• Mycobiology
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• v.42 no.1
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• pp.73-78
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• 2014

Cryptococcal infection is primarily caused by two species, Cryptococcus neoformans and C. gattii. Between the two species, C. neoformans var. grubii is the major causative agent of cryptococcosis in Asia. We investigated the molecular characteristics of 46 isolates of C. neoformans from patients with cryptococcosis between 2008 and 2012 in Seoul, Korea. All the isolates were determined to be C. neoformans var. grubii (serotype A), mating type $MAT{\alpha}$, and molecular type VNI by PCR-restriction fragment length polymorphism of the URA5 gene. Multilocus sequencing type (MLST) analysis using the International Society of Human and Animal Mycoses (ISHAM) consensus MLST scheme identified two sequence types (ST). Out of the 46 strains, 44 (95.7%) were identified as ST5, and remaining 2 were identified as ST31. Our study revealed that the clinical strains of C. neoformans in Korea are genetically homogeneous with the VNI/ST5 genotypes, and new appearance of VNI/ST31 genotype may serve as an important indicator of global genetic analysis.

• Parasites, Hosts and Diseases
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• v.46 no.2
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• pp.105-108
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• 2008

Although the Korean isolate KI-1 of Toxoplasma gondii has been considered to be a virulent type I lineage because of its virulent clinical manifestations, its genotype is unclear. In the present study, genotyping of the KI-1 was performed by multilocus PCR-RFLP and microsatellite sequencing. For 9 genetic markers (c22-8, c29-2, L358, PK1, SAG2, SAG3, GRA6, BTUB, and Apico), the KI-1 and RH strains exhibited typical PCR-RFLP patterns identical to the type I strains. DNA sequencing of tandem repeats in 5 microsatellite markers (B17, B18, TUB2, W35, and TgM-A) of the KI-1 also revealed patterns characteristic of the type I. These results provide strong genetic evidence that KI-1 is a type I lineage of T. gondii.

• 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.

• Korean Journal of Clinical Laboratory Science
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• v.54 no.4
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• pp.265-272
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• 2022

The emergence and dissemination of carbapenemase-producing Enterobacteriaceae (CPE), particularly the Klebsiella pneumoniae carbapenemase-2 (KPC-2) producing Klebsiella pneumoniae, has been rapidly increasing worldwide and is becoming a serious public health threat. Since the epidemiology and characteristics of these KPC-2-producing K. pneumoniae vary according to the region and period under consideration, this study investigated the prevalence of carbapenemases and the epidemiological relationship of 78 carbapenem-resistant K. pneumoniae (CRKP) isolated from a tertiary hospital in Daejeon, from March 2017 to December 2020. The antimicrobial susceptibility tests were identified using the disk-diffusion method. PCR and DNA sequencing were used to determine the carbapenemase genes. In addition, molecular epidemiology was performed by multilocus sequence typing (MLST). Among the 78 CRKP isolates, 35 isolates (44.9%) were carbapenemase-producing K. pneumoniae (CPKP) and the major carbapenemase type was KPC-2 (30 isolates, 85.7%). The New Delhi metallo-enzyme-1 (NDM-1) and NDM-5 were identified in 4 isolates (11.4%) and 1 isolate (2.9%), respectively. Multilocus sequence typing (MLST) analysis showed 10 sequence types (STs) and the most prevalent ST was ST307 (51.4%, 18/35). All the ST307 isolates were KPC-2-producing K. pneumoniae and were multidrug-resistant (MDR). In addition, ST307 has gradually emerged during a four-year period. These findings indicate that continuous monitoring and proper infection control are needed to prevent the spread of KPC-2-producing K. pneumoniae ST307.

• Mycobiology
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• v.46 no.2
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• pp.92-100
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• 2018

The filamentous Ascomycota Colletotrichum gloeosporioides sensu lato is a fungus that has been reported worldwide as a causal agent of anthracnose disease in avocado and other crops. In Mexico, this species affects fruits from an early stage of development in the orchard until the post-harvest stage. Although fungicides are continuously applied to control Colletotrichum species, pericarp cankers and soft rot mesocarp in fruits are still frequently observed. Considering the lack of a precise description of the causative agent, the aim of the current study was to determine the pathogens involved in this symptomatology. Twenty-four isolates were consistently obtained from the pericarp of avocado fruits cv. "Hass" collected in the central avocado-producing area of Mexico. Morphological features such as colony growth, conidia size, and mycelial appressorium were assessed. Bayesian multilocus phylogenetic analyses were performed using amplified sequences of the internal transcribed spacer region of the nuclear ribosomal DNA; actin, chitin synthase, glyceraldehyde-3-phosphate dehydrogenase partial genes; and APn2-Mat1-2 intergenic spacer and mating type Mat1-2 partial gene from the nine selected isolates. In addition, fruits were inoculated with a conidial suspension and reproducible symptoms confirmed the presence of Colletotrichum fructicola in this area. This pathogenic species can now be added to those previously reported in the country, such as C. acutatum, C. boninense, C. godetiae, C. gloeosporioides, and C. karstii. Disease management programs to reduce the incidence of anthracnose should include C. fructicola to determine its response to fungicides that are routinely applied, considering that the appearance of new species is affecting the commercial quality of the fruits and shifting the original population structure.

• Journal of Microbiology and Biotechnology
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• v.30 no.7
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• pp.974-981
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• 2020

Sequence type 410 (ST410) of Escherichia coli is an extraintestinal pathogen associated with multi drug resistance. In this study, we aimed to investigate the horizontal propagation pathway of a high-risk clone of E. coli ST410 that produces Klebsiella pneumoniae carbapenemase (KPC). blaKPC-encoding E. coli and K. pneumoniae isolates were evaluated, and complete sequencing and comparative analysis of blaKPC-encoding plasmids from E. coli and K. pneumoniae, antimicrobial susceptibility tests, polymerase chain reaction, multilocus sequence typing, and conjugal transfer of plasmids were performed. Whole-genome sequencing was performed for plasmids mediating KPC-2 production in E. coli and K. pneumoniae clinical isolates. Strains E. coli CPEc171209 and K. pneumoniae CPKp171210 were identified as ST410 and ST307, respectively. CPEc171209 harbored five plasmids belonging to serotype O8:H21, which is in the antimicrobial-resistant clade C4/H24. The CPKp171210 isolate harbored three plasmids. Both strains harbored various additional antimicrobial resistance genes. The IncX3 plasmid pECBHS_9_5 harbored blaKPC-2 within a truncated Tn4401a transposon, which also contains blaSHV-182 with duplicated conjugative elements. This plasmid displayed 100% identity with the IncX3 plasmid pKPBHS_10_3 from the K. pneumoniae CPKp171210 ST307 strain. The genes responsible for the conjugal transfer of the IncX3 plasmid included tra/trb clusters and pil genes coding the type IV pilus. ST410 can be transmitted between patients, posing an elevated risk in clinical settings. The emergence of a KPC-producing E. coli strain (ST410) is concerning because the blaKPC-2-bearing plasmids may carry treatment resistance across species barriers. Transgenic translocation occurs among carbapenem-resistant bacteria, which may spread rapidly via horizontal migration.

• Korean Journal of Clinical Laboratory Science
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• v.50 no.4
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• pp.406-413
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• 2018

The emergence of carbapenem resistance among Pseudomonas aeruginosa has become an increasing problem worldwide. In particular, $metallo-{\beta}-lactamases$ (MBLs) are responsible for the high-level resistance to carbapenem. Sequence type 235 (ST235) has been found internationally in a multidrug-resistant clone and is involved in the dissemination of genes encoding IMP-6 and VIM-2. This study examined the prevalence of MBLs and the epidemiological relationship in carbapenem-resistant P. aeruginosa (CRPA) isolates obtained from a tertiary hospital in Daejeon, Korea, between March 2008 and June 2014. The antimicrobial susceptibilities were determined using the disk-diffusion method and PCR and DNA sequencing were used to identify the MBL genes. In addition, an epidemiological relationship was investigated by multilocus sequence typing (MLST). Among the 110 CRPA isolates, 32 isolates (29.1%) were MBL-producers; the major type was IMP-6 (29 isolates, 90.6%). VIM-2 was identified in 3 isolates (9.4%) of ST357. IMP-6-producing isolates were multidrug-resistant (MDR) and belonged to ST235. ST235 (55 isolates, 50.0%) was the clone most frequently detected and has gradually emerged during a seven-year period. To prevent the spread of MDR ST235 P. aeruginosa isolates, the current widespread use of carbapenems needs to be curtailed, and novel continuous monitoring strategies should be developed as soon as possible.

• The Plant Pathology Journal
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• v.39 no.4
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• pp.409-416
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• 2023

Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.3
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• pp.301-308
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• 2019

The emergence and spread of multidrug resistant (MDR) Pseudomonas aeruginosa is a critical problem worldwide. The pathogenesis of P. aeruginosa is due partly to the production of several cell-associated and extracellular virulence factors. This study examined the distribution of virulence factors and antimicrobial resistance patterns of carbapenem-resistant P. aeruginosa (CRPA) isolated from a tertiary hospital in Daejeon, Korea. Antimicrobial susceptibility testing was performed using the disk diffusion method, and PCR and DNA sequencing were performed to determine for the presence of virulence genes. In addition, the sequence type (ST) of MDR P. aeruginosa was investigated by multilocus sequence typing (MLST). Among 32 CRPA isolates, 14 (43.8%) were MDR and the major ST was ST235 (10 isolates, 71.4%). All isolates were positive for the presence of virulence genes and the most prevalent virulence genes were toxA, plcN, and phzM (100%). All isolates carried at least eight or more different virulence genes and nine (28.1%) isolates had 15 virulence genes. The presence of the exoU gene was detected in 71.4% of the MDR P. aeruginosa isolates. These results indicate that the presence of the exoU gene can be a predictive marker for the persistence of MDR P. aeruginosa isolates.

• Mycobiology
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• v.44 no.3
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• pp.121-130
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• 2016

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade.