• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1683-1690
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• 2020

Objective: The rapid and reliable detection of the African swine fever virus (ASFV) plays an important role in emergency control and preventive measures of ASF. Some methods have been recommended by FAO/OIE to detect ASFV in clinical samples, including realtime polymerase chain reaction (PCR). However, mismatches in primer and probe binding regions may cause a false-negative result. Here, a slight modification in probe sequence has been conducted to improve the qualification of real-time PCR based on World Organization for Animal Health (OIE) protocol for accurate detection of ASFV in field samples in Vietnam. Methods: Seven positive confirmed samples (four samples have no mismatch, and three samples contained one mutation in probe binding sites) were used to establish novel real-time PCR with slightly modified probe (Y = C or T) in comparison with original probe recommended by OIE. Results: Both real-time PCRs using the OIE-recommended probe and novel modified probe can detect ASFV in clinical samples without mismatch in probe binding site. A high correlation of cycle quantification (Cq) values was observed in which Cq values obtained from both probes arranged from 22 to 25, suggesting that modified probe sequence does not impede the qualification of real-time PCR to detect ASFV in clinical samples. However, the samples with one mutation in probe binding sites were ASFV negative with OIE recommended probe but positive with our modified probe (Cq value ranked between 33.12-35.78). Conclusion: We demonstrated for the first time that a mismatch in probe binding regions caused a false negative result by OIE recommended real-time PCR, and a slightly modified probe is required to enhance the sensitivity and obtain an ASF accurate diagnosis in field samples in Vietnam.

• Parasites, Hosts and Diseases
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• v.51 no.2
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• pp.231-236
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• 2013

The present study was conducted to investigate the clinical outcomes of Entamoeba histolytica infection in symptomatic and asymptomatic Orang Asli (aborigine) communities in Malaysia. Examination was performed on 500 stool samples obtained from Orang Asli communities in 3 different states using formalin-ether concentration, trichrome staining, and single-round PCR techniques. Out of 500 stool samples, single infection of E. histolytica, Entamoeba dispar, and Entamoeba moshkovskii was identified in 3.2%, 13.4%, and 1%, respectively. In addition, 10 samples had mixed infections with E. histolytica and E. dispar. Six samples containing E. dispar were also positive for E. moshkovskii, and only 2 samples had E. histolytica in association with E. dispar and E. moshkovskii. Seventeen E. histolytica-positive samples were from symptomatic subjects, whereas the remaining 11 samples came from asymptomatic subjects. These findings suggest a predominant distribution of pathogenic potential of E. histolytica strains in this community. Therefore, further studies on genotyping of E. histolytica is required, to find out association between E. histolytica genotype and the outcome of the infection.

• Korean Journal of Clinical Laboratory Science
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• v.36 no.2
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• pp.137-143
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• 2004

Erythrocyte sedimentation rate(ESR) measurements were performed in a total of 191 blood samples from patients below a hematocrit of 35% by both the Test-1(SIRE Analytical Systems, Udine, Italy) and the Westergren method, endorsed as the reference method for ESR by the International Council for Standardization in Hematology(ICSH). The corrected Westergren ESR values were also obtained applying the formula of Fabry (corrected ESR = ESR measured x 15/55-Hct). Linear regression analysis showed a close correlation (r=0.85) between the two methods both before and after ESR correction in total samples. There was no significant correlation difference between two methods in both two groups with hemoglobin $${\geq_-}9g/dl$$ and <9g/dl before and after ESR correction (r=0.873, r=0.827 respectively before correction and r=0.867, r=0.830 respectively after correction). Also, for two groups with hematocrit $${\geq_-}24%$$ and <24%, no significant difference was observed (r=0.859, r=0.792 respectively before correction and r=0.782, r=0.842 respectively after correction). However, for samples with <60mm of Westergren ESR before correction, a better correlation coefficient was obtained than samples with $${\geq_-}60mm$$(r=0.701, r=0.541 respectively). In corrected Westergren ESR, also samples that were obtained with <40mm showed better correlation than samples with $${\geq_-}40mm$$ (r=0.690, r=0.347 respectively). In conclusion, we found a good correlation between Test-1 and Westergren measurements in patients with anemia but an expert group discussion is required to solve discrepancy between two methods in blood samples with very high ESR.

• Journal of Microbiology and Biotechnology
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• v.23 no.2
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• pp.246-250
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• 2013

In this study, a loop-mediated isothermal amplification (LAMP) method to rapidly detect Staphylococcus aureus strains was developed and evaluated by extensively applying a large number of S. aureus isolates from clinical and food samples. Six primers were specially designed for recognizing eight distinct sequences on the species-specific femA gene of S. aureus. The detection limits were 100 fg DNA/tube and $10^4$ CFU/ml. The LAMP assay was applied to 432 S. aureus strains isolated from 118 clinical and 314 food samples. Total detection rates for the LAMP and polymerase chain reaction assays were 98.4% (306/311) and 89.4% (278/311), respectively.

• Clinical Endoscopy
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• v.56 no.2
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• pp.221-228
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• 2023

Background/Aims: Endoscopic ultrasound-guided tissue acquisition (EUS-TA) is essential for the diagnosis of pancreatic cancer. The feasibility of comprehensive genomic profiling (CGP) using samples obtained by EUS-TA has been under recent discussion. This study aimed to evaluate the utility of EUS-TA for CGP in a clinical setting. Methods: CGP was attempted in 178 samples obtained from 151 consecutive patients with pancreatic cancer at the Aichi Cancer Center between October 2019 and September 2021. We evaluated the adequacy of the samples for CGP and determined the factors associated with the adequacy of the samples obtained by EUS-TA retrospectively. Results: The overall adequacy for CGP was 65.2% (116/178), which was significantly different among the four sampling methods (EUS-TA vs. surgical specimen vs. percutaneous biopsy vs. duodenal biopsy, 56.0% [61/109] vs. 80.4% [41/51] vs. 76.5% [13/17] vs. 100.0% [1/1], respectively; p=0.022). In a univariate analysis, needle gauge/type was associated with adequacy (22 G fine-needle aspiration vs. 22 G fine-needle biopsy [FNB] vs. 19 G-FNB, 33.3% (5/15) vs. 53.5% (23/43) vs. 72.5% (29/40); p=0.022). The sample adequacy of 19 G-FNB for CGP was 72.5% (29/40), and there was no significant difference between 19 G-FNB and surgical specimens (p=0.375). Conclusions: To obtain adequate samples for CGP with EUS-TA, 19 G-FNB was shown to be the best in clinical practice. However, 19 G-FNB was not still sufficient, so further efforts are required to improve adequacy for CGP.

• Journal of Genetic Medicine
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• v.12 no.2
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• pp.79-84
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• 2015

Purpose: We developed and validated a fetal trisomy detection method for use as a noninvasive prenatal test (NIPT) including a Clinical Laboratory Improvement Amendments (CLIA)-certified bioinformatics pipeline on a cloud-based computing system using both Illumina and Life Technology sequencing platforms for 221 Korean clinical samples. We determined the necessary proportions of the fetal fraction in the cell-free DNA (cfDNA) sample for NIPT of trisomies 13, 18, and 21 through a limit of quantification (LOQ) test. Materials and Methods: Next-generation sequencing libraries from 221 clinical samples and three positive controls were generated using Illumina and Life Technology chemistries. Sequencing results were uploaded to a cloud and mapped on the human reference genome (GRCh37/hg19) using bioinformatics tools. Based on Z-scores calculated by normalization of the mapped read counts, final aneuploidy reports were automatically generated for fetal aneuploidy determination. Results: We identified in total 29 aneuploid samples, and additional analytical methods performed to confirm the results showed that one of these was a false-positive. The LOQ test showed that the proportion of fetal fraction in the cfDNA sample would affect the interpretation of the aneuploidy results. Conclusion: Noninvasive chromosome examination (NICE), a CLIA-certified NIPT with a cloud-based bioinformatics platform, showed unambiguous success in fetus aneuploidy detection.

• Clinical and Experimental Reproductive Medicine
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• v.38 no.1
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• pp.10-17
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• 2011

Objective: To explore potential relationships between sperm DNA integrity and both semen parameters and clinical outcomes. Methods: Semen analysis of 498 samples was performed according to the 2010 criteria of the World Health Organization. The sperm DNA fragmentation Index (DFI) of the semen samples was assessed using a neutral comet assay. Results: Sperm DFI showed a significant correlation with semen parameters, including the patient's age, sperm viability, motility, morphology, and number of leukocytes (p<0.05). The sperm DFI values for asthenozoospermic (15.2%), oligoteratozoospermic (18.3%), asthenoteratozoospermic (17.5%), and oligoasthenoteratozoospermic semen samples (21.3%) were significantly higher than that observed in normozoospermic semen samples (10.5%, p<0.05). A sperm DFI value of 14% was used as a threshold of sperm DFI in assessing whether DNA was highly damaged. In 114 IVF-ET cycles, the fertilization rate of the sperm DFI <14% group (70 cycles, 61.7%) was significantly higher than that observed for the ${\geq}14%$ group (44 cycles, 55.3%), but there was no difference in the other clinical outcomes between the two groups. In the ${\geq}14%$ group, the pregnancy rates of the ICSI cycles (40.0%) and half-ICSI (44.0%) were higher than conventional IVF cycles (30.7%), but the difference was not statistically significant. Conclusion: Along with the conventional semen analysis, the sperm DFI assessed using the comet assay was shown to improve the quality of the semen evaluation. To evaluate the precise effect of ICSI on pregnancy rates in the patients who demonstrate high sperm DFI values, further study is necessary.

• Korean Journal of Clinical Laboratory Science
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• v.46 no.3
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• pp.99-105
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• 2014

Isolating total DNA from small samples using traditional methods is difficult and inefficient mainly due to loss of DNA during filtration and precipitation. With advances in molecular pathology, DNA extraction from micro-dissected cells has become essential in handling clinical samples. Genomic DNA extraction using small numbers of cells can be very important to successfully PCR amplify DNA from small biopsy specimens. We compared our experimental genomic DNA extraction method (A) with two other commercially available methods: using spin columns (B), and conventional resins (C), and determined the efficacy of DNA extraction from small numbers of cells smeared on a glass slide. Approximately 50, 100, 200, 500 and 1000 cells were isolated from fine needle aspiration biopsy (FNAB) slides aspirated from histologically proven papillary thyroid carcinoma masses. DNA was extracted using the three techniques. After measuring DNA quantity, PCR amplification was performed to detect the ${\beta}$-globin and $BRAF^{V600E}$ gene mutations. DNA extracted by method (A) showed better yield than the other methods in all cell groups. With our method, a suitable amount of genomic DNA to produce amplification was extracted from as few as 50 cells, while more than 100 to 200 cells were required when methods (B) or (C) were applied. Our genomic DNA extraction method provides high quality and improved yields for molecular analysis. It will be especially useful for paucicellular clinical samples which molecular pathologists often confront when handling fine needle aspiration cytology, exfoliative cytology and small biopsy specimens.

• Journal of Microbiology
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• v.40 no.4
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• pp.301-304
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• 2002

Is a multiple number of sputum specimens necessary for the diagnosis of pulmonary tuberculosis? To answer this question, 6844 respiratory specimens obtained from previously untreated patients suspected of having pulmonary tuberculosis between 1998 and 2001 were evaluated retrospectively. All of the specimens were evaluated by acid fast bacilli smear and BACTEC 460 TB culture system. A total of 785 (11%) specimens from 353 patients were positive for Mycobacterium tuberculosis complex. For 76% (270/353) of these patients the organism was detected from sputum specimens collected sequentially for daily basis. Mycobacterium tuberculosis was isolated in the first, second and third samples of the majority (98%,195/199) of patients who had three or more sputum samples sent to the laboratory. Our results indicate that, we could carry out Mycobacterium tuberculosis isolation in the first, second and third sputum samples of the overwhelming majority of the patients and the diagnostic value of four or more sputum specimens submitted to the laboratory was very low (2%). We recommend that, for definitive and cost-effective diagnosis of pulmonary tuberculosis at least three sequential sputum specimens be collected for all patients suspected pulmonary tuberculosis.

• Korean Journal of Clinical Pharmacy
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• v.6 no.2
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• pp.28-31
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• 1996

The in vitro inactivation of gentamicin and tobramycin by four cephalosporins (cefotetan, cefuroxime, cefodizime, cefotiam) in human serum was investigated. Each cephalosporin was added to human serum samples containing gentamicin sulfate or tobramycin sulfate. Blank samples containing only aminoglycosides were used as controls. Samples were stored at -20, 4 and $25^{\circ}C$ and were analyzed for aminoglycoside concentrations by fluorescence polarization immunoassay ($TDxFLx^{TM}$ system) at 0, 2, 4, 8, 12, 24, 48 and 72 hours after mixing. The serum containing cefotiam stored at $25^{\circ}C$ showed significant inactivation of gentamicin by $12\%$ at 72 hours. The results indicate that cefotitan, cefuroxime and cefodizime do not inactivate gentamicin and tobramycin while cefotiam inactivates gentamicin.