• Mycobiology
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• 제31권4호
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• pp.196-199
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• 2003

A very reliable and specific method for the identification of fungi in ectotrophic mycorrhizal symbiosis was developed using a specific PCR assay based on the amplification of the ITS1 region. To obtain specific data, an ITS-diagnostic assay was carried out that reveals genera and species specific sequences. Here, an application of one method is presented, which covers the identification of pure mycelia, basidiocarps as well as mixed samples such as ectomycorrhizal roots that were mingled with remains of the host plant. For this purpose a protocol was established that allowed the extraction of DNA from single mycorrhizal roots. In order to perform a specific ITS analysis we generated a new ITS-primer(ITS8) by a multiple alignment of five different genera and species of mycorrhizal fungi. The utilization of ITS1 and ITS8 resulted in specific PCR amplicons, which were characterized by sequencing without purification steps, even when the template DNA was associated with roots.

• 식물병연구
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• 제27권1호
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• pp.38-44
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• 2021

Xylella fastidiosa is the most damaging pathogen in many parts of the world. To increase diagnostic capability of X. fastidiosa in the field, the loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assay were developed to mqsA gene of citrate-synthase (XF 1535) X. fastidiosa and evaluated for specificity and sensitivity. Both assays were more robust than current published tests for detection of X. fastidiosa when screened against 16 isolates representing the four major subgroups of the bacterium from a range of host species. No cross reaction with DNA from healthy hosts or other species of bacteria has been observed. The LAMP and PCR assays could detect 10-4 pmol and 100 copies of the gene, respectively. Hydroxynaphthol blue was evaluated as an endpoint detection method for LAMP. There was a significant color shift that signaled the existence of the bacterium when at least 100 copies of the target template were present.

• Journal of Veterinary Science
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• 제21권5호
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• pp.71.1-71.10
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• 2020

Background: Feline calicivirus (FCV) is a major and highly infectious pathogen in cats worldwide. However, there have been limited studies about the status of FCV infections in Korea. Objectives: To investigate the current status of FCV infections in stray cats in Korea. Methods: A novel reverse transcription polymerase chain reaction (RT-PCR) assay was developed based on the conserved nucleotide sequences of reported FCV strains. Field swab samples were collected from 122 cats (2 hospital admitted cats and 120 stray cats) in 2016 and 2017. All the samples were tested by virus isolation and 2 different RT-PCRs, including the novel RT-PCR, for the detection of FCV. Results: The novel RT-PCR assay showed no cross-reactivity to the nucleic acids of the other feline pathogens tested, and the limit of detection was calculated as 10⁰ TCID₅₀/mL based on an in vitro assessment. The novel RT-PCR assay detected 5 positive samples from the 122 field samples, which showed perfect agreement with the results of the virus isolation method. In contrast, another RT-PCR assay used in a previous study in Korea detected no positive samples. The prevalence of FCV infection in stray cats was 2.5% (3/120) based on the results of virus isolation and the novel RT-PCR assays. Conclusions: The current study is the first report of the detection and prevalence of FCV in stray cats in Korea. The novel RT-PCR assay developed in this study showed high sensitivity and specificity, which indicates a useful diagnostic assay to identify FCV infection in cats.

• 농업과학연구
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• 제47권1호
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• pp.173-182
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• 2020

Human Astrovirus (HuAstV), known as a waterborne virus, is a group IV positive-sense single-stranded RNA that belongs to Astroviridae. The first outbreak of HuAstV was reported in England in 1975. HuAstV can exist not only among clinical patients but also in various water environments, such as water for agriculture and vegetables. For diagnosis of HuAstV from water samples, a polymerase chain reaction (PCR) system has been developed. However, the PCR-based diagnostic method has problems in field application, such as reaction time, sensitivity and specificity. For this reason, in this study we developed the loop-mediated isothermal amplification assay (LAMP) system, aimed specifically at HuAstV. Three prepared LAMP primer sets were tested by specificity, non-specificity and sensitivity; one LAMP primer set was selected with optimum reaction temperature. The developed LAMP primer set reaction conditions were confirmed at 62℃, and detection sensitivity was 1 fg/μL. In addition, restriction enzyme HaeIII (GG/CC) was introduced to confirm that the LAMP reaction was positive. As a result, selected LAMP primer set was 100 - 1000 times more specific, rapid, and sensitive than conventional-nested PCR methods. For verification of the developed LAMP assay, twenty samples of cDNA from groundwater samples were tested. We expect that the developed LAMP assay will be used to diagnose HuAstV from various samples.

• 대한의생명과학회지
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• 제25권4호
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• pp.426-430
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• 2019

Currently, molecular diagnostic assays based on nucleic acid amplification tests have been shown to effectively detect mycobacterial infections in various types of specimen, however, variable sensitivity was shown in FFPE samples according to the kind of commercial kit used. The present study therefore used automated PCR-reverse blot hybridization assay (REBA) system, REBA Myco-ID HybREAD 480^®, for the rapid identification of Mycobacterium species in various types of human tissue and compared the conventional one-tube nested-PCR assay for detecting Mycobacterium tuberculosis (MTB). In conventional nested-PCR tests, 25 samples (48%) were MTB positive and 27 samples (52%) were negative. In contrast, when conducted PCR-REBA assay, 11 samples (21%) were MTB positive, 20 samples (39%) were NTM positive, 8 samples (15%) were MTB-NTM double positive, and 13 samples (25%) were negative. To determine the accuracy and reliability of the two molecular diagnostic tests, the one-tube nested-PCR and PCR-REBA assays, were compared with histopathological diagnosis in discordant samples. When conducted nested-PCR assay, 10 samples (59%) were MTB positive and seven samples (41%) were negative. In contrast, when conducted PCR-REBA test, three samples (17%) were MTB positive, 10 samples (59%) were NTM positive and four samples (24%) were negative. In conclusion, the automated PCR-REBA system proved useful to identify Mycobacterium species more rapidly and with higher sensitivity and specificity than the conventional molecular assay, one-tube nested-PCR; it might therefore be the most suitable tool for identifying Mycobacterium species in various types of human tissue for precise and accurate diagnosis of mycobacterial infection.

• 한국미생물·생명공학회지
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• 제45권4호
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• pp.358-364
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• 2017

Asymmetric PCR preferentially amplifies one DNA strand for use in DNA hybridization studies. Linear-After-The-Exponential-PCR (LATE-PCR) is an advanced asymmetric PCR method which uses innovatively designed primers at different concentrations. This study aimed to optimise LATE-PCR parameters to produce single-stranded DNA of Candida spp. and Aspergillus spp. for detection via probe hybridisation. The internal transcribed spacer (ITS) region was used to design limiting primer and excess primer for LATE-PCR. Primer annealing and melting temperature, difference of melting temperature between limiting and excess primer and concentration of primers were optimized. In order to confirm the presence of single-stranded DNA, the LATE-PCR product was hybridised with digoxigenin labeled complementary oligonucleotide probe specific for each fungal genus and detected using anti-digoxigenin antibody by dot blotting. Important parameters that determine the production of single-stranded DNA in a LATE-PCR reaction are difference of melting temperature between the limiting and excess primer of at least $5^{\circ}C$ and primer concentration ratio of excess primer to limiting primer at 20:1. LATE-PCR products of Candida albicans, Candida parapsilosis, Candida tropicalis and Aspergillus terreus at up to 1:100 dilution and after 1 h hybridization time, successfully hybridised to respective oligonucleotide probes with no cross reactivity observed between each fungal genus probe and non-target products. For Aspergillus fumigatus, LATE-PCR products were detected at 1:10 dilution and after overnight hybridisation. These results indicate high detection sensitivity for single-stranded DNA produced by LATE-PCR. In conclusion, this advancement of PCR may be utilised to detect fungal pathogens which can aid the diagnosis of invasive fungal disease.

• 대한수의학회지
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• 제43권3호
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• pp.471-476
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• 2003

Malignant catarrhal fever (MCF) is a systemic disease of ruminants caused by ovine herpesvirus 2 (OvHV-2). OvHV-2 is a gamma herpesvirus, which induces frequent latent infection and often difficult to detect its antigens and even specific nucleic acids because of its low viral copies in the infected tissues. Histopathology, serology and polymerase chain reaction (PCR) were compared for the diagnosis of MCF using 10 bison infected with OvHV-2. Histopathological diagnosis was performed using the criteria which was based upon the pathognomic lesions. Serological diagnosis was conducted using its serum with competitive ELISA for the detection of antibodies of OvHV-2. Also, the nest PCR was performed with peripheral blood leukocytes for the detection of OvHV-2-specific DNAs. Primers 556 and 775 were used for the primary amplification, and primers 556 and 555 were used for the secondary amplification. As the results, positive cases were 6 by histopahology, 9 by serology and 10 by PCR. As comparing with other diagnostic methods, PCR was found to be more sensitive than histopathology and serology. The recent development of molecular diagnostic assays has provided powerful tools for investigating how viruses survive in nature. Development of PCR specific for viruses has dramatically improved the accuracy of diagnosis of viruses in clinically infected animals. Furthermore, amplification of viral genomic material by nest PCR represents the most sensitive method for the detection of viruses and might be detected successfully even though very low viral DNA copies. So, it could be used as the first choice for the detection of viral DNAs with low copies such as the status of latent infection. However, it has also some limitation of application like as false negative results by PCR inhibitors and false positive results by contamination. The results of this study suggest that the use of molecular biological methods like PCR may increase the accuracy for the diagnosis of infectious diseases. However, in diagnostic laboratory, it is recommended that PCR assay must be conducted with other diagnostic methods for more reliable diagnosis.

• 한국임상수의학회지
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• 제24권2호
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• pp.77-81
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• 2007

본 연구는 개에서 심장사상충을 검출하기 위하여 표준검사를 적용하지 않은 상황에서 중합연쇄반응검사 (PCR)의 진단 능력을 평가하였다. 효소면역검사법 (ELISA)과 PCR 검사를 동시에 사용한 경우 PCR 검사의 민감도와 특이도는 두 검사의 조건부 독립을 가정한 상태에서expectation-maximization (EM) 알고리즘을 이용한 최대우도법과 Bayesian 기법으로 두 집단 검사 모형으로 분석하였다 2002-2004년 기간 중 심장사상충검사 결과를 기록한 의무기록에서 무작위로 266개 결과를 추출하여 133개씩 2회의 시험으로 배치하였다. 2회의 분석결과를 종합할 때 EM 알고리즘에서 PCR 검사의 민감도와 특이도는 각각 96.4-96.7%와 97.6-98.8%, Bayesian기법에서는 94.4-94.8h와 97.1-98%로 추정되었다. PCR 검사는 심장사상충을 스크리닝하는 도구로 유용하며, 표준검사를 적용하지 않은 상황에서 진단검사의 특성을 추론하는 방법으로 Bayesian 기법은 매우 유용함을 확인하였다.

• 한국초지조사료학회지
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• 제42권3호
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• pp.201-207
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• 2022

Fescues, which are widely cultivated as grasses and forages around the world, are often naturally infected with the endophyte, Epichloë. This fungus, transmitted through seeds, imparts resistance to drying and herbivorous insects in its host without causing any external damage, thereby contributing to the adaptation of the host to the environment and maintaining a symbiosis. However, some endophytes, such as E. coenophialum synthesize ergovaline or lolitrem B, which accumulate in the plant and impart anti-mammalian properties. For example, when livestock consume excessive amounts of grass containing toxic endophytes, problems associated with neuromuscular abnormalities, such as convulsions, paralysis, high fever, decreased milk production, reproductive disorders, and even death, can occur. Therefore, pre-inoculation with non-toxic endogenous fungi or management with endophyte-free grass is important in preventing damage to livestock and producing high-quality forage. To date, the diagnosis of endophytes has been mainly performed by observation under a microscope following staining, or by performing an immune blot assay using a monoclonal antibody. Recently, the polymerase chain reaction (PCR)-based molecular diagnostic method is gaining importance in the fields of agriculture, livestock, and healthcare given the method's advantages. These include faster results, with greater accuracy and sensitivity than those obtained using conventional diagnostic methods. For the diagnosis of endophytes, the nested PCR method is the only available option developed; however, it is limited by the fact that the level of toxic alkaloid synthesis cannot be estimated. Therefore, in this study, we aimed to develop a triplex real-time PCR diagnostic method that can determine the presence or absence of endophyte infection using DNA extracted from seeds within 1 h, while simultaneously detecting easD and LtmC genes, which are related to toxic alkaloid synthesis. This new method was then also applied to real field samples.

• Journal of Microbiology and Biotechnology
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• 제19권11호
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• pp.1464-1469
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• 2009

To achieve more accurate and rapid detection of macrolide-lincosamide-streptogramin B resistance genes, erm(A), erm(B), and erm(C), we developed a TaqMan probe-based real-time PCR (Q-PCR) method and compared it with conventional PCR (C-PCR), which is the most widely using erm gene identification method. The detection limit of Q-PCR was 5 fg of genomic DNA or 5-8 CFU of bacterial cells of Staphylococcus aureus. The utilization of Q-PCR might shorten the time to erm detection from 3-4 h to about 50 min. These data indicated that Q-PCR assay appears to be not only highly sensitive and specific, but also the most rapid diagnostic method. Therefore, the appropriate application of the Q-PCR assay will permit rapid and accurate identification of erm genes from clinical and other samples.