Detection and identification of Xanthomonas arboricola pv. pruni from symptomless plant material: results of an Italian test performance study

EPPO Bulletin ◽  
2015 ◽  
Vol 45 (1) ◽  
pp. 41-51 ◽  
Author(s):  
S. Loreti ◽  
N. Pucci ◽  
G. Perez ◽  
V. Catara ◽  
M. Scortichini ◽  
...  
Keyword(s):  
Test Performance ◽  
Plant Material ◽  
Performance Study ◽  
Detection And Identification ◽  
Symptomless Plant ◽  
Xanthomonas Arboricola

Assessment of a new qPCR tool for the detection and identification of the root-knot nematode Meloidogyne enterolobii by an international test performance study

2015 ◽  
Vol 144 (1) ◽  
pp. 97-108 ◽  
Author(s):  
Andrea Braun-Kiewnick ◽  
Nicole Viaene ◽  
Laurent Folcher ◽  
Fabrice Ollivier ◽  
Géraldine Anthoine ◽  
...  
Keyword(s):  
Test Performance ◽  
Performance Study ◽  
Root Knot Nematode ◽  
Detection And Identification ◽  
Meloidogyne Enterolobii

scholarly journals Development of a loop-mediated isothermal amplification assay for the detection of Tilletia controversa based on genome comparison

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Somayyeh Sedaghatjoo ◽  
Monika K. Forster ◽  
Ludwig Niessen ◽  
Petr Karlovsky ◽  
Berta Killermann ◽  
...  
Keyword(s):  
Test Performance ◽  
Genomic Dna ◽  
Lamp Assay ◽  
Fungal Species ◽  
Isothermal Amplification ◽  
Genome Comparison ◽  
Performance Study ◽  
Loop Mediated Isothermal Amplification ◽  
Tilletia Controversa ◽  
Genomic Regions

AbstractTilletia controversa causing dwarf bunt of wheat is a quarantine pathogen in several countries. Therefore, its specific detection is of great phytosanitary importance. Genomic regions routinely used for phylogenetic inferences lack suitable polymorphisms for the development of species-specific markers. We therefore compared 21 genomes of six Tilletia species to identify DNA regions that were unique and conserved in all T. controversa isolates and had no or limited homology to other Tilletia species. A loop-mediated isothermal amplification (LAMP) assay for T. controversa was developed based on one of these DNA regions. The specificity of the assay was verified using 223 fungal samples comprising 43 fungal species including 11 Tilletia species, in particular 39 specimens of T. controversa, 92 of T. caries and 40 of T. laevis, respectively. The assay specifically amplified genomic DNA of T. controversa from pure cultures and teliospores. Only Tilletia trabutii generated false positive signals. The detection limit of the LAMP assay was 5 pg of genomic DNA per reaction. A test performance study that included five laboratories in Germany resulted in 100% sensitivity and 97.7% specificity of the assay. Genomic regions, specific to common bunt (Tilletia caries and Tilletia laevis together) are also provided.

scholarly journals Multiple DNA Markers for Identification of Xanthomonas arboricola pv. juglandis Isolates and its Direct Detection in Plant Samples

Plant Disease ◽  
2017 ◽  
Vol 101 (6) ◽  
pp. 858-865 ◽  
Author(s):  
Camila Fernandes ◽  
Pedro Albuquerque ◽  
Rui Sousa ◽  
Leonor Cruz ◽  
Fernando Tavares
Keyword(s):  
Dna Markers ◽  
Plant Material ◽  
Juglans Regia ◽  
Infected Plant ◽  
Geographic Origin ◽  
Large Set ◽  
Dot Blot ◽  
Plant Samples ◽  
Culture Independent ◽  
Xanthomonas Arboricola

Xanthomonas arboricola pv. juglandis (Xaj) is the etiological agent of walnut (Juglans regia L.) bacterial blight (WBB), and has been associated to other walnut emerging diseases, namely brown apical necrosis (BAN) and vertical oozing canker (VOC), altogether severely affecting the walnut production worldwide. Despite the research efforts carried out to disclose Xaj genetic diversity, reliable molecular methods for rapid identification of Xaj isolates and culture-independent detection of Xaj in infected plant samples are still missing. In this work, we propose nine novel specific DNA markers (XAJ1 to XAJ9) selected by dedicated in silico approaches to identify Xaj isolates and detect these bacteria in infected plant material. To confirm the efficacy and specificity of these markers, dot blot hybridization was carried out across a large set of xanthomonads. This analysis, which confirmed the pathovar specificity of these markers, allowed to identify four broad-range markers (XAJ1, XAJ4, XAJ6, and XAJ8) and five narrow-range markers (XAJ2, XAJ3, XAJ5, XAJ7, and XAJ9), originating 12 hybridization patterns (HP1 to HP12). No evident relatedness was observed between these hybridization patterns and the geographic origin from which the isolates were obtained. Interestingly, four isolates that clustered together according the gyrB phylogenetic analysis (CPBF 1507, 1508, 1514, and 1522) presented the same hybridization pattern (HP11), suggesting that these nine markers might be informative to rapidly discriminate and identify different Xaj lineages. Taking into account that a culture-independent detection of Xaj in plant material has never been described, a multiplex PCR was optimized using markers XAJ1, XAJ6, and XAJ8. This triplex PCR, besides confirming the dot blot data for each of the 52 Xaj, was able to detect Xaj in field infected walnut leaves and fruits. Altogether, these nine Xaj-specific markers allow conciliating the specificity of DNA-detection assays with typing resolution, contributing to rapid detection and identification of potential emergent and acutely virulent Xaj genotypes, infer their distribution, disclose the presence of this phytopathogen on potential alternative host species and improve phytosanitary control.

scholarly journals Point of Care Testing using rapid automated Antigen Testing for SARS-COV-2 in Care Homes – an exploratory safety, usability and diagnostic agreement evaluation

2021 ◽  
Author(s):  
Massimo Micocci ◽  
Peter Buckle ◽  
Gail Hayward ◽  
A. Joy Allen ◽  
Kerrie Davies ◽  
...  
Keyword(s):  
Test Performance ◽  
Point Of Care ◽  
Care Home ◽  
Immunofluorescence Assay ◽  
Careful Consideration ◽  
Care Homes ◽  
Performance Study ◽  
Mixed Methods Evaluation ◽  
Point Of Care Tests ◽  
Positive Agreement

AbstractIntroductionSuccessful adoption of POCTs (Point-of-Care tests) for COVID-19 in care homes requires the identification of ideal use cases and a full understanding of contextual and usability factors that affect test results and minimise biosafety risks. This paper presents findings from a scoping-usability and test performance study of a microfluidic immunofluorescence assay for COVID-19 in care homes.MethodsA mixed-methods evaluation was conducted in four UK care homes to scope usability and to assess the agreement with qRT-PCR. A dry run with luminescent dye was carried out to explore biosafety issues.ResultsThe agreement analysis was carried out on 227 asymptomatic participants (159 staff and 68 residents) and 14 symptomatic participants (5 staff and 9 residents). Asymptomatic specimens showed 50% (95% CI: 1.3%-98.7%) positive agreement and 96% (95% CI: 92.5%-98.1%) negative agreement with overall prevalence and bias-adjusted Kappa (PABAK) of 0.911 (95% CI: 0.857-0.965). Symptomatic specimens showed 83.3% (95% CI: 35.9%-99.6%) positive agreement and 100% (95% CI: 63.1%-100%) negative agreement with overall prevalence and bias-adjusted Kappa (PABAK) of 0.857 (95% CI: 0.549-1).The dry run showed four main sources of contamination that led to the modification of the standard operating procedures. Simulation after modification showed no further evidence of contamination.ConclusionCareful consideration of biosafety issues and contextual factors associated with care home are mandatory for safe use the POCT. Whilst POCT may have some utility for ruling out COVID-19, further diagnostic accuracy evaluations are needed to promote effective adoption.

Detection and identification of bacterial canker of tomato Clavibacter michiganensis subsp. michiganensis

2021 ◽  
Author(s):  
I.N. Pisareva ◽  
◽  
O.Yu. Slovareva ◽  
Keyword(s):  
Sample Preparation ◽  
Plant Material ◽  
Plant Sample ◽  
Bacterial Canker ◽  
Clavibacter Michiganensis ◽  
Diagnostic Protocol ◽  
Clavibacter Michiganensis Subsp ◽  
Detection And Identification ◽  
Bacterial Canker Of Tomato

The study is devoted to the diagnosis of bacterial canker of tomato (Cmm). The method of sampling and plant sample preparation has been adapted. PCR recommended by the international diagnostic protocol and other sources have been tested. The use of methods made it possible to identify Cmm in plant material

Test performance study of diagnostic procedures for identification and detection ofGibberella circinatain pine seeds in the framework of a EUPHRESCO project

EPPO Bulletin ◽  
2013 ◽  
Vol 43 (2) ◽  
pp. 267-275 ◽  
Author(s):  
R. Ioos ◽  
T. Annesi ◽  
C. Fourrier ◽  
C. Saurat ◽  
A. Chandelier ◽  
...  
Keyword(s):  
Test Performance ◽  
Diagnostic Procedures ◽  
Performance Study

scholarly journals Point of care testing using rapid automated antigen testing for SARS-COV-2 in care homes – an exploratory safety, usability and diagnostic agreement evaluation

2021 ◽  
pp. 251604352110542
Author(s):  
Massimo Micocci ◽  
Peter Buckle ◽  
Gail Hayward ◽  
A Joy Allen ◽  
Kerrie Davies ◽  
...  
Keyword(s):  
Test Performance ◽  
Point Of Care ◽  
Care Home ◽  
Immunofluorescence Assay ◽  
Careful Consideration ◽  
Care Homes ◽  
Performance Study ◽  
Post Modification ◽  
Point Of Care Tests ◽  
Positive Agreement

Introduction Successful adoption of POCTs (Point-of-Care tests) for COVID-19 in care homes requires the identification of ideal use cases and a full understanding of the contextual and usability factors that affect test results and minimise biosafety risks. This paper presents a scoping-usability and test performance study of a microfluidic immunofluorescence assay for COVID-19 in care homes. Methods A mixed-methods evaluation was conducted in four UK care homes to scope usability and to assess the agreement with qRT-PCR. A dry run with luminescent dye was conducted to explore biosafety issues. Results The agreement analysis was conducted on 227 asymptomatic participants (159 staff and 68 residents) and 14 symptomatic participants (5 staff and 9 residents). Asymptomatic specimens showed 50% (95% CI:1.3%−98.7%) positive agreement and 96% (95% CI: 92.5%−98.1%) negative agreement with overall prevalence and bias-adjusted Kappa (PABAK) of 0.911 (95% CI: 0.857−0.965). Symptomatic specimens showed 83.3% (95% CI: 35.9%−99.6%) positive agreement and 100% (95% CI: 63.1%−100%) negative agreement with overall prevalence and bias-adjusted Kappa (PABAK) of 0.857 (95% CI: 0.549−1). The dry run highlighted four main sources of contamination that led to the modification of the standard operating procedures. Simulation post-modification showed no further evidence of contamination. Conclusion Careful consideration of biosafety issues and contextual factors associated with care home are mandatory for safe use the POCT. Whilst POCT may have some utility for ruling out COVID-19, further diagnostic accuracy evaluations are needed to promote effective adoption.

scholarly journals Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

2019 ◽  
Author(s):  
Luigi Faino ◽  
Valeria Scala ◽  
Alessio Albanese ◽  
Vanessa Modesti ◽  
Alessandro Grottoli ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Plant Material ◽  
Xylella Fastidiosa ◽  
Infected Plant ◽  
Diagnostic Tools ◽  
Nanopore Sequencing ◽  
Direct Dna Sequencing ◽  
Detection And Identification ◽  
Infected Plant Material

SummaryXylella fastidiosa (Xf) is a polyphagous gram-negative bacterial plant pathogen that can infect more than 300 plant species. It is endemic in America while, in 2013, Xf subsp. pauca was for the first time reported in Europe on olive tree in the Southern Italy. The availability of fast and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf.In this work, we used the Oxford Nanopore Technologies (ONT) device MinION platform for detecting and identifying Xf at species, subspecies and Sequence Type (ST) level straight from infected plant material. The study showed the possibility to detect Xf by direct DNA sequencing and identify the subspecies in highly infected samples. In order to improve sensitivity, Nanopore amplicon sequencing was assessed. Using primers within the set of the seven MLST officially adopted for identifying Xf at type strain level, we developed a workflow consisting in a multiple PCR and an ad hoc pipeline to generate MLST consensus after Nanopore-sequencing of the amplicons. The here-developed combined approach achieved a sensitivity higher than real-time PCR allowing within few hours, the detection and identification of Xf at ST level in infected plant material, also at low level of contamination.Originality Significance StatementIn this work we developed a methodology that allows the detection and identification of Xylella fastidiosa in plant using the Nanopore technology portable device MinION. The approach that we develop resulted more sensitive than methods currently used for detecting X. fastidiosa, like real-time PCR. This approach can be extensively used for X. fastidiosa detection and it may pave the road for the detection of other tedious vascular pathogens.

DNA barcoding as an identification tool for selected EU-regulated plant pests: an international collaborative test performance study among 14 laboratories

EPPO Bulletin ◽  
2013 ◽  
Vol 43 (2) ◽  
pp. 216-228 ◽  
Author(s):  
B. T. L. H. van de Vossenberg ◽  
M. Westenberg ◽  
P. J. M. Bonants
Keyword(s):  
Dna Barcoding ◽  
Test Performance ◽  
Performance Study ◽  
Plant Pests ◽  
Collaborative Test ◽  
International Collaborative ◽  
Identification Tool

Test performance study of isothermal amplification tests for the detection of Grapevine flavescence dorée phytoplasma and ‘ Candidatus Phytoplasma solani’

EPPO Bulletin ◽  
2017 ◽  
Vol 47 (1) ◽  
pp. 18-23 ◽  
Author(s):  
N. Mehle ◽  
P. Kogovšek ◽  
F. Constable ◽  
K. De Jonghe ◽  
M. Loiseau ◽  
...  
Keyword(s):  
Test Performance ◽  
Isothermal Amplification ◽  
Performance Study ◽  
Flavescence Dorée
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