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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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Gétaz M, Puławska J, Smits TH, Pothier JF. Host-Pathogen Interactions between Xanthomonas fragariae and Its Host Fragaria × ananassa Investigated with a Dual RNA-Seq Analysis. Microorganisms 2020; 8:E1253. [PMID: 32824783 PMCID: PMC7465820 DOI: 10.3390/microorganisms8081253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 12/31/2022] Open
Abstract
Strawberry is economically important and widely grown, but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, the gene expression of both plant and bacteria in planta was analyzed at two time points, 12 and 29 days post inoculation, in order to compare the pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28,588 known genes in strawberry and 4046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis-related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most X. fragariae genes involved in host interaction, recognition, and pathogenesis were lower expressed at late-phase infection. This study gives a first insight into the interaction of X. fragariae with its host. The strawberry plant changed gene expression in order to consistently adapt its metabolism with the progression of infection.
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Affiliation(s)
- Michael Gétaz
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, 96-100 Skierniewice, Poland;
| | - Theo H.M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland; (M.G.); (T.H.S.)
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Wang H, Turechek WW. Detection of Viable Xanthomonas fragariae Cells in Strawberry Using Propidium Monoazide and Long-Amplicon Quantitative PCR. PLANT DISEASE 2020; 104:1105-1112. [PMID: 32040389 DOI: 10.1094/pdis-10-19-2248-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas fragariae causes angular leaf spot in strawberry. The pathogen's association with its host tissue is thought to be a condition for its survival. Consequently, transmission of the pathogen to field production sites occurs almost exclusively through the movement of contaminated planting stock. The aim of this study was to develop a propidium monoazide (PMA)-quantitative PCR (qPCR) protocol for specific detection of viable X. fragariae cells. The qPCR procedure was developed for two different primer pairs: one producing a long amplicon (863 bp) and the other a short amplicon (61 bp). Both pairs were tested on mixtures of viable and heat-killed bacteria cells, bacteria-spiked strawberry petiole samples, and petioles collected from symptomatic, inoculated plants. The results showed that long-amplicon PMA-qPCR enabled specific and sensitive detection of X. fragariae with a detection limit of 103 CFU/ml, and it significantly improved PMA efficiency in differentiating viable from dead bacterial cells relative to short-amplicon PMA-qPCR. Based on the delta threshold cycle (Ct) values (i.e., the difference in Ct values between PMA-treated and nontreated samples), the long-amplicon PMA-qPCR was able to suppress the detection of dead X. fragariae cells 1.9- to 3.1-fold across all petiole samples tested. The quantification results from PMA-qPCR for mixtures of viable and dead cells were highly correlated with the predicted bacterial concentrations in a linear relationship (R2 = 0.981). This assay can be useful for identifying inoculum sources in the strawberry production cycle, which may lead to improved disease management strategies.
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Affiliation(s)
- Hehe Wang
- Department of Agricultural and Environmental Sciences, Clemson University, Blackville, SC
| | - William W Turechek
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL
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Martins L, Fernandes C, Albuquerque P, Tavares F. Assessment of Xanthomonas arboricola pv. juglandis Bacterial Load in Infected Walnut Fruits by Quantitative PCR. PLANT DISEASE 2019; 103:2577-2586. [PMID: 31347945 DOI: 10.1094/pdis-12-18-2253-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonas arboricola pv. juglandis is the etiologic agent of important walnut (Juglans regia L.) diseases, causing severe fruit drop and high economic losses in walnut production regions. Rapid diagnostics and knowledge of bacterial virulence fitness are key to hinder disease progression and apply timely phytosanitary measures. This work describes an X. arboricola pv. juglandis-specific real-time quantitative PCR (qPCR) using X. arboricola pv. juglandis-specific DNA markers to quantify the bacterial load in infected walnut plant tissues. Method validation was achieved using calibration curves obtained with serial dilutions of X. arboricola pv. juglandis chromosomal DNA and standard curves obtained from walnut samples spiked with X. arboricola pv. juglandis cells. High correlations (R2 > 0.990 and > 0.995) and low limits of detection (35 chromosomes/qPCR reaction and 2.7 CFU/qPCR reaction) were obtained for both markers considering the calibration and standard curves, respectively. Assessment of qPCR repeatability, reproducibility, and specificity allowed us to demonstrate the reliability and consistency of the method. Furthermore, in planta quantification of X. arboricola pv. juglandis bacterial load using infected walnut fruit samples showed a higher detection resolution compared with standard PCR detection. By allowing quantification of virulence fitness of distinct X. arboricola pv. juglandis strains in planta, the proposed qPCR method may contribute to assertive risk assessment of walnut diseases caused by X. arboricola pv. juglandis and ultimately help to improve phytosanitary practices.
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Affiliation(s)
- Leonor Martins
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Camila Fernandes
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
- INIAV - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, Oeiras, Portugal
| | - Pedro Albuquerque
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Fernando Tavares
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
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Wang H, Turechek WW. A Loop-Mediated Isothermal Amplification Assay and Sample Preparation Procedure for Sensitive Detection of Xanthomonas fragariae in Strawberry. PLoS One 2016; 11:e0147122. [PMID: 26766068 PMCID: PMC4713083 DOI: 10.1371/journal.pone.0147122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/29/2015] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. Asymptomatic infection is common and contributes to the difficulties in disease management. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay as an efficient method for detection of asymptomatic infections of X. fragariae. In addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate in real-life samples. The sample preparation procedure includes an overnight incubation of strawberry tissues in phosphate-buffered saline (PBS), followed by a quick sample concentration and a boiling step to extract DNA for amplification. The detection limit of the LAMP assay was approximately 2×10(3) CFU/mL for pure bacteria culture and 300 CFU/mL for bacteria spiked strawberry leaf and petiole samples. LAMP provided a 2-3 fold lower detection limit than the standard qPCR assay but was faster, and more user-friendly. The LAMP assay should serve as a rapid, sensitive and cost-effective tool for detecting asymptomatic infections of X. fragariae in strawberry nursery stock and contribute to improved disease management.
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Affiliation(s)
- Hehe Wang
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
| | - William W. Turechek
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States of America
- * E-mail:
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Diagnostics of Seed-Borne Plant Pathogens for Safe Introduction and Healthy Conservation of Plant Genetic Resources. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Robène I, Perret M, Jouen E, Escalon A, Maillot MV, Chabirand A, Moreau A, Laurent A, Chiroleu F, Pruvost O. Development and validation of a real-time quantitative PCR assay to detect Xanthomonas axonopodis pv. allii from onion seed. J Microbiol Methods 2015; 114:78-86. [DOI: 10.1016/j.mimet.2015.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/30/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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Mirmajlessi SM, Destefanis M, Gottsberger RA, Mänd M, Loit E. PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Syst Rev 2015; 4:9. [PMID: 25588564 PMCID: PMC4320524 DOI: 10.1186/2046-4053-4-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/02/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique. METHODS The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided. RESULTS A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed. CONCLUSIONS From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.
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Affiliation(s)
- Seyed Mahyar Mirmajlessi
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Marialaura Destefanis
- />Pesticides, Plant Health and Seed Testing Laboratories, Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare Ireland
| | - Richard Alexander Gottsberger
- />Department for Molecular Diagnostics of Plant Diseases, Institute for Sustainable Plant Production, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Marika Mänd
- />Department of Plant Protection, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Evelin Loit
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
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Albuquerque P, Caridade CMR, Marcal ARS, Cruz J, Cruz L, Santos CL, Mendes MV, Tavares F. Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. Appl Environ Microbiol 2011; 77:5619-28. [PMID: 21705524 PMCID: PMC3165254 DOI: 10.1128/aem.05189-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/05/2011] [Indexed: 11/20/2022] Open
Abstract
Phytosanitary regulations and the provision of plant health certificates still rely mainly on long and laborious culture-based methods of diagnosis, which are frequently inconclusive. DNA-based methods of detection can circumvent many of the limitations of currently used screening methods, allowing a fast and accurate monitoring of samples. The genus Xanthomonas includes 13 phytopathogenic quarantine organisms for which improved methods of diagnosis are needed. In this work, we propose 21 new Xanthomonas-specific molecular markers, within loci coding for Xanthomonas-specific protein domains, useful for DNA-based methods of identification of xanthomonads. The specificity of these markers was assessed by a dot blot hybridization array using 23 non-Xanthomonas species, mostly soil dwelling and/or phytopathogens for the same host plants. In addition, the validation of these markers on 15 Xanthomonas spp. suggested species-specific hybridization patterns, which allowed discrimination among the different Xanthomonas species. Having in mind that DNA-based methods of diagnosis are particularly hampered for unsequenced species, namely, Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans, for which comparative genomics tools to search for DNA signatures are not yet applicable, emphasis was given to the selection of informative markers able to identify X. fragariae, X. axonopodis pv. phaseoli, and X. fuscans subsp. fuscans strains. In order to avoid inconsistencies due to operator-dependent interpretation of dot blot data, an image-processing algorithm was developed to analyze automatically the dot blot patterns. Ultimately, the proposed markers and the dot blot platform, coupled with automatic data analyses, have the potential to foster a thorough monitoring of phytopathogenic xanthomonads.
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Affiliation(s)
- Pedro Albuquerque
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Departamento de Biologia (FCUP), Edifício FC4, Via Panorâmica no. 36, Universidade do Porto, 4150-564 Porto, Portugal
| | - Cristina M. R. Caridade
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Instituto Superior de Engenharia de Coimbra (ISEC), Rua Pedro Nunes-Quinta da Nora, 3030-199 Coimbra, Portugal
| | - Andre R. S. Marcal
- Centro de Investigação em Ciências Geo-Espaciais (CICGE), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
- Centro de Matemática da Universidade do Porto (CMUP), Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal
| | - Joana Cruz
- Instituto Nacional de Recursos Biológicos (INRB), Unidade de Investigação de Protecção de Plantas, Tapada da Ajuda, 1349-018 Lisbon, Portugal
| | - Leonor Cruz
- Instituto Nacional de Recursos Biológicos (INRB), Unidade de Investigação de Protecção de Plantas, Tapada da Ajuda, 1349-018 Lisbon, Portugal
| | - Catarina L. Santos
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Marta V. Mendes
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Fernando Tavares
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Departamento de Biologia (FCUP), Edifício FC4, Via Panorâmica no. 36, Universidade do Porto, 4150-564 Porto, Portugal
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Rose HL, Dewey CA, Ely MS, Willoughby SL, Parsons TM, Cox V, Spencer PM, Weller SA. Comparison of eight methods for the extraction of Bacillus atrophaeus spore DNA from eleven common interferents and a common swab. PLoS One 2011; 6:e22668. [PMID: 21818364 PMCID: PMC3144239 DOI: 10.1371/journal.pone.0022668] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 06/28/2011] [Indexed: 11/19/2022] Open
Abstract
Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit) were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum) and one solid (Underarm deodorant), the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar), and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method.
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Affiliation(s)
- Helen L. Rose
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Caroline A. Dewey
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Morgan S. Ely
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Sarah L. Willoughby
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Tanya M. Parsons
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Victoria Cox
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Phillippa M. Spencer
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Simon A. Weller
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
- * E-mail:
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