Development of a loop-mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis.

Genome, Bacterial Micrococcaceae / classification Nucleic Acid Amplification Techniques / methods Sensitivity and Specificity
Clavibacter michiganensis LAMP diagnostics isothermal amplification plant pathogenic bacteria surveillance

Journal

Journal of applied microbiology
ISSN: 1365-2672
Titre abrégé: J Appl Microbiol
Pays: England
ID NLM: 9706280

Informations de publication

Date de publication:
Feb 2019
Historique:
received: 19 07 2018
revised: 03 10 2018
accepted: 05 10 2018
pubmed: 12 10 2018
medline: 5 3 2019
entrez: 12 10 2018
Statut: ppublish

Résumé

Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis. Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples. The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries. The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care.

Identifiants

DOI: 10.1111/jam.14128 PMID: 30307676
pubmed: 30307676
doi: 10.1111/jam.14128
doi:

Banques de données

GENBANK
['MH560478', 'MH560479', 'MH560477', 'MH560480', 'MH560481', 'MH560482', 'MH560483', 'MH560496', 'MH560484', 'MH560485', 'MH560486', 'MH560487', 'MH560488', 'MH56089', 'MH560490', 'MH560491', 'MH560492', 'MH560462', 'MH560463', 'MH560464', 'MH560466', 'MH560467', 'MH560468', 'MH560469', 'MH560471', 'MH560472', 'MH560473', 'MH560493', 'MH560494', 'ZUM3936', 'MH560495', 'MH560497', 'MH560498', 'MH560499', 'MH560500', 'MH560501', 'MH560502', 'MH605380', 'MH605381', 'MH605375', 'MH605382', 'MH547375', 'MH547381', 'MH547376', 'MH547385', 'MH547387', 'MH547382', 'MH547379', 'MH547377', 'MH547378', 'MH605378', 'MH605379', 'MH605376', 'MH605377', 'MH453512', 'MH453511', 'MH453525', 'MH453518', 'MH453533', 'MH453537', 'MH453538', 'MH510046', 'MG847369', 'NC_009480', 'NC_010407', 'NC_020891', 'NC_00439', 'NC_003295']

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

388-401

Subventions

Organisme : USDA National Institute of Food and Agriculture
ID : 9038H
Organisme : National Science Foundation
ID : DBI-1561663

Informations de copyright

© 2018 The Society for Applied Microbiology.

Auteurs

S Dobhal (S)

Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
ORCID: 0000-0001-9946-8348

A Larrea-Sarmiento (A)

Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.

A M Alvarez (AM)

Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.

M Arif (M)

Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
ORCID: 0000-0002-5887-2050

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Development of a loop-mediated isothermal...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Cocci à Gram positif › Micrococcaceae › Development of a loop-mediated isothermal...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Techniques d'amplification d'acides nucléiques › Development of a loop-mediated isothermal...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Sensibilité et spécificité › Development of a loop-mediated isothermal...