• Food Science of Animal Resources
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• v.34 no.5
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• pp.665-673
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• 2014

We compared standard culture methods as well as conventional PCR and real-time PCR for the detection of Listeria monocytogenes (L. monocytogenes) in milk, cheese, fresh-cut vegetables, and raw beef that have different levels of background microflora. No statistical differences were observed in sensitivity between the two selective media in all foods. In total, real-time PCR assay exhibited statistically excellent detection sensitivity (p<0.05) and was less time consuming and laborious as compared with standard culture methods. Conventional culture methods showed poor performance in detecting L. monocytogenes in food with high levels of background microflora, generating numerous false negative results. While the detection of L. monocytogenes in fresh cut vegetable by culture methods was hindered only by L. innocua, various background microflora, such as L. innocua, L. welshimeri, L. grayi, and Enterococcus faecalis appeared on the two selective media as presumptive positive colonies in raw beef indicating the necessity of improvement of current selective media. It appears that real-time PCR is an effective and sensitive presumptive screening tool for L. monocytogenes in various types of foods, especially foods samples with high levels of background microflora, thus complementing standard culture methodologies.

• Journal of Food Hygiene and Safety
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• v.34 no.6
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• pp.557-561
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• 2019

This study investigated the efficacy of DNA extraction methods for real-time PCR detection of foodborne pathogenic bacteria in livestock manure composts. Livestock manure composts were inoculated with Escherichia coli O157:H7, Salmonella Typhimurium, Listeria monocytogenes, Bacillus cereus and incubated in enrichment broth. For DNA extraction, enriched samples were treated following boiling method, by chloroform, C₁₈ powder, and proteinase K. As a result, 4 species of bacteria were detected by real-time PCR when subjected to boiling for 30 min and treated with proteinase K. These results suggest that detection of foodborne pathogens by real-time PCR from livestock manure composts could be applicable using effective DNA extraction methodology such as the boiling method or proteinase K.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.25-32
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• 2019

Influenza A (H1N1) virus caused a worldwide pandemic in 2009-2010 and still remains in seasonal circulation. Continuous surveillance activities are encouraged in the post pandemic phase to watch over the trend of occurrence every year, this is better to be done by a rapid and sensitive method for its detection. This study was conducted to detect proportions of occurrence of influenza A virus (H1N1) in patients with influenza-like illness. Samples from 500 patients with influenza or influenza-like clinical presentation were tested by real-time reverse transcription polymerase chain reaction (RT-PCR) and virus tissue culture. Among the total 500 participants, 193 (38.6%) were females and 307 (61.4%) males. Seventy-one patients (14.2%) were positive for H1N1 virus infection with real-time RT-PCR while 52 (10.4%) were positive by tissue culture. Non-statistically significant relation was found between age and gender with the positivity of H1N1. Sensitivity and specificity of real-time RT-PCR was 98.08% and 95.54%, respectively, in comparison to virus isolation with accuracy 95.8%. This study showed that H1N1 virus was responsible for a good proportion of influenza during the post-pandemic period. Real-time RT-PCR provides rapidity and sensitivity for the detection of influenza A virus (H1N1) compared with virus isolation and thus it is recommended as a diagnostic tool.

• Journal of Dairy Science and Biotechnology
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• v.31 no.2
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• pp.127-131
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• 2013

The aim of this study was to investigate adulteration of caprine milk products by bovine milk using biomolecular techniques with bovine-specific primers for the mitochondrial cytochrome b gene. Polymerase chain reaction (PCR) and real-time PCR assays were applied to caprine milk products including infant formula, city milk, and fermented milk. The results indicated that six out of the eight caprine infant formula products tested contained bovine milk components. In addition, two of the three tested caprine city milk products and two caprine fermented milk products were shown to be adulterated with bovine milk. Conventional PCR results corroborated with results obtained by real-time PCR. This study demonstrates that DNA-based species identification procedures would be useful and applicable in routine examinations of the dairy industry to ensure the quality and safety of dairy foods.

• Biomedical Science Letters
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• v.19 no.2
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• pp.153-157
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• 2013

Although culture is the gold standard method to identify mycobacteria, its use in tuberculous lymphadenitis (TBL) is limited due to formalin fixation of the submitted specimens. We evaluated the performance of quantitative real-time PCR (q-PCR) for Mycobacterium Tuberculosis (MTB) in granulomatous lymphadenitis using formalin-fixed paraffin-embedded (FFPE) tissues. From 2000 to 2010, a total number of 117 cases of lymph node samples with granulomatous inflammation which were surgically removed and fixed in formalin were studied. Hematoxylin & Eosin (H&E) and Ziehl-Neelsen-stained (ZN) slides were reviewed. qPCR using Real TB-Taq$^{(R)}$ was performed for all cases to identify Mycobacterium tuberculosis. Thirteen non-tuberculous lymphadenopathy cases were used as negative control. Cervical lymph nodes were more frequently affected (60%, 70/117) than other sites. ZN stain for acid fast bacilli was positive in 19 (16.24%) cases. qPCR for tuberculosis was positive in 92 (78.63%) cases. Caseous necrosis was found in 103 (88.03%) cases. While the ZN stain and qPCR were both negative in all control cases, the qPCR showed a significantly higher positive rate (78.63% vs. 16.24%) compared to ZN stain in histologically diagnosed TBL. Quantitative real-time PCR proves to be more sensitive than ZN stain for diagnosis of tuberculous lymphadenitis.

• Biomedical Science Letters
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• v.26 no.4
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• pp.302-309
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• 2020

Human Coxsackievirus B5 (HuCoxV-B5) infection has been associated with various diseases such as myocarditis, aseptic meningitis, hand-foot-and mouth-disease, and insulin-dependent diabetes. HuCoxV-B5 is a virus transmitted through the fecal-oral route and is detected in clinics, aquatic environments, food, shellfish, etc. and is one of the more important viruses in public health because of its incidence rate reported worldwide. In this study, a combination of SYBR Green-based real-time PCR primers for molecular diagnosis including monitoring of HuCoxV-B5 was selected and the optimal reaction conditions were established. Compared with the previously reported TaqMan probe-based real-time PCR method, assessments including a sample applicability test were performed. Results showed that the real-time PCR method developed in this study was suitable for a molecular diagnostic technique for detecting HuCoxV-B5. This study is expected to contribute to efforts in responding to safety accidents in public health because the proposed method facilitates rapid diagnosis of clinical patients. It can also be used as a specific monitoring tool of HuCoxV-B5 in non-clinical areas such as aquatic environments among others.

• Korean Journal of Microbiology
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• v.49 no.3
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• pp.270-274
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• 2013

The bumblebee, Bombus terrestris, has played an important role as one of the alternative pollinators since the outbreak of honeybee collapse disorder. Recently, pathogens and parasites such as viruses, bacteria and mites, which affect the life span and fecundity of their host, have been discovered in B. terristris. In order to detect the microsporidian pathogen, Nosema spp. in the field populations of B. terristris, we collected adults and isolated their genomic DNA for diagnostic PCR. The PCR primers specific for Nosema spp. were newly designed and applied to gene amplification for cloning. Only small subunit ribosomal RNA (SSU rRNA) gene of N. ceranae was successfully amplified among examined genes and sequenced, which indicates that N. ceranae mainly infects the examined field population of B. terristris. To detect of SSU rRNA gene, two regions of SSU rRNA gene were selected by primary PCR analysis and further analyzed in quantitative real-time PCR (qRT-PCR). The qRT-PCR analysis demonstrated that SSU rRNA of N. ceranae was detected at concentration as low as $0.85ng/{\mu}l$ genomic DNA. This result suggests that the detection via qRT-PCR can be applied for the rapid and sensitive diagnosis of N. ceranae infection in the field population as well as risk assessment of B. terristris.

• Environmental Engineering Research
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• v.14 no.1
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• pp.63-67
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• 2009

Escherichia coli K-12 (E. coli K-12) is a representative indicator globally used for distinguishing and monitoring dynamic fates of pathogenic microorganisms in the environment. This study investigated how to most critically quantify lacZ ($\beta$-galactosidase) gene in E. coli K-12 by two different real-time polymerase chain reaction (real-time PCR) in association with three different DNA extraction practices. Three DNA extractions, i.e., sodium dodecyl sulfate (SDS)/proteinase K, magnetic beads and guanidium thiocyanate (GTC)/silica matrix were each compared for extracting total genomic DNA from E. coli K-12. Among them, GTC/silica matrix and magnetic beads beating similarly worked out to have the highest (22-23 ng/${\mu}L$) concentration of DNA extracted, but employing SDS/proteinase K had the lowest (10 ng/${\mu}L$) concentration of DNA retrieved. There were no significant differences in the quantification of the copy numbers of lacZ gene between SYBR Green I qPCR and QProbe-qPCR. However, SYBR Green I qPCR obtained somewhat higher copy number as $1{\times}10^8$ copies. It was decided that GTC/silica matrix extraction or magnetic beads beating in combination with SYBR Green I qPCR can be preferably applied for more effectively quantifying specific gene from a pure culture of microorganism.

• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1778-1783
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• 2006

Event-specific PCR detection methods are the primary trend in genetically modified (GM) plant detection owing to their high specificity based on the flanking sequence of the exogenous integrant. Therefore, this study describes a real-time PCR system for event-specific GM canola GT73, consisting of a set of primers, TaqMan probe, and single target standard plasmid. For the specific detection of GT73 canola, the 3'-integration junction sequence between the host plant DNA and the integrated specific border was targeted. To validate the proposed method, test samples of 0, 1, 3, 5, and 10% GT73 canola were quantified. The method was also assayed with 15 different plants, and no amplification signal was observed in a real-time PCR assay with any of the species tested, other than GT73 canola.

• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.516-519
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• 2007

Enterobacter sakazakii is an emerging food pathogen, which induces severe meningitis and sepsis in neonates and infants, with a high fatality rate. The disease is generally associated with the ingestion of contaminated infant formula. In this study, we describe the development of a real-time PCR protocol to identify E. sakazakii using a TaqMan probe, predicated on the nucleotide sequence data of the 168 rRNA gene obtained from a variety of pathogens. To detect E. sakazakii, four primer sets and one probe were designed. Five strains of E. sakazakii and 28 non-E. sakazakii bacterial strains were used in order to ensure the accuracy of detection. The PCR protocol successfully identified all of the E. sakazakii strains, whereas the 28 non-E. sakazakii strains were not detected by this method. The detection limits of this method for E. sakazakii cells and purified genomic DNA were 2.3 CFU/ assay and 100 fg/assay, respectively. These findings suggest that our newly developed TaqMan real-time PCR method should prove to be a rapid, sensitive, and quantitative method for the detection of E. sakazakii.