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Wang L, Zhang T, Huo J, Wang Y, Lu Y, Zhu X. Rapid and specific detection of Enterococcus faecium with an isothermal amplification and lateral flow strip combined method. Arch Microbiol 2023; 206:28. [PMID: 38112880 DOI: 10.1007/s00203-023-03758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Enterococcus faecium is responsible for a highly contagious, drug-resistant nosocomial infection that often causes serious illness. In this study, a rapid and sensitive RPA-LFS (recombinase polymerase amplification-lateral flow strip) method for the detection of E. faecium was established based on specific primers and probes designed using the ddl gene. To verify the specificity and sensitivity of the method, 26 specific strains and 100-106 CFU/μL E. faecium were selected for detection. The results show that the proposed method can specifically detect E. faecium, and the minimum detection limit is 100 CFU/μL. To compare the clinical application of the method with qPCR, 181 clinical samples were collected for testing. RPA-LFS and qPCR had the same practical applicability, and 61 parts of E. faecium were detected in 183 clinical samples. The methods developed in this study not only have the advantages of rapid sensitivity and specificity but also meet the needs of remote areas with scarce medical resources.
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Affiliation(s)
- Lei Wang
- Central Laboratory of Hospital, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital, Lianyungang, China
| | - Ting Zhang
- Central Laboratory of Hospital, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital, Lianyungang, China
| | - Juan Huo
- Central Laboratory of Hospital, The First People's Hospital of Lianyungang, Xuzhou Medical University Affiliated Hospital, Lianyungang, China
| | - Yan Wang
- Department of Oncology, Lianyungang Second People's Hospital (Lianyungang Hospital Affiliated to Jiangsu University), Lianyungang, China
- Department of Laboratory Medicine, Lianyungang Second People's Hospital (Lianyungang Hospital Affiliated to Jiangsu University), Lianyungang, China
| | - Yingzhi Lu
- Department of Oncology, Lianyungang Second People's Hospital (Lianyungang Hospital Affiliated to Jiangsu University), Lianyungang, China
- Department of Laboratory Medicine, Lianyungang Second People's Hospital (Lianyungang Hospital Affiliated to Jiangsu University), Lianyungang, China
| | - Xinming Zhu
- Department of Laboratory Medicine, Lianyungang Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Lianyungang, China.
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Yang W, Su Y, Zeng L, Zhang Y, Ullah F, Wang X, Li X, Feng X, Li Z. LAMP Assay as a Rapid Identification Technique of Chinese Citrus Fly and Japanese Orange Fly (Diptera: Tephritidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:956-962. [PMID: 36946506 DOI: 10.1093/jee/toad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 06/14/2023]
Abstract
Bactrocera tsuneonis and Bactrocera minax are the most destructive pests that damage citrus in China. These key pests hinder the citrus trade, cause significant financial losses, drastically lower citrus production and quality, and decrease farmer enthusiasm for citrus planting. Bactrocera minax and B. tsuneonis are very similar in all life stages. There are limited morphological characteristics to differentiate the adult species, and it is nearly impossible to differentiate these two species in the egg and larval stages. Loop-mediated isothermal amplification (LAMP) is a rapid and robust diagnostic tool used to identify these two species accurately. We designed two sets of primers to distinguish B. minax and B. tsuneonis using DNA barcoding region of the COI gene. Only 50 min was needed under a constant temperature of 65ºC to determine the species of the two flies. The reaction system has high specificity and sensitivity, in which these two species can be accurately distinguished between different geographical populations and 1.0 ng/μL was the lowest DNA concentration that could be detected. Our primers can quickly identify these key pests without knowing their morphology, which could facilitate plant protection workers at the primary level to solve problems in plant quarantine.
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Affiliation(s)
- Wenzhao Yang
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yun Su
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lingyu Zeng
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yue Zhang
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Farman Ullah
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaoliang Wang
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Xiaonan Li
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Xiaodong Feng
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Zhihong Li
- Department of Plant Biosecurity, College of Plant Protection, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Razuvaeva AV, Ulyanova EG, Skolotneva ES, Andreeva IV. Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods. Vavilovskii Zhurnal Genet Selektsii 2023; 27:240-249. [PMID: 37293445 PMCID: PMC10244583 DOI: 10.18699/vjgb-23-30] [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: 07/14/2022] [Revised: 12/25/2022] [Accepted: 01/07/2022] [Indexed: 06/10/2023] Open
Abstract
Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agro- and biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed - from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region.
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Affiliation(s)
- A V Razuvaeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Ulyanova
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
| | - E S Skolotneva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Andreeva
- Siberian Federal Scientific Centre of Agro-BioTechnologies of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk Region, Russia
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Shimbori EM, Querino RB, Costa VA, Zucchi RA. Taxonomy and Biological Control: New Challenges in an Old Relationship. NEOTROPICAL ENTOMOLOGY 2023; 52:351-372. [PMID: 36656493 PMCID: PMC9851596 DOI: 10.1007/s13744-023-01025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/03/2023] [Indexed: 05/13/2023]
Abstract
Biological control and taxonomy are continuously developing fields with remarkable impacts on society. At least 80 years of literature have documented this relationship, which remains essentially the same in its mutualistic nature, as well as in its major challenges. From the perspective of Brazilian taxonomists, we discuss the impacts of important scientific and social developments that directly affect research in these areas, posing new challenges for this lasting relationship. The increasing restrictions and concerns regarding the international transit of organisms require improvements in research related to risk assessment for exotic biological control agents and also stimulate prospecting within the native biota. In our view, this is a positive situation that can foster a closer relationship between taxonomists and applied entomologists, as well as local surveys and taxonomic studies that are necessary before new programs and agents can be implemented. We discuss the essential role of molecular biology in this context, as an iconic example of the synergy between applied sciences and natural history. As our society comes to need safer and more sustainable solutions for food security and the biodiversity crisis, scientific progress will build upon this integration, where biological control and taxonomy play an essential role.
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Affiliation(s)
- Eduardo Mitio Shimbori
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
| | - Ranyse Barbosa Querino
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Cerrados, Planaltina, Distrito Federal Brazil
| | - Valmir Antonio Costa
- Centro Avançado de Pesquisa e Desenvolvimento em Sanidade Agropecuária, Instituto Biológico, São Paulo Campinas, Brazil
| | - Roberto Antonio Zucchi
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de São Paulo (USP), São Paulo Piracicaba, Brazil
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Agurto-Arteaga A, Vivas-Ruiz DE, Lazo F, Proleón Á, Torrejón D, Electo J, Cayo C, Urra FA, Chávez-Olórtegui C, Sánchez EF, Yarlequé A. Simultaneous identification of three clinically relevant peruvian pit vipers by multiplex loop-mediated isothermal amplification (mLAMP). Toxicon 2023; 223:107022. [PMID: 36621682 DOI: 10.1016/j.toxicon.2023.107022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Previous knowledge about the taxonomic distribution of venomous snake species is very useful for epidemiological aspects of ophidism. Here, we sought to develop an assay for the differential identification of clinically relevant snakes in Peru: Bothrops atrox, Lachesis muta, and Crotalus durissus using a multiplex loop-mediated isothermal amplification (mLAMP) assay. For this, DNA was extracted from the shed snake skins and the mitochondrial genes Cytb, COI, and 12S rRNA were amplified and further sequenced, for the design of mLAMP reaction primers. For each snake species the forward and reverse primers, internal forward and reverse primers, and the loop primers were obtained, bearing the latter different fluorophores for product identification. Finally, the reaction was standardized in the presence of all primer sets, and an optimal amount of low molecular weight polyethyleneimine. The precipitated products were observed in a UV light transilluminator, finding a differential fluorescence according to the DNA used, with a detection limit to the naked eye in the range of 0.2-25 ng of DNA, within 30 min. This study is the first report on the use of mLAMP technology for the identification of venomous snakes.
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Affiliation(s)
- Andres Agurto-Arteaga
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru.
| | - Dan E Vivas-Ruiz
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru.
| | - Fanny Lazo
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Álex Proleón
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Daniel Torrejón
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Jorge Electo
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Carmen Cayo
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
| | - Felix A Urra
- Laboratorio de Plasticidad Metabólica y Bioenergética, Programa de Farmacología Clínica y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Carlos Chávez-Olórtegui
- Departamento de Bioquímica-Inmunología, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Eladio F Sánchez
- Research and Development Center, Ezequiel Dias Foundation, 30510-010, Belo Horizonte, MG, Brazil
| | - Armando Yarlequé
- Laboratorio de Biología Molecular-Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima 01, Lima, Peru
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Benjakul S, Saetang J. Development of Loop-Mediated Isothermal Amplification (LAMP) Assays for the Rapid Authentication of Three Swimming Crab Species. Foods 2022; 11:2247. [PMID: 35954015 PMCID: PMC9368355 DOI: 10.3390/foods11152247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
Blue swimming crab meat is easily adulterated by other crab meats with a lower price. A potential authentication method is required to prevent mislabeling. LAMP assays were established to identify the meat of blue swimming crab, crucifix crab, and three spotted swimming crab. The primers were designed using PrimerExplorer V5. The specificity of the LAMP assay was tested compared to the PCR method. The sensitivity was conducted at the DNA concentrations of 0.4-50 ng/reaction. The results demonstrated that both LAMP and PCR could discriminate all species of crabs. LAMP showed a superior sensitivity to PCR in the three spotted swimming crab, while a similar result between LAMP and PCR was obtained in blue swimming crab. No changes in the detection efficacy were attained when boiled and steamed crab meats were applied. Therefore, the LAMP assay developed could potentially be applicable to detect the adulteration or mislabeling of raw or cooked crab meat in markets.
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Affiliation(s)
| | - Jirakrit Saetang
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand;
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