Fast and specific detection of the invasive forest pathogen Heterobasidion irregulare through a Loop-mediated isothermal AMPlification (LAMP) assay

2017 ◽  
Vol 48 (2) ◽  
pp. e12396 ◽  
Author(s):  
F. Sillo ◽  
L. Giordano ◽  
P. Gonthier
Keyword(s):  
Lamp Assay ◽  
Isothermal Amplification ◽  
Specific Detection ◽  
Loop Mediated Isothermal Amplification ◽  
Forest Pathogen ◽  
Heterobasidion Irregulare

scholarly journals A Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid and Specific Detection of Airborne Inoculum of Uromyces betae (Sugar Beet Rust)

Plant Disease ◽  
2019 ◽  
Vol 103 (3) ◽  
pp. 417-421 ◽  
Author(s):  
Agata M. Kaczmarek ◽  
Kevin M. King ◽  
Jonathan S. West ◽  
Mark Stevens ◽  
Debbie Sparkes ◽  
...  
Keyword(s):  
United Kingdom ◽  
Sugar Beet ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Specific Detection ◽  
Rust Disease ◽  
Loop Mediated Isothermal Amplification ◽  
The United Kingdom ◽  
Uromyces Betae ◽  
Forecasting System

Sugar beet rust disease (causal agent Uromyces betae) represents a serious threat to worldwide sugar beet (Beta vulgaris) crops, causing yield losses of up to 10% in the United Kingdom. Currently, the disease is managed mainly by application of fungicides after rust disease symptoms appear. Development of a future forecasting system, incorporating data on environmental factors and U. betae inoculum levels, would enable better disease control by more targeted application of fungicides. In this study, we developed a first molecular diagnostic, targeted to cytochrome b DNA sequences and based on loop-mediated isothermal amplification (LAMP) technology, for rapid (<30 min) and specific detection of U. betae. The new assay only detected U. betae strains (collected from across eastern England, the main sugar beet growing region in the United Kingdom) and Denmark; it did not detect other closely related pathogens (e.g., Puccinia sp., U. fabae) or others that are commonly found on sugar beet (Cercospora beticola, Erysiphe betae, Ramularia beticola). The assay could consistently detect down to small amounts of U. betae DNA (10 pg). Application of the new LAMP diagnostic to air spore tape samples collected between mid-June and mid-September from a single U.K. sugar beet field site revealed differences in temporal patterns of pathogen inoculum between the 2015 and 2016 seasons. The described LAMP assay could now be used as a component of a future automated inoculum-based forecasting system, enabling more targeted control of sugar beet rust disease.

scholarly journals Genome-informed loop-mediated isothermal amplification assay for specific detection of Pectobacterium parmentieri in infected potato tissues and soil

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryan Domingo ◽  
Cristian Perez ◽  
Diksha Klair ◽  
Huong Vu ◽  
Alika Candelario-Tochiki ◽  
...  
Keyword(s):  
Infected Plant ◽  
Field Tests ◽  
Lamp Assay ◽  
Soft Rot ◽  
Epidemiological Studies ◽  
Potato Industry ◽  
Isothermal Amplification ◽  
Specific Detection ◽  
Loop Mediated Isothermal Amplification

AbstractPectobacterium 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.

Species-specific detection of medically important aspergilli by a loop-mediated isothermal amplification method in chronic pulmonary aspergillosis

2019 ◽  
Vol 57 (6) ◽  
pp. 703-709
Author(s):  
Kazuya Tone ◽  
Junko Suzuki ◽  
Mohamed Mahdi Alshahni ◽  
Kazuyoshi Kuwano ◽  
Koichi Makimura
Keyword(s):  
Sensitivity And Specificity ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Lamp Method ◽  
Specific Detection ◽  
Pulmonary Aspergillosis ◽  
Loop Mediated Isothermal Amplification ◽  
Group A ◽  
Chronic Pulmonary Aspergillosis ◽  
Species Specific

AbstractChronic pulmonary aspergillosis (CPA) is a common subtype of pulmonary aspergillosis and a life-threatening disease. However, its diagnosis remains difficult due to the lack of specific clinical features and radiologic findings, as well as the difficulty of isolating Aspergillus spp. We developed a novel species-specific detection method of medically important aspergilli using a loop-mediated isothermal amplification (LAMP) for CPA. Specific LAMP primer sets for Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, and Aspergillus nidulans were designed. The use of the LAMP assay was validated using respiratory specimens (CPA cases, n = 21; nonaspergillosis cases, n = 23). A total of 15 cases were positive in the CPA group (A. fumigatus, n = 5; A. flavus, n = 1; A. niger, n = 1; A. terreus, n = 7; A. nidulans, n = 1), but only three in the non-CPA group (A. niger, n = 2; A. terreus n = 1). The sensitivity and specificity of the diagnosis of CPA by the LAMP system were 71.4% and 87.0%, respectively. In conclusion, we developed a species-specific detection approach for five medically important aspergilli using the LAMP method. The system showed high sensitivity and specificity for diagnosis of CPA.

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