• Korean Journal of Veterinary Service
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• v.37 no.4
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• pp.247-252
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• 2014

The economic impact of swine mycoplasma infection is high. An accurate diagnosis is often difficult and time consuming. We report the development and validation of an effective multiplex polymerase chain reaction (PCR) assay that detects Mycoplasma (M.) hyopneumoniae and M. hyorhinis. The multi detection of M. hyopneumoniae and M. hyorhinis primer set were employed to detect mycoplasma species and typing of the species was performed on the basis of sequence analysis of the PCR product. The target nucleic acid fragments were specifically amplified by M. hyopneumoniae and M. hyorhinis PCR with 16S ribosomal DNA primers. Single and mixed Mycoplasma species DNA templates were used to evaluate the specificity of the multiplex assay. The corresponding specific DNA products were amplified for each pathogen. The multiplex PCR assay provides a novel tool for simultaneous detection and differentiation of M. hyopneumoniae and M. hyorhinis.

• Journal of Microbiology and Biotechnology
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• v.24 no.3
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• pp.334-336
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• 2014

A new species named Aspergillus cumulatus sp. nov. is described in Aspergillus section Aspergillus (Eurotium state). The type strain (KACC $47316^T$) of this species was isolated from rice straw used in meju fermentations in Korea, and other strains were isolated from the air in a meju fermentation room. The species is characterized by growth at a wide range of water activities and the formation of aerial hyphae on malt extract 60% sucrose agar (ME60S) that resemble a cumulus cloud. Furthermore, A. cumulatus produces yellow ascomata containing small lenticular ascospores (5.1-5.7 ${\mu}m$) with a wide furrow, low equatorial crests, and tuberculate convex surface. The species is phylogenetically distinct from the other reported Aspergillus section Aspergillus species based on multilocus sequence typing using rDNA-ITS, ${\beta}$-tubulin, calmodulin, and RNA polymerase II genes.

• Parasites, Hosts and Diseases
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• v.41 no.4
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• pp.209-219
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• 2003

The evolutionary course of the CsRn1 long-terminal-repeat (LTR) retrotransposon was predicted by conducting a phylogenetic analysis with its paralog LTR sequences. Based on the clustering patterns in the phylogenetic tree, multiple CsRn1 copies could be grouped into four subsets, which were shown to have different integration times. Their differential sequence divergences and heterogeneous integration patterns strongly suggested that these subsets appeared sequentially in the genome of C. sinensis. Members of recently expanding subset showed the lowest level of divergence in their L TR and reverse transcriptase gene sequences. They were also shown to be highly polymorphic among individual genomes of the trematode. The CsRn1 element exhibited a preference for repetitive, agenic chromosomal regions in terms of selecting integration targets. Our results suggested that CsRn1 might induce a considerable degree of intergenomic variation and, thereby, have influenced the evolution of the C. sinensis genome.

• Journal of Microbiology and Biotechnology
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• v.28 no.12
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• pp.1992-1998
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• 2018

In 2015, Bacillus paralicheniformis was separated from B. licheniformis on the basis of phylogenomic and phylogenetic studies, and urease activity was reported as a phenotypic property that differentiates between the two species. Subsequently, we have found that the urease activity of B. paralicheniformis is strain-specific, and does not reliably discriminate between species, as strains having the same urease gene cluster were identified in B. licheniformis and B. sonorensis, the closest relatives of B. paralicheniformis. We developed a multilocus sequence typing scheme using eight housekeeping genes, adk, ccpA, glpF, gmk, ilvD, pur, spo0A, and tpi to clearly identify B. paralicheniformis from closely related Bacillus species and to find a molecular marker for the rapid identification of B. paralicheniformis. The scheme differentiated 33 B. paralicheniformis strains from 90 strains formerly identified as B. licheniformis. Among the eight housekeeping genes, spo0A possesses appropriate polymorphic sites for the design of a B. paralichenofomis-specific PCR primer set. The primer set designed in this study perfectly separated B. paralicheniformis from B. licheniformis and B. sonorensis.

• Tuberculosis and Respiratory Diseases
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• v.54 no.4
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• pp.367-377
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• 2003

Background : It is well known that only 10% of those infected with Mycobacterium tuberculosis actually develop clinical disease, indicating the existence of host genetic factors regulating disease expression. In this study, we investigated HLA-DRB1 and -DQB1 gene polymorphisms in Korean patients with pulmonary tuberculosis (PTB). Methods : HLA-DRB1 and -DQB1 gene polymorphisms were investigated in 67 PTB patients without previous treatment history, 38 drug-sensitive (DS) and 29 multidrug-resistant (MDR) cases, and 200 healthy controls. HLA-DRB1 typing was done using reverse SSO (sequence specific oligonucleotide) and PCR-SSCP (single strand conformational polymorphism) methods and DQB1 typing was done using PCR-RFLP (restriction fragment length polymorphism), PCR-SSCP and PCR-SSP (sequence specific primer) methods. Results : Among the PTB patients, MDR-TB cases showed frequencies of DRB1*0701 and *08032 increased by about two-fold compared to those of normal controls, and likewise for their associated DQB1 alleles, DQB1*0202 and *0601 (15.5% vs. 34.5%, p=0.01). The frequency of HLA-DQB1*0609 was significantly increased in PTB patients (4.0% vs. 14.9%, p=0.004), showing similar increases in both DS and MDR cases. There was also an association of HLA alleles with the clinical severity of the disease according to the extent of lung lesion. Significantly increased frequencies of DRB1*08032 (4.2% vs. 32.6%, p=0.007) and DQB1*0601 (12.5% vs. 34.9%, p=0.047) were observed in more advanced (moderately & far advanced/DS and far advanced/MDR), compared with less advanced (minimal/DS and moderately advanced/MDR) lung lesions. Although DRB1*0701, DQB1*0202 and DQB1*0609 showed significant increases in different subsets of the disease, these HLA alleles did not show consistent association with disease severity. Conclusion : HLA-DRB1*08032 and DQB1*0601 alleles were associated with genetic susceptibility to MDR-TB in Korean patients, and also with disease severity and progression of PTB.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.180-182
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• 2002

Substantial genomic diversity has been expected among clinical isolates of H. pylori. We have suggested that the two complete H. pylori genomes already sequenced may be insufficient for providing a discriminatory tool for typing clinical isolates as well as an insight into the genomic diversity, which enable to establish strategy for control of H. pylori infection. In this study, we determine the nucleotide sequence of the entire genome of Korean strain 51 and compare it with two reported genomic sequences to suggest validity for extensive genomic sequencing of H. pylori. The genome of H. pylori 51 consists of a circular chromosome with a size of 1,591,297 bp, which is corresponding to $95.4\%\;and\;96.8\%$ of the 26695 and J99 chromosome length, respectively. We predict that there are 1,454 open reading frames (ORFs) in 51, representing $91.4\%\;and\;97.2\%$ of the reported numbers of ORF of 26695 and J99, respectively. In contrast to 26695 and J99 that have 123 and 65 strain-specific genes, respectively, of the 1,454 genes, only 39 genes are unique to 51. Differences in genomic organization between 51 and each foreign strain were greater than between 2 foreign strains in pair wise entire sequence alignments by BLASTN. Particularly, the extent of genomic rearrangement observed between 51 and 26695 is higher than between 51 and J99. Multiple sequence alignment of orthologous genes among 3 strains showed that 51 is genetically closer to 26695 rather than J99. Phylogenetic analysis of nonsynonymous and synonymous mutation indicated J99 has the longest branch length in the unrooted phylogenetic tree, suggesting that J99 has higher mutation rate than the other 2 strains.

• Journal of Life Science
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• v.17 no.3 s.83
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• pp.402-406
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• 2007

This study was performed to develop the molecular marker for sex determination of hare (Lepus coreanus) distributed in Korea which focused on sexual dimorphism between X and Y chromosomal homologous genes, zinc finger-X (ZFX) and -Y (ZFY). The intron 7 regions of ZFX and ZFY genes exhibited differential amplification patterns between male and female hares. The lengths of intron 7 region of ZFX and ZFY genes were 538 and 233-bp, respectively. Especially, the ZFX intron 7 contained a repetitive sequence identified as member of RNA-mediated transposable elements which was similar to CSINE2 commonly found in the rabbit genome. However, it was not present in intron 7 of ZFY gene. The molecular sex typing by polymerase chain reaction (PCR) was also carried out to determine the sex of hare based on difference in lengths between the intron 7 regions of ZFX and ZFY genes. All DNA samples tested had common band amplified from ZFX. However, the male hare DNAs had two distinct bands which amplified from ZFX and ZFY genes, respectively. The results from ZFX-ZFY PCR sex typing were identical to those from phenotypic investigation and from amplification patterns using male-specific sex determining region Y (SRY) gene as well. Finally, this study suggested that the sexual dimorphism between intron 7 regions of ZFX and ZFY could be useful genetic marker to determine sex of hare.

• Journal of Veterinary Science
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• v.22 no.5
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• pp.68.1-68.15
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• 2021

Background: Colistin and carbapenem-resistant bacteria have emerged and become a serious public health concern, but their epidemiological data is still limited. Objectives: This study examined colistin and carbapenem resistance in Escherichia coli and Salmonella from pigs, pig carcasses, and pork in Thailand, Lao PDR, and Cambodia border provinces. Methods: The phenotypic and genotypic resistance to colistin and meropenem was determined in E. coli and Salmonella obtained from pigs, pig carcasses, and pork (n = 1,619). A conjugative experiment was performed in all isolates carrying the mcr gene (s) (n = 68). The plasmid replicon type was determined in the isolates carrying a conjugative plasmid with mcr by PCR-based replicon typing (n = 7). The genetic relatedness of mcr-positive Salmonella (n = 11) was investigated by multi-locus sequence typing. Results: Colistin resistance was more common in E. coli (8%) than Salmonella (1%). The highest resistance rate was found in E. coli (17.8%) and Salmonella (1.7%) from Cambodia. Colistin-resistance genes, mcr-1, mcr-3, and mcr-5, were identified, of which mcr-1 and mcr-3 were predominant in E. coli (5.8%) and Salmonella (1.7%), respectively. The mcr-5 gene was observed in E. coli from pork in Cambodia. Two colistin-susceptible pig isolates from Thailand carried both mcr-1 and mcr-3. Seven E. coli and Salmonella isolates contained mcr-1 or mcr-3 associated with the IncF and IncI plasmids. The mcr-positive Salmonella from Thailand and Cambodia were categorized into two clusters with 94%-97% similarity. None of these clusters was meropenem resistant. Conclusions: Colistin-resistant E. coli and Salmonella were distributed in pigs, pig carcasses, and pork in the border areas. Undivided-One Health collaboration is needed to address the issue.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.2
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• pp.260-264
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• 2019

An 84-year-old woman presented to the emergency department with a chief complaint of pressure sores of the anus. She had a urine catheter when she showed pyuria three times but had no fever. A microscopic examination revealed many grapevine-like Gram positive strains and neutrophils. After 24 hours of urine culture on blood agar, non-hemolytic mucous colonies were found and further enlarged after 48 hours of culture. The capsules were identified after India ink stain. The catalase was positive, but the tube coagulase and latex coagulase were both negative. The S. aureus was identified by Vitek-2 and mass spectrometer Vitek MS V-3 IVD. The strain was confirmed by 16S rRNA gene sequencing and multilocus sequence typing (MLST). The phenotypically atypical MRSA found in the tube coagulase and latex coagulase were both negative. MRSA often show no beta hemolysis as in this case but are rarely latex coagulase-negative. We report a woman whose urine culture showed non-hemolytic, tube coagulase-negative, and latex coagulase-negative MRSA.

• Korean Journal of Food Science and Technology
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• v.40 no.1
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• pp.101-105
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• 2008

Enterobacter sakazakii is implicated in severe forms of neonatal infections such as meningitis and sepsis. This organism has been isolated from a wide range of foods, including cheese, vegetables, grains, herbs, and spices, but its primary environment is still unknown. Generally, dried infant milk formula has been epidemiologically identified as the source of E. sakazakii. Sunsik (a powdered mixture of roasted grains and other foodstuffs) is widely consumed in Korea as a side dish or energy supplement. Sunsik is consumed without heat treatment; thus, lacking an additional opportunity to inactivate foodborne pathogens. Therefore, its microbiological safety should be guaranteed. In this study, the prevalence of E. sakazakii was monitored in 23 different sunsik component flours, using FDA recommended methods; but E. sakazakii medium (Neogen) and Chromogenic E. sakazakii medium (Oxoid) were used as the selective media. In total, presumptive E. sakazakii strains were isolated from 8 different sunsik powders. Subsequently, an API 20E test was conducted, and 15 strains from 5 different sunsik flours (sea tangle, brown rice, non-glutinous rice, cheonggukjang, dried anchovy) were confirmed as E. sakazakii. Fifteen strains were again confirmed by PCR amplification, using three different primer sets (tDNA sequence, ITS sequence, 16S rRNA sequence), and compared to ATCC strains (12868, 29004, 29544, 51329). They were once again confirmed by their enzyme production profiles using an API ZYM kit. Finally, RAPD (random amplified polymorphic DNA)-genotyping was carried out as a monitoring tool to determine the contamination route of E. sakazakii during processing.