scholarly journals Towards on-site testing of Phytophthora species

2015 ◽  
Vol 7 (1) ◽  
pp. 211-217 ◽  
Author(s):  
Lydia Schwenkbier ◽  
Sibyll Pollok ◽  
Stephan König ◽  
Matthias Urban ◽  
Sabine Werres ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Plant Pathogens ◽  
Phytophthora Species ◽  
Site Testing ◽  
Accurate Identification

Rapid detection and accurate identification of plant pathogens in the field is an ongoing challenge.

scholarly journals The Genus Phytophthora (Peronosporales) in Argentina

2020 ◽  
Vol 55 (2) ◽  
pp. 161-193
Author(s):  
Hemilse Elena Palmucci ◽  
Silvia Wolcan
Keyword(s):  
Plant Pathogens ◽  
Phytophthora Species ◽  
Molecular Techniques ◽  
Economic Losses ◽  
Late Nineteenth Century ◽  
Accurate Identification ◽  
Secondary Sources ◽  
Host Pathogen ◽  
The Status ◽  
Scientific Meetings

Background and aims: The genus Phytophthora includes plant pathogens that affect a wide host range and cause severe damage and economic losses. The aim of this study was to achieve a more comprehensive knowledge of Phytophthora in Argentina. To this end, a review was carried out from the first reports in the late nineteenth century until March 2019. M&M: Information was taken from printed and on-line primary and secondary sources such as Proceedings of National and International Scientific Meetings, Bulletins from National Institutions and Universities, periodical Journals, books and data bases, and then analyzed and categorized. Results: The revision allowed updating the status of Phytophthora species recorded in the country, considering their geographical distribution, groups of crops affected, host-pathogen relationships, symptoms and nomenclature changes, as well as presenting a quick and comparative access to different subjects related to these pathogens. The results showed that, to date, 20 Phytophthora spp., one species affinis and one taxon affect 223 host-pathogen relationships in Argentina. The diversity of Phytophthora species in the world suggests that a larger number of species, still not cited, could be present in Argentina. Conclusions: Researchers specialized in the genus Phytophthora, molecular techniques and phylogenetic studies, may allow progressing in the accurate identification of the species and knowledge of their genetic variability.

ANALYTICAL SYSTEMS BASED ON RECOMBINASE POLYMERASE AMPLIFICATION FOR RAPID DETECTION OF VIRAL, VIROID AND BACTERIAL PLANT PATHOGENS

2021 ◽  
Vol 1 (19) ◽  
pp. 242-244
Author(s):  
A.V. Ivanov ◽  
A.V. Zherdev ◽  
B.B. Dzantiev
Keyword(s):  
Potato Virus ◽  
Rapid Detection ◽  
Plant Pathogens ◽  
Potato Virus X ◽  
Potato Spindle Tuber Viroid ◽  
Recombinase Polymerase Amplification ◽  
Analysis Time ◽  
Potato Blackleg ◽  
Test Systems ◽  
Dickeya Solani

Test systems have been developed for the detection of phytopathogens, combining recombinase polymerase amplification and membrane test strips. Test systems provide detection of potato virus X, potato spindle tuber viroid, potato blackleg pathogen (Dickeya solani), as well as multi-analysis of three viruses. Amplification is carried out at 37 °C. The analysis time does n ot exceed 30 min.

scholarly journals Duplex Real-Time PCR Assay for Rapid Detection of Ampicillin-Resistant Enterococcus faecium

2004 ◽  
Vol 48 (2) ◽  
pp. 556-560 ◽  
Author(s):  
Stein Christian Mohn ◽  
Arve Ulvik ◽  
Roland Jureen ◽  
Rob J. L. Willems ◽  
Janetta Top ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Enterococcus Faecium ◽  
Rapid Detection ◽  
Resistant Bacteria ◽  
Pcr Assay ◽  
Culture Methods ◽  
Accurate Identification ◽  
Antibiotic Resistant ◽  
Highly Correlated

ABSTRACT Rapid and accurate identification of carriers of resistant microorganisms is an important aspect of efficient infection control in hospitals. Traditional identification methods of antibiotic-resistant bacteria usually take at least 3 to 4 days after sampling. A duplex real-time PCR assay was developed for rapid detection of ampicillin-resistant Enterococcus faecium (ARE). Primers and probes that are used in this assay specifically detected the d-Ala-d-Ala ligase gene of E. faecium and the modified penicillin-binding protein 5 gene (pbp5) carrying the Glu-to-Val substitution at position 629 (Val-629) in a set of 129 tested E. faecium strains with known pbp5 sequence. Presence of the Val-629 in the strain set from 11 different countries was highly correlated with ampicillin resistance. In a screening of hospitalized patients, the real-time PCR assay yielded a sensitivity and a specificity for the detection of ARE colonization of 95% and 100%, respectively. The results were obtained 4 h after samples were harvested from overnight broth of rectal swab samples, identifying both species and the resistance marker mutation in pbp5. This novel assay reliably identifies ARE 2 to 3 days more quickly than traditional culture methods, thereby increasing laboratory throughput, making it useful for rectal screening of ARE. The assay demonstrates the advantages of real-time PCR for detection of nosocomial pathogens.

scholarly journals Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae

2020 ◽  
Vol 8 (5) ◽  
pp. 653 ◽  
Author(s):  
Jamie McGowan ◽  
Richard O’Hanlon ◽  
Rebecca A. Owens ◽  
David A. Fitzpatrick
Keyword(s):  
Mass Spectrometry ◽  
Plant Pathogens ◽  
Genome Structure ◽  
Draft Genome ◽  
Phytophthora Species ◽  
Comparative Genomic ◽  
Tandem Gene Duplication ◽  
Widespread Species ◽  
Forest Pathogen ◽  
Extracellular Proteome

The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species—Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.

scholarly journals Simple and Portable Magnetic Immunoassay for Rapid Detection and Sensitive Quantification of Plant Viruses

2015 ◽  
Vol 81 (9) ◽  
pp. 3039-3048 ◽  
Author(s):  
Stefanie Rettcher ◽  
Felicitas Jungk ◽  
Christoph Kühn ◽  
Hans-Joachim Krause ◽  
Greta Nölke ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Plant Pathogens ◽  
High Sensitivity ◽  
Potato Virus X ◽  
Plant Viruses ◽  
Economic Losses ◽  
Virus Concentration ◽  
Content Type ◽  
Agricultural Industry ◽  
Sum Frequency

ABSTRACTPlant pathogens cause major economic losses in the agricultural industry because late detection delays the implementation of measures that can prevent their dissemination. Sensitive and robust procedures for the rapid detection of plant pathogens are therefore required to reduce yield losses and the use of expensive, environmentally damaging chemicals. Here we describe a simple and portable system for the rapid detection of viral pathogens in infected plants based on immunofiltration, subsequent magnetic detection, and the quantification of magnetically labeled virus particles.Grapevine fanleaf virus(GFLV) was chosen as a model pathogen. Monoclonal antibodies recognizing the GFLV capsid protein were immobilized onto immunofiltration columns, and the same antibodies were linked to magnetic nanoparticles. GFLV was quantified by immunofiltration with magnetic labeling in a double-antibody sandwich configuration. A magnetic frequency mixing technique, in which a two-frequency magnetic excitation field was used to induce a sum frequency signal in the resonant detection coil, corresponding to the virus concentration within the immunofiltration column, was used for high-sensitivity quantification. We were able to measure GFLV concentrations in the range of 6 ng/ml to 20 μg/ml in less than 30 min. The magnetic immunoassay could also be adapted to detect other plant viruses, includingPotato virus XandTobacco mosaic virus, with detection limits of 2 to 60 ng/ml.

scholarly journals Validation of a Preformulated, Field Deployable, Recombinase Polymerase Amplification Assay for Phytophthora Species

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 466
Author(s):  
Austin G. McCoy ◽  
Timothy D. Miles ◽  
Guillaume J. Bilodeau ◽  
Patrick Woods ◽  
Cheryl Blomquist ◽  
...  
Keyword(s):  
Plant Extract ◽  
Plant Pathogens ◽  
Limit Of Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Phytophthora Species ◽  
Recombinase Polymerase Amplification ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Liquid Form ◽  
Crude Plant Extract

Recombinase polymerase amplification (RPA) assays are valuable molecular diagnostic tools that can detect and identify plant pathogens in the field without time-consuming DNA extractions. Historically, RPA assay reagents were commercially available as a lyophilized pellet in microfuge strip tubes, but have become available in liquid form more recently—both require the addition of primers and probes prior to use, which can be challenging to handle in a field setting. Lyophilization of primers and probes, along with RPA reagents, contained within a single tube limits the risk of contamination, eliminates the need for refrigeration, as the lyophilized reagents are stable at ambient temperatures, and simplifies field use of the assays. This study investigates the potential effect of preformulation on assay performance using a previously validated Phytophthora genus-specific RPA assay, lyophilized with primers and probes included with the RPA reagents. The preformulated lyophilized Phytophthora RPA assay was compared with a quantitative polymerase chain reaction (qPCR) assay and commercially available RPA kits using three qPCR platforms (BioRad CFX96, QuantStudio 6 and Applied Biosystems ViiA7) and one isothermal platform (Axxin T16-ISO RPA), with experiments run in four separate labs. The assay was tested for sensitivity (ranging from 500 to 0.33 pg of DNA) and specificity using purified oomycete DNA, as well as crude extracts of Phytophthora-infected and non-infected plants. The limit of detection (LOD) using purified DNA was 33 pg in the CFX96 and ViiA7 qPCR platforms using the preformulated kits, while the Axxin T16-ISO RPA chamber and the QuantStudio 6 platform could detect down to 3.3 pg with or without added plant extract. The LOD using a crude plant extract for the BioRad CFX96 was 330 pg, whereas the LOD for the ViiA7 system was 33 pg. These trials demonstrate the consistency and uniformity of pathogen detection with preformulated RPA kits for Phytophthora detection when conducted by different labs using different instruments for measuring results.

scholarly journals Fluorescein Isothiocyanate Labeling Antigen-Based Immunoassay Strip for Rapid Detection of Acidovorax citrulli

Plant Disease ◽  
2018 ◽  
Vol 102 (3) ◽  
pp. 527-532 ◽  
Author(s):  
Haijuan Zeng ◽  
Xuzhao Zhai ◽  
Manman Xie ◽  
Qing Liu
Keyword(s):  
Rapid Detection ◽  
Culture Medium ◽  
Plant Pathogens ◽  
Fluorescein Isothiocyanate ◽  
Enzyme Linked Immunosorbent Assay ◽  
Green Fluorescence ◽  
Nitrocellulose Membrane ◽  
Inexpensive Method ◽  
Acidovorax Citrulli ◽  
Field Samples

A simple and fast immunoassay strip to detect Acidovorax citrulli (Ac) using fluorescein isothiocyanate as a marker was developed. Fluorescein isothiocyanate (FITC) was added to sample culture medium for bacteria incubation, and the bacteria could emit a yellow-green fluorescence under ultraviolet light and become a fluorescent probe. This immunofluorescence strip (IFS) was based on the binding between fluorescent bacteria and the unlabeled monoclonal antibody (McAb) immobilized on the test area in nitrocellulose membrane. The detection limit of the strip was 106 CFU/ml with a result that could be observed within 10 min. The IFS could detect eight strains of Ac and display no cross-reactions with 30 other pathogenic strains. The detection results would not be affected by impurities in plant or unknown microorganisms in natural field samples and were consistent with PCR results, indicating that the IFS has high accuracy. This is the first report of using only one unlabeled McAb to develop a direct-type immunofluorescence strip for the rapid detection of Ac. The IFS reduced detection time and simplified operation procedures compared with the traditional enzyme-linked immunosorbent assay (ELISA) and PCR methods. In addition, this simple and inexpensive method will play a significant role in monitoring plant pathogens on field detection.

scholarly journals A Lucid Key to the Common Species of Phytophthora

Plant Disease ◽  
2012 ◽  
Vol 96 (6) ◽  
pp. 897-903 ◽  
Author(s):  
Jean Beagle Ristaino
Keyword(s):  
Plant Pathogens ◽  
Common Species ◽  
Morphological Characters ◽  
Phytophthora Species ◽  
Molecular Characteristics ◽  
Character State ◽  
Disease Symptoms ◽  
Fact Sheet ◽  
The Common ◽  
Simple Search

The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 features are used to make a correct species identification. Once a culture is obtained, the user enters responses to known character state options into Lucid Player, and the correct species is identified. Illustrations of each character state for a feature are included in the key. The main morphological features included in the key are: asexual structures, sexual structures, and chlamydospore, hyphae, and cultural characteristics. The user can read an illustrated “Fact Sheet” on each species that includes pictures of morphological characters, disease symptoms, host range, and relevant references. A cross-linked glossary of terminology is included in each fact sheet. In addition, a DNA search function that contains a simple search of internal transcribed spacer (ITS) and Barcode of Life (BOL, 5′ end of the cox 1 gene) sequences for each species can be queried. The key was created to provide teachers, diagnosticians, and regulatory personnel with easily accessible tools to distinguish common species in the genus Phytophthora based on a number of important morphological and molecular characteristics. The key is available for purchase from APS Press and should provide another useful tool for the identification of members of this destructive group of Oomycete plant pathogens.

scholarly journals Clinical and mycological characteristics of keratitis caused by Colletotrichum gloeosporioides: A case report and review of literature

2021 ◽  
Vol 15 (02) ◽  
pp. 301-305
Author(s):  
Alireza Izadi ◽  
Mohammad Soleimani ◽  
Roshanak Daie Ghazvini ◽  
Seyed Jamal Hashemi ◽  
Mohssen Gramishoar ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Plant Pathogens ◽  
Colletotrichum Gloeosporioides ◽  
Morphological Characteristics ◽  
Fungal Keratitis ◽  
Slit Lamp ◽  
Review Of Literature ◽  
Internal Transcribed Spacer Region ◽  
Accurate Identification ◽  
Case Presentation

Introduction: Colletotrichum species are well-known plant pathogens, which have been increasingly reported as the cause of keratitis or subcutaneous lesions in humans. In this study we reported a rare case of fungal keratitis from Iran and reviewed the literature. Case Presentation: A 69-year-old man whose right eye was injured by herbal material was examined by slit-lamp biomicroscopy and mycology investigation of corneal scrapings was done. The grown filamentous fungal was identified as Colletotrichum gloeosporioides based on morphological characteristics and DNA sequence of the internal transcribed spacer region. The isolated strain was sensitive to amphotericin B, caspofungin, anidolafungin, micafungin, voriconazole, and relatively resistant to fluconazole, and itraconazole. Patient was successfully treated with voriconazole. Conclusions: This report highlights that the early and accurate identification and therapy can helpful to management keratitis caused by C. gloeosporioides.

scholarly journals Rapid Detection of Babesia motasi Responsible for Human Babesiosis by Cross-priming Amplification combined with a vertical flow

2020 ◽  
Author(s):  
Jinming Wang ◽  
Shandian Gao ◽  
Shangdi Zhang ◽  
Xin He ◽  
Junlong Liu ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Clinical Performance ◽  
Clinical Care ◽  
Epidemiological Studies ◽  
Gansu Province ◽  
Molecular Diagnostic ◽  
Rrna Gene ◽  
Vertical Flow ◽  
Accurate Identification ◽  
Human Babesiosis

Abstract Background: Babesia motasi is known as an etiological agent of human and ovine babesiosis. Diagnosis of babesiosis is traditionally performed by microscopy, examining Giemsa-stained thin peripheral blood smears. Rapid detection and accurate identification of species are desirable for clinical care and epidemiological studies. Methods: An easy to operate molecular method, which requires less capital equipment and incorporates cross priming amplification combined with a vertical flow (CPA-VF) visualization strip for rapid detection and identification of B. motasi. Results: The CPA-VF targets the 18S rRNA gene and has a detection limit of 50 fg per reaction; no cross reaction was observed with other piroplasms infective to sheep or Babesia infective to humans. CPA-VF and real-time (RT)-PCR had sensitivities of 95.2% (95% confidence interval [CI], 78.1-99.4%) and 90.5% (72-97.6%) and specificities of 95.8 (80.5-99.5%) and 97.9 (83.5-99.9%), respectively, versus microscopy and nested (n) PCR combined with gene sequencing. The clinical performance of the CPA-VF assay was evaluated with field blood samples from sheep (n = 240) in Jintai county, Gansu Province, and clinical specimens (n = 492) obtained from patients bitten by ticks. Conclusions: Our results indicate that the CPA-VF is a rapid, accurate, nearly instrument-free molecular diagnostic approach for identification of B. motasi. Therefore, it could be an alternative technique for epidemiological investigations and diagnoses of ovine and/or human babesiosis caused by B. motasi, especially in resource-limited regions.Keywords: Ovine babesiosis, human babesiosis, Babesia motasi, cross priming amplification, vertical flow visualization strip, detection, identification

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