Development and application of a LAMP method for rapid detection of apple blotch caused by Marssonina coronaria

2021 ◽  
Vol 141 ◽  
pp. 105452
Author(s):  
Weichao Ren ◽  
Na Liu ◽  
Baohua Li
Keyword(s):  
Rapid Detection ◽  
Lamp Method ◽  
Marssonina Coronaria

Rapid Detection of Mycoplasma pneumoniae by Loop-Mediated Isothermal Amplification (LAMP) in Clinical Respiratory Specimens

2019 ◽  
Author(s):  
Maryam ARFAATABAR ◽  
Narjes NOORI GOODARZI ◽  
Davoud AFSHAR ◽  
Hamed MEMARIANI ◽  
Ghasem AZIMI ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Rapid Detection ◽  
Lamp Assay ◽  
Culture Method ◽  
Isothermal Amplification ◽  
Lamp Method ◽  
Culture Methods ◽  
Loop Mediated Isothermal Amplification ◽  
Specificity And Sensitivity ◽  
Respiratory Specimens

  Background: Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP) worldwide, especially among children and debilitated populations. The present study aimed to investigate a loop-mediated isothermal amplification (LAMP) technique for rapid detection of M. pneumoniae in clini-cal specimens collected from patients with pneumonia. Methods: Throat swabs were collected from 110 outpatients who suffered from pneumonia. Throat swab samples were obtained from patients referred to the hospital outpatient clinics of Tehran University hospitals, Iran in 2017. The presence of M. pneumoniae in the clinical specimens was evaluated by LAMP, PCR and culture methods. Sensitivity and specificity of the LAMP and PCR assays were also determined. Results: Out of 110 specimens, LAMP assay detected M. pneumoniae in 35 specimens. Detection limit of the LAMP assay was determined to be 33fg /μL or ~ 40 genome copies/reaction. Moreover, no cross-reaction with genomic DNA from other bacteria was observed. Only 25 specimens were positive by the culture method. The congruence between LAMP assay and culture method was ‘substantial’ (κ=0.77). Specificity and sensitivity of LAMP assay were 88.2%, 100% in compare with culture. However, the con-gruence between LAMP assay and PCR assay was ‘almost perfect’ (κ=0.86). Specificity and sensitivity of LAMP assay were 92.5%, 100% in compare with PCR. Conclusion: Overall, the LAMP assay is a rapid and cost-efficient laboratory test in comparison to other methods including PCR and culture. Therefore, the LAMP method can be applied in identification of M. pneumoniae isolates in respiratory specimens.

scholarly journals Loop-Mediated Isothermal Amplification (LAMP) Method for Rapid Detection of Trypanosoma brucei rhodesiense

2008 ◽  
Vol 2 (2) ◽  
pp. e147 ◽  
Author(s):  
Zablon Kithinji Njiru ◽  
Andrew Stanislaw John Mikosza ◽  
Tanya Armstrong ◽  
John Charles Enyaru ◽  
Joseph Mathu Ndung'u ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Rapid Detection ◽  
Isothermal Amplification ◽  
Lamp Method ◽  
Trypanosoma Brucei Rhodesiense ◽  
Loop Mediated Isothermal Amplification

scholarly journals Establishment of a Rapid Detection Method for Rice Blast Fungus Based on One-Step Loop-Mediated Isothermal Amplification (LAMP)

Plant Disease ◽  
2019 ◽  
Vol 103 (8) ◽  
pp. 1967-1973 ◽  
Author(s):  
Ling Li ◽  
Shu Ya Zhang ◽  
Chuan-Qing Zhang
Keyword(s):  
Rapid Detection ◽  
Rice Blast ◽  
Detection System ◽  
Fungal Spores ◽  
Lamp Assay ◽  
Rice Blast Fungus ◽  
Isothermal Amplification ◽  
Lamp Method ◽  
Loop Mediated Isothermal Amplification ◽  
Blast Fungus

Rice blast is one of the most serious diseases for rice, and controlling the filamentous fungus Magnaporthe oryzae that causes rice blast is crucial for global food security. Typically, early infected rice does not show symptoms. Therefore, the early diagnosis of rice blast is particularly important to avoid uncontrollable propagation of rice blast fungus. In the present work, a rapid and efficient loop-mediated isothermal amplification (LAMP) method was developed to detect the pathogen at the early infected stage of rice. The Alb1 superfamily hypothetical protein MGG_04322, a nuclear shuttling factor involved in ribosome and melanin biogenesis, was chosen as the target for designing the LAMP primers. The LAMP assay enabled rapid detection of as little as 10 pg of pure genomic DNA of M. oryzae. In addition, we established the quantitative LAMP (q-LAMP) detection system to quantify the conidia of rice blast fungus. The q-LAMP assay enabled rapid detection (within 35 min) of the fungal spores at a sensitivity of 3.2 spores/ml. In addition, the assay sets up the linearization formula of the standard curve as y = 0.3066 + 15.33x (where x = amplification of time), inferring that spore number = 100.60y. In addition, the q-LAMP assay was successfully used to detect the presence of the virulence strains of M. oryzae (wild type) in comparison with that of the two mutant strains by quantifying the biomass within host tissue. These results provide a useful and convenient tool for detecting M. oryzae that could be applied in the incubation period of rice blast before symptoms appear.

scholarly journals Sensitive and Rapid Detection of Koi Herpesvirus by LAMP Method

2006 ◽  
Vol 41 (1) ◽  
pp. 19-27 ◽  
Author(s):  
Manabu Yoshino ◽  
Hajime Watari ◽  
Tadashi Kojima ◽  
Masanari Ikedo
Keyword(s):  
Rapid Detection ◽  
Lamp Method ◽  
Koi Herpesvirus

Development and Application of a Novel Nucleic Amplification Kit on Rapid Detection of Various Types of Staphylococci Strains

2014 ◽  
Vol 618 ◽  
pp. 288-292
Author(s):  
Yang Deng ◽  
Yan Rui Liang ◽  
Lin Li ◽  
Bing Li ◽  
Jian Yu Su
Keyword(s):  
Antibiotic Resistance ◽  
Predictive Value ◽  
Rapid Detection ◽  
Detection Rate ◽  
Lamp Method ◽  
Gram Negative ◽  
Optimal Reaction Condition ◽  
Optimal Reaction ◽  
Reference Strains ◽  
Antibiotic Resistance Determinant

A loop-mediated isothermal amplification (LAMP) method for rapid detection of various staphylococci strains and associated antibiotic resistance determinant had been developed and evaluated in this study. Six primers, including outer primers, inner primers and loop primers, were specially designed for recognizing eight distinct sequences on four targets: 16Sr RNA,femA,mecA, andorfX. Twenty-seven reference strains, including various species of gram-negative and-positive isolates, were included in this study to evaluate and optimize LAMP assays. The optimal reaction condition was found to be 65°C for 45 min, with detection limits at 100 fg DNA/tube and 10 CFU/reaction for 16S rRNA, 100 fg DNA/tube and 10 CFU/reaction forfemA, 1 pg DNA/tube and 100 CFU/reaction formecA, 10 DNA/tube and 10 CFU/reaction fororfX, respectively. Application of LAMP assays were performed on 166 various types of staphylococci isolates, the detection rate of LAMP assays for the 16Sr RNA,femA,mecA, andorfXwas 100% (166/166), 98.5% (64/65), 94.3% (66/70), and 98.6% (69/70) and the negative predictive value (NPV) was 100%, 98.1%, 92.3%, and 92.7% respectively; with a 100% positive predictive value (PPV) for all three targets. In conclusion, LAMP assays were demonstrated to be useful and powerful tools for rapid detection of various staphylococci strains.

scholarly journals Rapid Detection of Cercospora beticola in Sugar Beet and Mutations Associated with Fungicide Resistance Using LAMP or Probe-Based qPCR

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1654-1661 ◽  
Author(s):  
Subidhya Shrestha ◽  
Jonathan Neubauer ◽  
Rebecca Spanner ◽  
Mari Natwick ◽  
Joshua Rios ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Fungicide Resistance ◽  
Rapid Detection ◽  
Lamp Assay ◽  
Qpcr Assay ◽  
Cercospora Beticola ◽  
Lamp Method ◽  
In Planta ◽  
Cercospora Leaf Spot

Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is the most destructive disease of sugar beet worldwide. Although growing CLS-tolerant varieties is helpful, disease management currently requires timely application of fungicides. However, overreliance on fungicides has led to the emergence of fungicide resistance in many C. beticola populations, resulting in multiple epidemics in recent years. Therefore, this study focused on developing a fungicide resistance detection “toolbox” for early detection of C. beticola in sugar beet leaves and mutations associated with different fungicides in the pathogen population. A loop-mediated isothermal amplification (LAMP) method was developed for rapid detection of C. beticola in infected sugar beet leaves. The LAMP primers specific to C. beticola (Cb-LAMP) assay was able to detect C. beticola in inoculated sugar beet leaves as early as 1 day postinoculation. A quinone outside inhibitor (QoI)-LAMP assay was also developed to detect the G143A mutation in cytochrome b associated with QoI resistance in C. beticola. The assay detected the mutation in C. beticola both in vitro and in planta with 100% accuracy. We also developed a probe-based quantitative PCR (qPCR) assay for detecting an E198A mutation in β-tubulin associated with benzimidazole resistance and a probe-based qPCR assay for detection of mutations in cytochrome P450-dependent sterol 14α-demethylase (Cyp51) associated with resistance to sterol demethylation inhibitor fungicides. The primers and probes used in the assay were highly efficient and precise in differentiating the corresponding fungicide-resistant mutants from sensitive wild-type isolates.

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