbreaks of food poisoning. The aim of this work was to assess the toxinogenic and antibiotic susceptibility profiles of the strains of Staphylococcus spp isolated from three types of fermented dairy products (yoghourt, millet dêguê, and couscous dêguê). The isolation of the Staphylococcus strains was performed on selective media, and their identification was done using biochemical and molecular methods. The susceptibility at 15 antibiotics tested was assessed using the disc diffusion method. The immunodiffusion method was used to evaluate the toxin (luk-E/D, luk-S/F, ETA, and ETB) production. Biofilm formation was qualitatively researched on microplates. Less than half (42.77%) of the collected samples were contaminated with Staphylococcus spp. The yoghourt and millet dêguê samples collected in the afternoon were more contaminated than those collected in the morning. The S. aureus, S. capitis, and S. xylosus strains, respectively, were the most present. S. aureus was the only coagulase-positive species identified in our samples. The highest resistance to antibiotics was observed with penicillin (100%) irrespective of the nature of the sample. S. aureus strains were highly (71.4%) resistant to methicillin. The S. aureus strains were the most biofilm-forming (27.6%), followed by S. capitis strains. Panton and Valentine's leukocidin (luk-S/F) was produced by only S. aureus strains at a rate of 8.33%. Only coagulase-negative Staphylococcus (CNS) produced Luk-E/D. The high rates of Staphylococci contamination indicate bad hygiene quality during the production and distribution of dairy products. It is, therefore, necessary to improve the quality of fermented milk products.
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Affiliation(s)
- Majoie Géroxie Tohoyessou
- Laboratory Biology and Typing Molecular in Microbiology, Faculty of Science and Technology, University of Abomey-Calavi, 05 BP 1604, Cotonou, Benin
| | - Wassiyath Mousse
- Laboratory Biology and Typing Molecular in Microbiology, Faculty of Science and Technology, University of Abomey-Calavi, 05 BP 1604, Cotonou, Benin
| | - Haziz Sina
- Laboratory Biology and Typing Molecular in Microbiology, Faculty of Science and Technology, University of Abomey-Calavi, 05 BP 1604, Cotonou, Benin
| | - Fernique Kona
- Antibiotics, Natural Substances and Surveillance of Resistance of Microorganisms to Anti-Infective Unit (ASSURMI), Institute Pasteur of Ivory Coast, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Tania Azanghadji
- Laboratory Biology and Typing Molecular in Microbiology, Faculty of Science and Technology, University of Abomey-Calavi, 05 BP 1604, Cotonou, Benin
| | - Nathalie Guessennd
- Antibiotics, Natural Substances and Surveillance of Resistance of Microorganisms to Anti-Infective Unit (ASSURMI), Institute Pasteur of Ivory Coast, 01 BP 490, Abidjan 01, Côte d'Ivoire
| | - Farid Baba-Moussa
- Laboratory of Microbiology and Food Technology, Faculty of Science and Technology, University of Abomey-Calavi, ISBA-Champ de Foire, 01 BP 526, Cotonou, Benin
| | - Thomas Dadie
- Laboratory of Biotechnology and Food Microbiology, University Nangui Abrogoua, 02 B.P. 801, Abidjan 02, Côte d'Ivoire
| | | | - Lamine Baba-Moussa
- Laboratory Biology and Typing Molecular in Microbiology, Faculty of Science and Technology, University of Abomey-Calavi, 05 BP 1604, Cotonou, Benin
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DNA-based techniques for seafood species authentication. ADVANCES IN FOOD AND NUTRITION RESEARCH 2020; 95:207-255. [PMID: 33745513 DOI: 10.1016/bs.afnr.2020.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Global trade of seafood has increased in the last decade, leading to significant concerns associated with seafood fraud. Seafood fraud involves the intentional misrepresentation of fish or shellfish for the purpose of economic gain and includes acts such as species substitution, illegal transshipment, overtreatment/short weighting, and mislabeling country of origin or production method. These fraudulent acts have had economic, environmental, and public health consequences on a global level. DNA-based techniques for seafood authentication are utilized by regulatory agencies and can be employed as part of a food fraud risk mitigation plan. This chapter will focus specifically on the use of DNA-based methods for the detection of seafood species substitution. Various methods have been developed for DNA-based species identification of seafood, including polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), species-specific PCR, real-time PCR, Sanger sequencing, microarrays, and high-resolution melting (HRM). Emerging techniques for seafood authentication include droplet digital PCR, isothermal amplification, PCR-enzyme-linked immunosorbent assay (ELISA), and high-throughput or next-generation sequencing. Some of these DNA-based methods target specific species, such as real-time PCR and droplet digital PCR, while other methods allow for simultaneous differentiation of a wide range of fish species, including Sanger sequencing and high-throughput sequencing. This chapter will begin with an introduction on seafood fraud and species substitution, followed by an analysis of the main DNA-based authentication methods and emerging techniques for species identification.
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40
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Feng J, Zhu Q, Wang Y. Colorimetric detection of Gadidae species using probe-modified gold nanoparticles. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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41
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Pecoraro C, Crobe V, Ferrari A, Piattoni F, Sandionigi A, Andrews AJ, Cariani A, Tinti F. Canning Processes Reduce the DNA-Based Traceability of Commercial Tropical Tunas. Foods 2020; 9:E1372. [PMID: 32992465 PMCID: PMC7650566 DOI: 10.3390/foods9101372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022] Open
Abstract
Canned tuna is one of the most widely traded seafood products internationally and is of growing demand. There is an increasing concern over the vulnerability of canned tuna supply chains to species mislabelling and fraud. Extensive processing conditions in canning operations can lead to the degradation and fragmentation of DNA, complicating product traceability. We here employed a forensically validated DNA barcoding tool (cytochrome b partial sequences) to assess the effects of canning processes on DNA degradation and the identification of four tropical tuna species (yellowfin, bigeye, skipjack and longtail tuna) collected on a global scale, along their commercial chains. Each species was studied under five different canning processes i.e., freezing, defrosting, cooking, and canning in oil and brine, in order to investigate how these affect DNA-based species identification and traceability. The highest percentage of nucleotide substitutions were observed after brine-canning operations and were greatest for yellowfin and skipjack tuna. Overall, we found that DNA degradation significantly increased along the tuna canning process for most specimens. Consequently, most of the specimens canned in oil or brine were misidentified due to the high rate of nucleotide substitution in diagnostic sequences.
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Affiliation(s)
- Carlo Pecoraro
- Physalia-Courses, 10249 Berlin, Germany;
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
| | - Valentina Crobe
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
| | - Federica Piattoni
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
| | - Anna Sandionigi
- Department of Electronics Information and Bioengineering, Politecnico di Milano, 20133 Milano, Italy;
| | - Adam J. Andrews
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 48121 Ravenna, Italy; (A.F.); (F.P.); (A.J.A.); (A.C.); (F.T.)
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42
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Galal-Khallaf A. Multiplex PCR and 12S rRNA gene sequencing for detection of meat adulteration: A case study in the Egyptian markets. Gene 2020; 764:145062. [PMID: 32860900 DOI: 10.1016/j.gene.2020.145062] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 01/06/2023]
Abstract
Recently, DNA-based methods have proved to be accurate, fast and sensitive for meat authentication. According to the European Union, the food safety standards require accurate and detailed composition information of the meat products. Therefore, an accurate, fast and cost-effective identification methodology is needed. In this study, multiplex PCR coupled with 12S rDNA sequencing was employed for the detection of meat adulteration in two red meat products (frozen beef liver and cold cut samples, respectively) in Egypt. Multiplex PCR allowed the identification of ruminant, poultry, pork, and donkey residuals in processed red meat products (cold cuts) in a single step PCR reaction. Preliminary uniplex PCR was performed to evaluate primers specificity using DNA extracted from the positive control samples. The primers produced specific fragments for ruminant, poultry, pork, and donkey as follows: 271, 183, 531 and 145 bp, respectively. Multiplex PCR revealed that none of the samples was contaminated by porcine or donkey residuals, but 62.5% of all tested processed beef samples contained poultry contaminants. The sensitivity of this method was 0.01 ng/μL for beef, poultry and donkey and 0.1 ng/μL for pig. Another promising finding is the identification of all frozen beef liver samples as a cattle species (Bos taurus) through PCR-sequencing of a short fragment of 12S rRNA gene. Finally, we recommend the employment of multiplex PCR and PCR-sequencing of 12S rDNA for quality control in routine analysis of processed and frozen meat products.
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Affiliation(s)
- Asmaa Galal-Khallaf
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, Egypt.
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43
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Rampazzo F, Tosi F, Tedeschi P, Gion C, Arcangeli G, Brandolini V, Giovanardi O, Maietti A, Berto D. Preliminary multi analytical approach to address geographic traceability at the intraspecific level in Scombridae family. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2020; 56:260-279. [PMID: 32216466 DOI: 10.1080/10256016.2020.1739671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Globalization of seafood product marketing caused the increase of request of an effective fish traceability that enhances the consumer confidence in food safety. In this study, an integrated multi analytical approach based on two different and independent analytical techniques (carbon and nitrogen stable isotopes and fatty acids analysis) was applied in order to identify different fish species and trace their geographical provenience. The investigation was focused on four species (Thunnus thynnus, Thunnus alalunga, Auxis rochei and Scomber scombrus) belonging to the Scombridae family. The DNA barcoding method confirmed genus and species for S. scombrus and A. rochei, but only genus for T. alalunga and T. thynnus. Carbon and nitrogen stable isotopes results evidenced different fish diets and trophic positions, whereas fatty acids analysis displayed that the unsaturated prevailed (∼60 %) over the saturated compounds with a variation among the species and the geographical area in particular for docosahexaenoic and eicosapentaenoic acids percentage. The principal component analysis applied to stable isotopes and fatty acids evidenced a good discrimination among species and their geographical catching area. This multi-disciplinary analytical approach could represent a promising tool to identify the commercial fish and trace their origin in order to guarantee the health of consumers.
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Affiliation(s)
- Federico Rampazzo
- Italian National Institute for Environmental Protection and Research (ISPRA), Chioggia (VE), Italy
| | - Federica Tosi
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Paola Tedeschi
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara (FE), Ferrara (FE), Italy
| | - Claudia Gion
- Italian National Institute for Environmental Protection and Research (ISPRA), Chioggia (VE), Italy
| | - Giuseppe Arcangeli
- Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (PD), Italy
| | - Vincenzo Brandolini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara (FE), Ferrara (FE), Italy
| | - Otello Giovanardi
- Italian National Institute for Environmental Protection and Research (ISPRA), Chioggia (VE), Italy
| | - Annalisa Maietti
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara (FE), Ferrara (FE), Italy
| | - Daniela Berto
- Italian National Institute for Environmental Protection and Research (ISPRA), Chioggia (VE), Italy
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44
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Xing B, Zhang Z, Sun R, Wang Y, Lin M, Wang C. Mini-DNA barcoding for the identification of commercial fish sold in the markets along the Taiwan Strait. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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Curk T, Brackley CA, Farrell JD, Xing Z, Joshi D, Direito S, Bren U, Angioletti-Uberti S, Dobnikar J, Eiser E, Frenkel D, Allen RJ. Computational design of probes to detect bacterial genomes by multivalent binding. Proc Natl Acad Sci U S A 2020; 117:8719-8726. [PMID: 32241887 PMCID: PMC7183166 DOI: 10.1073/pnas.1918274117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target-probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.
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Affiliation(s)
- Tine Curk
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Chris A Brackley
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - James D Farrell
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhongyang Xing
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Darshana Joshi
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Susana Direito
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia
| | | | - Jure Dobnikar
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Erika Eiser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rosalind J Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom;
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46
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Aranguren Caro LF, Mai HN, Nunan L, Lin J, Noble B, Dhar AK. Assessment of transmission risk in WSSV-infected shrimp Litopenaeus vannamei upon cooking. JOURNAL OF FISH DISEASES 2020; 43:403-411. [PMID: 32048310 DOI: 10.1111/jfd.13128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
White spot syndrome virus has been a threat to the global shrimp industry since it was discovered in Taiwan in 1992. Thus, shrimp-producing countries have launched regulations to prevent import of WSSV-infected commodity shrimp from endemic areas. Recently, cooked shrimp that is infected with WSSV tested positive by PCR. However, there is no study to determine the infectivity of WSSV in cooked shrimp that tested positive by PCR. In the present study, WSSV-infected shrimp were cooked at boiling temperature for different times including 0, 1, 3, 5, 10 and 30 min. Upon exposure to boiling temperature, WSSV-infected shrimp were fed to SPF shrimp (Litopenaeus vannamei). The result showed experimentally challenged shrimp from 0-min treatment (positive control) indeed got infected with WSSV. However, experimentally challenged shrimp that were fed tissues boiled at 1, 3, 5, 10 and 30 min were not infected with WSSV. Mortality data showed that only the positive control (0-min) treatment displayed high mortality, whereas no mortality was observed in any other treatment category. These findings suggest that cooking shrimp at boiling temperature for at least 1 min might prevent any potential spread of WSSV from endemic countries to other geographical areas where WSSV has not yet been reported.
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Affiliation(s)
- Luis Fernando Aranguren Caro
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Hung N Mai
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Linda Nunan
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Joshua Lin
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Brenda Noble
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
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47
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Xiong X, Yuan F, Huang M, Cao M, Xiong X. Development of a rapid method for codfish identification in processed fish products based on SYBR Green real‐time PCR. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Xiong Xiong
- College of Food Science and Light Industry Nanjing Tech University Nanjing 211800 China
| | - Fangying Yuan
- College of Food Science and Light Industry Nanjing Tech University Nanjing 211800 China
| | - Manhong Huang
- College of Food Science and Light Industry Nanjing Tech University Nanjing 211800 China
| | - Min Cao
- College of Food Science and Light Industry Nanjing Tech University Nanjing 211800 China
| | - Xiaohui Xiong
- College of Food Science and Light Industry Nanjing Tech University Nanjing 211800 China
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48
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Xiong X, Huang M, Xu W, Cao M, Li Y, Xiong X. Tracing Atlantic Salmon (Salmo salar) in Processed Fish Products Using the Novel Loop-Mediated Isothermal Amplification (LAMP) and PCR Assays. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01738-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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49
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Jiang S, Ma X, Li T, Zhu C, You X. Developing Single Nucleotide Polymorphisms for Identification of Cod Products by RAD-Seq. Animals (Basel) 2020; 10:E423. [PMID: 32138187 PMCID: PMC7142540 DOI: 10.3390/ani10030423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 11/30/2022] Open
Abstract
The increase in the rate of seafood fraud, particularly in the expensive fishes, forces us to verify the identity of marine products. Meanwhile, the definition of cod lacks consistency at the international level, as few standards and effective application methods are capable of accurately detecting cod species. Genetic fingerprinting is important for both certifying authenticity and traceability of fish species. In this study, we developed a method that combines DNA barcoding and the restriction-site associated DNA sequencing (RAD-Seq) approach for the identification of cod products. We first obtained 6941 high-quality single nucleotide polymorphism (SNP)s from 65.6 gigabases (Gb) of RAD-Seq raw data, and two sequences that contain SNPs were finally used to successfully identify three different cod product species, which are Atlantic cod (Gadus morhua), Greenland turbot (Reinhardtius hippoglossoides), and Patagonian toothfish (Dissostichus eleginoides). This SNP-based method will help us to identify the products, which are sold under the name of "Xue Yu" (Cod) in China, and works in parallel with existing fish identification techniques to establish an efficient framework to detect and prevent fraud at all points of the seafood supply chain.
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Affiliation(s)
- Shoujia Jiang
- BGI Zhenjiang Detection Co., LTD, Zhenjiang 212132, China; (S.J.); (X.M.); (T.L.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xingyu Ma
- BGI Zhenjiang Detection Co., LTD, Zhenjiang 212132, China; (S.J.); (X.M.); (T.L.)
| | - Tao Li
- BGI Zhenjiang Detection Co., LTD, Zhenjiang 212132, China; (S.J.); (X.M.); (T.L.)
| | - Changqing Zhu
- Childhood Food Institute, School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Xinxin You
- BGI Zhenjiang Detection Co., LTD, Zhenjiang 212132, China; (S.J.); (X.M.); (T.L.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
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50
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Dou X, Zhang L, Wang X, Yang R, Wang X, Ma F, Yu L, Mao J, Li H, Wang X, Li P. Identification and Validation of Metabolic Markers for Adulteration Detection of Edible Oils Using Metabolic Networks. Metabolites 2020; 10:E85. [PMID: 32121379 PMCID: PMC7143555 DOI: 10.3390/metabo10030085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/23/2020] [Accepted: 02/28/2020] [Indexed: 12/03/2022] Open
Abstract
Food adulteration is a challenge faced by consumers and researchers. Due to DNA fragmentation during oil processing, it is necessary to discover metabolic markers alternative to DNA for adulteration detection of edible oils. However, the contents of metabolic markers vary in response to various factors, such as plant species, varieties, geographical origin, climate, and cultivation measures. Thus, it is difficult to identify a universal marker for all adulterants that may be present in some authentic samples. Currently, the specificity and selectivity of metabolic biomarkers are difficult to validate. Therefore, this study developed a screening strategy based on plant metabolic networks by developing a targeted analytical method for 56 metabolites in a metabolic network, using liquid/liquid extraction-liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified a chain of 11 metabolites that were related to isoflavonoid biosynthesis, which were detected in soybean oils but not rapeseed oils. Through multiple-marker mutual validation, these metabolites can be used as species-specific universal markers to differentiate soybean oil from rapeseed oil. Moreover, this method provides a model for screening characteristic markers of other edible vegetable oils and foods.
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Affiliation(s)
- Xinjing Dou
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Liangxiao Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Laboratory of Quality and Safety Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiao Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Ruinan Yang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xuefang Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Fei Ma
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Laboratory of Quality and Safety Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Li Yu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Jin Mao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Hui Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiupin Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Peiwu Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (X.D.); (X.W.); (R.Y.); (X.W.); (F.M.); (L.Y.); (J.M.); (H.L.); (X.W.); (P.L.)
- Laboratory of Quality and Safety Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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