• Korean Journal of Clinical Laboratory Science
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• v.50 no.3
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• pp.331-336
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• 2018

In this study, multi-locus sequence typing (MLST) analysis of 40 clinically isolated Candida albicans in tertiary hospitals in Daejeon, Korea, confirmed the nucleotide sequence and phylogenetic relationships of the strains collected from different specimen sources. The general variations found in seven different housekeeping genes of C. albicans, collected from urine and sputum, peripheral blood, central line blood, and other specimens, were analyzed. The phylogenetic tree was divided into 18 sub-clusters (1), a central line blood (2), others (5), sputum (1), peripheral blood (6), sputum (1), and urine (1), and the isolates at the same site were confirmed to have genetic similarity. Consequently, genetic similarity and the potential relevance were found in the strains collected from the same specimen sources. MLST analysis of C. albicans suggests that persistent data accumulation of phylogenetic gene variations of C. albicans may help establish infectious disease studies and epidemiological surveillance systems.

• Journal of fish pathology
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• v.36 no.2
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• pp.277-286
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• 2023

Korean rockfish, Sebastes schlegelii, is a representative bony fish that belongs to the family Scorpaenidae and the order Scorpaeniformes. It has high ecological and economic value and is widely cultivated in many East Asian countries, including South Korea, Japan and China. One of streptococci, Streptococcus iniae, is Gram-positive cocci with a negative reaction for catalase and oxidase. The Korean rockfish shows clinical signs when infected with S. iniae, such as body darkening, bleeding, enlarged kidneys, blurred eyes, abdominal distension, etc., ultimately leading to death. The Korean rockfish causes significant economic losses every year in South Korea due to streptococcosis. In this study, we identified bacteria from the fish using polymerase chain reaction and conducted analyses of hemolytic activity and biochemical tests using API 20 STREP and API ZYM systems. Results of confirming the hemolytic activity (n=4) observed in alpha-type hemolysis (25%), beta-type hemol- ysis (50%), and gamma-type hemolysis (25%) of isolates. The biochemical test results exhibited sig- nificant variation among S. iniae. Additionally, we performed intraperitoneal injection with S. iniae in the fish and analyzed the phylogenetic tree using housekeeping genes of S. iniae, including cpsD, arcC, glnA, groEL, gyrB, mutS, pheT, prkC, rpoB, and tkt, via multilocus sequence typing (MLST). The lethal dose (LD₅₀) showed strong pathogenicity, such as 3.34 × 10 colony-forming unit (CFU)/ml for 23FBStr0601 strain and 7.16 × 10 CFU/ml for 23FBStr0602 strain. 23FBStr0603 strain showed relatively low pathogenicity at 1.73 × 10⁵ CFU/ml. The strains 23FBStr0601 and 23FBStr0602, which showed strong pathogenicity, clustered into one monophyletic group. The 23FBStr0603 strain showed weak pathogenicity and formed a monophyletic group with KCTC 3657.

• Clinical and Experimental Pediatrics
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• v.58 no.1
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• pp.20-27
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• 2015

Purpose: We investigated the molecular types of uropathogenic Escherichia coli (UPEC) by using conventional phylogrouping, multilocus sequence typing (MLST), and fimH genotyping. Methods: Samples of patients younger than 18 years of age were collected from the Chung-Ang University Hospital over 2 years. Conventional phylogenetic grouping for UPEC strains was performed by polymerase chain reaction (PCR). Bacterial strain sequence types (STs) were classified on the basis of the results of partial sequencing of seven housekeeping genes. In addition, we analyzed nucleotide variations in a 424-base pair fragment of fimH, a major virulence factor in UPEC. Results: Sixty-four UPEC isolates were analyzed in this study. Phylogenetic grouping revealed that group B2 was the most common type (n=54, 84%). We identified 16 distinctive STs using MLST. The most common STs were ST95 (35.9%), ST73 (15.6%), ST131 (12.5%), ST69 (7.8%), and ST14 (6.3%). Fourteen fimH allele types were identified, of which 11 had been previously reported, and the remaining three were identified in this study. f1 (n=28, 45.2%) was found to be the most common allele type, followed by f6 and f9 (n=7, 11.3% each). Comparative analysis of the results from the three different molecular typing techniques revealed that both MLST and fimH typing generated more discriminatory UPEC types than did PCR-based phylogrouping. Conclusion: We characterized UPEC molecular types isolated from Korean children by MLST and fimH genotyping. fimH genotyping might serve as a useful molecular test for large epidemiologic studies of UPEC isolates.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.421-429
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• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• Journal of Microbiology and Biotechnology
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• v.25 no.9
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• pp.1410-1416
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• 2015

Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.953-958
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• 2015

Background: Expression of KRT13, FAIM2 and CYP2W1 appears to be influenced by risk habits, thus exploring the associations of these genes in oral squamous cell cancer (OSCC) with risk habits, clinico-pathological parameters and patient survival may be beneficial in identifying relevant biomarkers with different oncogenic pathways. Materials and Methods: cDNAs from 41 OSCC samples with and without risk habits were included in this study. Quantitative real-time PCR was used to analyze KRT13, FAIM2 and CYP2W1 in OSCC. The housekeeping gene (GAPDH) was used as an endogenous control. Results: Of the 41 OSCC samples, KRT13 was down-regulated in 40 samples (97.6%), while FAIM2 and CYP2W1 were down-regulated in 61.0% and 48.8%, respectively. Overall, there were no associations between KRT13, FAIM2 and CYP2W1 expression with risk habits, selected socio-demographic and clinico-pathological parameters and patient survival. Conclusions: Although this study was unable to show significance, there were some tendencies in the associations of KRT13, FAIM2 and CYP2W1 expression in OSCC with selected clinic-pathological parameters and survival.

• Clinical and Experimental Pediatrics
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• v.60 no.7
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• pp.221-226
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• 2017

Purpose: Escherichia coli sequence type (ST) 131, a multidrug-resistant clone causing extraintestinal infections, has rapidly become prevalent worldwide. However, the epidemiological and clinical features of pediatric infections are poorly understood. We aimed to explore the characteristics of ST131 Escherichia coli isolated from Korean children with urinary tract infections. Methods: We examined 114 uropathogenic E. coli (UPEC) isolates from children hospitalized at Chung-Ang University Hospital between 2011 and 2014. Bacterial strains were classified into STs by partial sequencing of seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA). Clinical characteristics and antimicrobial susceptibility were compared between ST131 and non-ST131 UPEC isolates. Results: Sixteen UPEC isolates (14.0%) were extended-spectrum ${\beta}-lactamase$ (ESBL)-producers; 50.0% of ESBL-producers were ST131 isolates. Of all the isolates tested, 13.2% (15 of 114) were classified as ST131. There were no statistically significant associations between ST131 and age, sex, or clinical characteristics, including fever, white blood cell counts in urine and serum, C-reactive protein, radiologic abnormalities, and clinical outcome. However, ST131 isolates showed significantly lower rates of susceptibility to cefazolin (26.7%), cefotaxime (40.0%), cefepime (40.0%), and ciprofloxacin (53.3%) than non-ST131 isolates (65.7%, 91.9%, 92.9%, and 87.9%, respectively; P<0.001 for all). ESBL was more frequently produced in ST131 (53.3%) than in non-ST131 (8.1%) isolates (P<0.01). Conclusion: ST131 E. coli isolates were prevalent uropathogens in children at a single medical center in Korea between 2011 and 2014. Although ST131 isolates showed higher rates of antimicrobial resistance, clinical presentation and outcomes of patients were similar to those of patients infected with non-ST131 isolates.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.11
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• pp.1673-1679
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• 2008

In order to study the biological function of gapdh gene in yak, and prove whether the gapdh gene was a useful intra-reference gene that can be given an important role in molecular biology research of yak, the cDNA sequence encoding glyceraldehyde-3-phosphate dehydrogenase from yak was cloned by the RT-PCR method using gene specific PCR primers. The sequence results indicated that the cloned cDNA fragment (1,008 bp) contained a 1,002 bp open reading frame, encoding 333 amino acids (AAs) with a molecular mass of 35.753 kDa. The deduced amino acids sequence showed a high level of sequence identity to Bos Taurus (99.70%), Xenopus laevis (94.29%), Homo sapiens (97.01%), Mus musculus (97.90%) and Sus scrofa (98.20%). The expression of yak's gapdh gene in heart, spleen, kidney and brain tissues was also detected; the results showed that the gapdh gene was expressed in all these tissues. Further analysis of yak GAPDH amino acid sequence implied that it contained a complete glyceraldehyde-3-phosphate dehydrogenase active site (ASCTTNCL) which ranged from 148 to 155 amino acid residues. It also contained two conserved domains, a NAD binding domain in its N-terminal and a complete catalytic domain of sugar transport in its C-terminal. The phylogenetic analysis showed that yak and Bos taurus were the closest species. The prediction of secondary structures indicated that GAPDH of yak had a similar secondary structure to other isolated GAPDH. The results of this study suggested that the gapdh gene of yak was similar to other species and could be used as the intra-reference to analyze the expression of other genes in yak.

• The Plant Pathology Journal
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• v.32 no.5
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• pp.431-440
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• 2016

In 2004, bacterial spot-causing xanthomonads (BSX) were reclassified into 4 species-Xanthomonas euvesicatoria, X. vesicatoria, X. perforans, and X. gardneri. Bacterial spot disease on pepper plant in Korea is known to be caused by both X. axonopodis pv. vesicatoria and X. vesicatoria. Here, we reidentified the pathogen causing bacterial spots on pepper plant based on the new classification. Accordingly, 72 pathogenic isolates were obtained from the lesions on pepper plants at 42 different locations. All isolates were negative for pectolytic activity. Five isolates were positive for amylolytic activity. All of the Korean pepper isolates had a 32 kDa-protein unique to X. euvesicatoria and had the same band pattern of the rpoB gene as that of X. euvesicatoria and X. perforans as indicated by PCR-restriction fragment length polymorphism analysis. A phylogenetic tree of 16S rDNA sequences showed that all of the Korean pepper plant isolates fit into the same group as did all the reference strains of X. euvesicatoria and X. perforans. A phylogenetic tree of the nucleotide sequences of 3 housekeeping genes-gapA, gyrB, and lepA showed that all of the Korean pepper plant isolates fit into the same group as did all of the references strains of X. euvesicatoria. Based on the phenotypic and genotypic characteristics, we identified the pathogen as X. euvesicatoria. Neither X. vesicatoria, the known pathogen of pepper bacterial spot, nor X. perforans, the known pathogen of tomato plant, was isolated. Thus, we suggest that the pathogen causing bacterial spot disease of pepper plants in Korea is X. euvesicatoria.

• Research in Plant Disease
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• v.28 no.3
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• pp.172-178
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• 2022

The graft cactus (Gymnocalycium mihanovichii) continues to be exported to more than 20 countries worldwide. In April 2021, typical bacterial symptoms of soft rot were observed in the graft cactus (cv. Yeonbit) in Goyang, Gyeonggi-do, Korea, resulting in economic losses in cactus production. The stems turned dark brown and the flowers were covered with black rot. The bacterial strain designated as KNUB-01-21 was isolated from infected stems and flowers. The results of the morphological and biochemical tests of the isolate were similar to those of Pectobacterium brasiliense. For molecular analysis, the 16S rRNA region and three housekeeping genes (dnaX, leuS, and recA) of the strain KNUB-01-21 were amplified. Based on the results of the molecular analysis and morphological and biochemical tests, KNUB-01-21 was identified as P. brasiliense. The pathogenicity of KNUB-01-21 on graft cactus was confirmed by an inoculation test. Artificial inoculation using P. brasiliense KNUB-01-21 produced soft rot symptoms on the grafted cactus, and the same bacterium was re-isolated and re-identified. This is the first report of P. brasiliense causing soft rot in graft cactus in Korea.