• The Plant Pathology Journal
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• v.29 no.4
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• pp.435-439
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• 2013

Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980's. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.50 no.4
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• pp.447-452
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• 2017

In this study, we tried to identify a sea anemone collected from the coast of Gijang, Busan. The anemone was morphologically similar to species belonging to the genus Anthopleura, but its morphological characteristics did not allow for confirmed identification to species level. Multiple genes from mitochondrial cytochrome oxidase III, 12S and 16S rRNA, and nuclear 18S and 28S rRNA, were amplified for multilocus sequence typing (MLST) analysis using genomic DNA extracted from the sampled anemone and a different primer set. Based on the MLST analysis, the anemone obtained in this study was identified as Anthopleura artemisia. Also, the sequence of internal transcribed spacer-2 was most closely related to A. artemisia, indicating that this single region might be useful for anemone identification. This study shows significance of molecular identification for sea anemones, and will be helpful in studies of sea anemone identification using genotyping-by-sequencing.

• Research in Plant Disease
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• v.29 no.4
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• pp.445-451
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• 2023

Zamioculcas zamiifolia is a popular indoor ornamental plant in Korea. In August 2021, a severe outbreak of soft rot disease affected Z. zamiifolia in Emseong, Chungcheongbuk-do, Korea. Infected plants displayed wilting, water-soaked lesions, stem collapse, and green-brown discoloration. The bacterial strain KNUB-05-21 was isolated from infected stems and identified as Pectobacterium aroidearum using 16S rRNA nucleotide sequencing and multilocus sequence analysis based on partial sequences of dnaX, leuS, and recA genes. Confirmation of its affiliation with P. aroidearum was also obtained through biochemical and morphological characterization. To confirm the pathogenicity of strain KNUB-05-21, its suspension was injected into Z. zamiifolia stems. Within a week, soft rot developed on the stems, exhibiting symptoms similar to those observed in field-infected plants. The reisolated strain was identical to those of P. aroidearum. Before this study, P. aroidearum was not reported as a causative pathogen of Z. zamiifolia soft rot in Korea.

• Korean Journal of Poultry Science
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• v.47 no.2
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• pp.115-119
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• 2020

Fowl cholera is an infectious disease caused by Pasteurella multocida that contributes to high economic loss in the commercial chicken industry. Three Pasteurella multocida strains were isolated from outbreaks of acute fowl cholera in the Korean layer farms from 2018 to 2019. One strain was identified and serotyped using capsular PCR typing. This strain was also genotyped by lipopolysaccharide (LPS) PCR typing as A: L3, whereas other strains were non-typable. The multilocus sequence typing (MLST) result showed that the A: L3 strain is sequence type (ST) 134; the non-typable strains were recorded as the following new STs: ST 366 and ST 374. Using phylogenetic tree analysis based on MLST sequences, we determined that ST 366 and ST 374 are closely related to the reference strains that were previously isolated from duck and chicken in Korea, and they were highly prevalent within the Korean cluster. In conclusion, Pasteurella multocida strains were identified and isolated in this study. Furthermore, this is the first report of using MLST to determine the prevalence of fowl cholera in Korea.

• 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.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.916-924
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• 2017

Eighty-five Enterococcus faecalis isolates collected from animals (40 isolates), meju (a Korean fermented soybean product; 27 isolates), humans (10 isolates), and various environmental samples (8 isolates) were subjected to multilocus sequence typing (MLST) to identify genetic differences between samples of different origins. MLST analysis resulted in 44 sequence types (STs), and the eBURST algorithm clustered the STs into 21 clonal complexes (CCs) and 17 singletons. The predominant STs, ST695 (21.1%, 18/85) and ST694 (9.4%, 8/85), were singletons, and only contained isolates originating from meju. None of the STs in the current study belonged to CC2 or CC9, which comprise clinical isolates with high levels of antibiotic resistance. The E. faecalis isolates showed the highest rates of resistance to tetracycline (32.9%), followed by erythromycin (9.4%) and vancomycin (2.4%). All isolates from meju were sensitive to these three antibiotics. Hence, MLST uncovered genetic diversity within E. faecalis, and clustering of the STs using eBURST revealed a correlation between the genotypes and origins of the isolates.

• Journal of Preventive Medicine and Public Health
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• v.45 no.1
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• pp.1-7
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• 2012

Using three Austrian case studies, the variegated applications of molecular typing in today's public health laboratories are discussed to help illustrate preventive management strategies relying on DNA subtyping. DNA macrorestriction analysis by pulsed field gel electrophoresis has become the gold standard for subtyping of food borne pathogens like listeria, salmonella, campylobacter and Bacillus cereus. Using a Salmonella Mbandaka outbreak from the year 2010 as example, it is shown how the comparison of patterns from human isolates, food isolates, animal isolates and feed isolates can allow to identify and confirm a source of disease. An epidemiological connection between the simultaneous occurrence of tuberculosis in cattle and deer with cases of human tuberculosis due to Mycobacterium caprae in 2010 was excluded using mycobacterial interspersed repetitive units variable-number tandem repeats subtyping. Also in 2010, multilocus sequence typing with nonselective housekeeping genes, the so-called sequence based typing protocol, was used to elucidate connections between an environmental source (a hospital drinking water system) and a case of legionellosis. During the last decades, molecular typing has evolved to become a routine tool in the daily work of public health laboratories. The challenge is now no longer to simply type microorganisms, but to type them in a way that allows for data exchange between public health laboratories all over the world.

• 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.28 no.5
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• pp.796-808
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• 2018

The intracellular bacterium Wolbachia pipientis is widespread in arthropods. Recently, possibilities of novel Wolbachia-mediated hosts, their distribution, and natural rate have been anticipated, and the coconut leaf beetle Brontispa longissima (Gestro) (Coleoptera: Chrysomelidae), which has garnered attention as a serious pest of palms, was subjected to this interrogation. By adopting Wolbachia surface protein (wsp) and multilocus sequence type (MLST) genotypic systems, we determined the Wolbachia infection density within host developmental stages, body parts, and tissues, and the results revealed that all the tested samples of B. longissima were infected with the same Wolbachia strain (wLog), suggesting complete vertical transmission. The MLST profile elucidated two new alleles (ftsZ-234 and coxA-266) that define a new sequence type (ST-483), which indicates the particular genotypic association of B. longissima and Wolbachia. The quantitative real-time PCR analysis revealed a higher infection density in the eggs and adult stage, followed by the abdomen and reproductive tissues, respectively. However, no significant differences were observed in the infection density between sexes. Moreover, the wsp and concatenated MLST alignment analysis of this study with other known Wolbachia-mediated arthropods revealed similar clustering with distinct monophyletic supergroup B. This is the first comprehensive report on the prevalence, infection dynamics, and phylogeny of the Wolbachia endosymbiont in B. longissima, which demonstrated that Wolbachia is ubiquitous across all developmental stages and distributed in the entire body of B. longissima. Understanding the Wolbachia infection dynamics would provide useful insight to build a framework for future investigations, understand its impacts on host physiology, and exploit it as a potential biocontrol agent.

• Food Science of Animal Resources
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• v.40 no.5
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• pp.758-771
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• 2020

This study was to investigate the prevalence and characteristics of antimicrobial-resistant Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) from 4,264 retail meat samples including beef, pork, and chicken in Korea between 2013 and 2018. A broth microdilution antimicrobial susceptibility testing was performed for S. aureus. Molecular typing by multilocus sequence typing (MLST), spa typing, and pulsed-field gel electrophoresis (PFGE), was performed on mecA-positive S. aureus strain. S. aureus was isolated at a rate of 18.2% (777/4,264), of which MRSA comprised 0.7% (29 strains). MLST analysis showed that 11 out of the 29 MRSA isolates were predominantly sequence type (ST) 398 (37.9%). In addition, ST72, ST692, ST188, ST9, and ST630 were identified in the MRSA isolates. The spa typing results were classified into 11 types and showed a high correlation with MLST. The antimicrobial resistance assays revealed that MRSA showed 100% resistance to cefoxitin and penicillin. In addition, resistance to tetracycline (62.1%), clindamycin (55.2%), and erythromycin (55.2%) was relatively high; 27 of the 29 MRSA isolates exhibited multidrug resistance. PFGE analysis of the 18 strains excluding the 11 ST398 strains exhibited a maximum of 100% homology and a minimum of 64.0% homology. Among these, three pairs of isolates showed 100% homology in PFGE; these results were consistent with the MLST and spa typing results. Identification of MRSA at the final consumption stage has potential risks, suggesting that continuous monitoring of retail meat products is required.