Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
09 11 2021
09 11 2021
Historique:
received:
05
06
2021
accepted:
19
10
2021
entrez:
10
11
2021
pubmed:
11
11
2021
medline:
29
1
2022
Statut:
epublish
Résumé
Pectobacterium parmentieri (formerly Pectobacterium wasabiae), which causes soft rot disease in potatoes, is a newly established species of pectinolytic bacteria within the family Pectobacteriaceae. Despite serious damage caused to the potato industry worldwide, no field-deployable diagnostic tests are available to detect the pathogen in plant samples. In this study, we aimed to develop a reliable, rapid, field-deployable loop-mediated isothermal amplification (LAMP) assay for the specific detection of P. parmentieri. Specific LAMP primers targeting the petF1 gene region, found in P. parmentieri but no other Pectobacterium spp., were designed and validated in silico and in vitro using extensive inclusivity (15 strains of P. parmentieri) and exclusivity (94 strains including all other species in the genus Pectobacterium and host DNA) panels. No false positives or negatives were detected when the assay was tested directly with bacterial colonies, and with infected plant and soil samples. Sensitivity (analytical) assays using serially diluted bacterial cell lysate and purified genomic DNA established the detection limit at 10 CFU/mL and 100 fg (18-20 genome copies), respectively, even in the presence of host crude DNA. Consistent results obtained by multiple users/operators and field tests suggest the assay's applicability to routine diagnostics, seed certification programs, biosecurity, and epidemiological studies.
Identifiants
pubmed: 34753982
doi: 10.1038/s41598-021-01196-4
pii: 10.1038/s41598-021-01196-4
pmc: PMC8578433
doi:
Substances chimiques
DNA, Bacterial
0
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
21948Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM103466
Pays : United States
Organisme : USDA-ARS
ID : 58-2040-9-011
Organisme : National Science Foundation
ID : DBI-1561663
Informations de copyright
© 2021. The Author(s).
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