• The Plant Pathology Journal
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• 제29권4호
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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.

• Clinical and Experimental Pediatrics
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• 제58권1호
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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 Veterinary Science
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• 제21권4호
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• pp.57.1-57.11
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• 2020

Background: Streptococcus dysgalactiae subspecies equisimilis (SDSE) acts as an etiological agent for lameness, neurological signs, and high mortality in pigs. Despite its importance in pig industries and zoonotic potential, little is known about the effects of this pathogen. Objectives: This study aimed to determine the molecular characteristics and antimicrobial resistance of SDSE strains isolated from diseased pigs. Methods: A total 11 SDSE isolates were obtained from diseased pigs. Bacterial identification, PCR for virulence genes, emm typing, and antimicrobial resistance genes, multilocus sequence typing, and antimicrobial susceptibility test were performed. Results: Nine isolates were from piglets, and 8 showed lameness, sudden death, or neurological signs. The isolates were PCR-positive for sla (100%), sagA (100%), and scpA (45.5%), and only 1 isolate amplified the emm gene (stL2764). Eight different sequence types were detected, categorized into 2 clonal complexes and 4 singletons. All the isolates in this study were included in a small cluster, which also contained other strains derived from humans and horses. The minimum inhibitory concentrations for the tested beta-lactams were low, while those for macrolides, tetracyclines, and fluoroquinolones were relatively high. PCR analysis of the macrolide and tetracycline resistance genes demonstrated that the isolates carried erm(B) (18.2%, n = 2), mef(A/E) (9.1%, n = 1), tet(M) (18.2%, n = 2), and tet(O) (90.2%, n = 10). Two isolates presented a mutation in parC, which is associated with fluoroquinolone resistance. Conclusion: This study provided insight into swine-derived SDSE, as it is related to veterinary medicine, and elucidated its zoonotic potential, in the context of molecular epidemiology and antimicrobial resistance in public health.

• 대한수의학회지
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• 제60권3호
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• pp.183-186
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• 2020

This paper describes the development of neurological signs of two prematurely born calves four days after birth. The pathological examination results indicated fibrinopurulent polyserositis, including meningoencephalitis with suppurative bronchopneumonia. Bovine viral diarrhea virus subtype 2a was detected in most of the internal organs, and the bacterial colonies cultured from the samples were identified as Klebsiella (K.) pneumoniae. Molecular analysis via multilocus sequence typing identified a different K. pneumoniae isolate in each calf-type 14 in calf A and type 65 in calf B. This is the first report identifying K. pneumoniae sequence types 14 and 65 in cattle.

• Journal of Microbiology and Biotechnology
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• 제32권10호
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• pp.1307-1314
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• 2022

In this study, we sought to investigate the various characteristics of Salmonella spp. isolated from raw chicken meats available in Korean markets. The data collected, such as food source of isolation, sampling information, serotype, virulence, and genetic profile including sequence type, were registered in the database for further comparative analysis of the strains isolated from the traceback investigation samples. To characterize serotype, virulence and gene sequences, we examined 113 domestically distributed chicken meat samples for contamination with Salmonella spp. Phylogenetic analysis was conducted on 24 strains (21.2%) of Salmonella isolated from 113 commercially available chicken meats and by-products, using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Serotyping of the isolated Salmonella spp. revealed S. Enteritidis in 11 strains (45.8%), S. Virchow in 6 strains (25%), S. Montevideo in 2 strains (8.3%), S. Bsilla in 2 strains (8.3%), S. Bareilly in 1 strain (4.2%), S. Dessau in 1 strain (4.2%), and S. Albany in 1 strain (4.2%). The genetic correlation indicated that 24 isolated strains were classified into 18 clusters with a genetic similarity of 64.4-100% between them. Eleven isolated S. Enteritidis strains were classified into 9 genotypes with a sequence identity of 74.4%, whereas the most distantly related S. Virchow was divided into five genotypes with 85.9% identity. Here, the MLST analysis indicated that the major Sequence Type (ST) of the Salmonella spp. isolated from domestic chicken sold in Chungcheong Province belongs to the ST 11 and 16, which differs from the genotype of Salmonella isolated from imported chicken. The differential sequence characteristics can be a genetic marker for identifying causative bacteria for epidemiological investigations of food poisoning.

• 대한의생명과학회지
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• 제24권3호
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• pp.221-229
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• 2018

Trichophyton rubrum is one of the well-known pathogenic fungi and causes dermatophytosis and cutaneous mycosis in human world widely. However, there are not an available sequence type (ST) classification methods and previous studies for T. rubrum until now. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to characterize the genetic diversity and the phylogenetic relation of T. rubrum clinical isolates, five different housekeeping genes, such as actin (ACT), calmodulin (CAL), RNA polymerase II (RPB2), superoxide dismutase 2 (SOD2), and ${\beta}$-tubulin (BT2) were analyzed using by multilocus sequence typing (MLST). Also, DNA sequence analysis was performed to examine the differences between the sequences of Trichophyton strains and the identified genetic variations sequence. As a result, most of the sequences were shown to have highly matched rates in their housekeeping genes. However, genetic variations were found on three different positions of ${\beta}$-tubulin gene and were shown to have changed from $C{\rightarrow}G$ (1766), $G{\rightarrow}T$ (1876), and $C{\rightarrow}A$ (1886). To confirm the association with T. rubrum inheritance, a phylogenetic tree analysis was performed. It was classified as four clusters, but there was little significant correlation. Even so, MLST analysis is believed to be helpful for determining the genetic variations of T. rubrum in cases where there is more large-scale data accumulation. In conclusion, the present study demonstrated the first MLST analysis of T. rubrum in Korea and explored the possibility that MLST could be a useful tool for studying the epidemiology and evolution of T. rubrum through further studies.

• 한국미생물·생명공학회지
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• 제51권4호
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• pp.500-506
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• 2023

Carbapenem 내성 Klebsiella pneumoniae (Carbapenem-resistant K. pneumonia, CRKP)는 전 세계적인 공중 보건 문제로 대두되고 있다. 최근 Klebsiella pneumoniae carbapenemase-2 (KPC-2) 생성 sequence type (ST)307은 CRKP의 주요 클론으로 확인되었으며, 국내에서 ST307의 확산이 보고되었다. 본 연구에서는 2020년 3월부터 2021년 12월까지 대전지역의 3차 병원에서 분리된 CRKP 50균주를 대상으로, 분자 특성과 항균제 내성 양상을 조사하였다. 역학적 관계는 multilocus sequence typing (MLST)를 통해 분석하였고, 항균제 감수성 검사는 디스크 확산법을 통해 확인하였다. PCR과 DNA 염기서열분석은 carbapenemase 유전자 확인을 위해 수행하였다. CRKP감염은 남성과 60세 이상의 환자에서 훨씬 더 빈번하게 확인되었다. CRKP 50균주 중 46균주(92.0%)는 다제내성(MDR)을 보였고, 44균주(88.0%)는 carbapenemase-producing K. pneumoniae (CPKP)로 확인되었다. 주요 carbapenemase 유형은 KPC-2 (36균주, 72.0%)였으며, New Delhi metallo-enzyme-1 (NDM-1)과 NDM-5는 각각 7균주(14.0%)와 1균주(2.0%)에서 확인되었다. 특히, KPC-2 생성 K. pneumoniae의 88.9% (32/36)가 ST307에 속한 반면, NDM-1,-5 생성 K. pneumoniae의 87.5% (7/8)가 non-ST307에 속한 것을 확인하였다. 이러한 결과는 ST307의 확산 뿐만 아니라 non-ST307의 발달을 예방하기 위한 적절한 감염관리와 효과적인 감시체계가 필요하다고 사료된다.

• Mycobiology
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• 제42권4호
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• pp.412-415
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• 2014

Alternaria from different Allium plants was characterized by multilocus sequence analysis. Based on sequences of the ${\beta}$-tubulin (BT2b), the Alternaria allergen a1 (Alt a1), and the RNA polymerase II second largest subunit (RPB2) genes and phylogenetic data analysis, isolates were divided into two groups. The two groups were identical to representative isolates of A. porri (EGS48-147) and A. vanuatuensis (EGS45-018). The conidial characteristics and pathogenicity of A. vanuatuensis also well supported the molecular characteristics. This is the first record of A. vanuatuensis E. G. Simmons & C. F. Hill from Korea and China.

• 대한임상검사과학회지
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• 제50권4호
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• pp.406-413
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• 2018

최근 P. aeruginosa의 carbapenem에 대한 내성은 전 세계적으로 증가하고 있는 실정이다. 특히 $metallo-{\beta}-lactamases$ (MBLs)는 carbapenem의 고도 내성에 관여하고 있는 것으로 보고되고 있다. 한편, Sequence type 235 (ST235)는 다제내성 클론으로써 국제적으로 보고되고 있으며, IMP-6와 VIM-2 유전자의 확산에도 관여하는 것으로 알려져 있다. 본 연구에서는 2008년 3월부터 2014년 6월까지, 대전지역의 3차 병원에서 분리된 carbapenem 내성 P. aeruginosa에서 MBL 유전자를 분석하고 이에 대한 역학관계를 조사하고자 하였다. 항균제 감수성 양상은 디스크 확산법으로 확인하였고, MBL 유전자의 분석을 위해 PCR과 염기서열분석을 수행하였다. 더불어, 역학 관계를 조사하기 위해 multilocus sequence typing (MLST)를 실시하였다. 110 균주의 carbapenem 내성 P. aeruginosa 중, 32균주(29.1%)가 MBL를 생성하였고, IMP-6 (29균주, 90.6%)가 주요하게 확인되었다. VIM-2는 3균주(9.4%)에서 확인되었으며, 모두 ST357로 확인되었다. IMP-6를 생성하는 P. aeruginosa는 모두 다제내성을 보였고, ST235로 확인되었다. ST235 (55균주, 50.0%)는 가장 높은 비율로 확인된 클론이며 7년 동안 지속적으로 확인되었다. 이러한 다제내성 ST235의 확산을 방지하기 위해, carbapenem의 과도한 사용을 제한하고, 지속적으로 모니터링하는 전략이 개발되어야 할 것으로 사료된다.

• Pediatric Infection and Vaccine
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• 제23권3호
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• pp.172-179
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• 2016

목적: Bacillus cereus 는 암환자들에서 기회감염을 일으킬 수 있다. 2013년에서 2014년 기간 동안 삼성서울병원 소아 암 병동에서 B. cereus 균혈증의 급격한 증가가 관찰되었다. 이에 증가된 B. cereus 균혈증에 대해 분자역학적 연구를 시행하였다. 방법: 2001년 1월부터 2014년 6월까지의 기간 동안 B. cereus 균혈증이 발생한 소아 암 환자들을 확인하였다. 이번 연구에서 B. cereus 균혈증은, 오염여부와는 상관없이, 혈액배양검사에서 적어도 한번 이상 B. cereus 가 확인된 경우로 정의하였다. 획득 가능한 균주들에 대해 multilocus sequence typing (MLST) 분석을 시행하였고, 후향적 챠트 리뷰를 실시하였다. 결과: 연구 기간 동안 총 19명의 B. cereus 균혈증 환자가 확인되었다. 그러나, 2013년도에는 B. cereus 균혈증 환자가 급격하게 증가하였다. 또한, 응급실 공사 중이던 2013년 7월의 1주, 2013년 10월의 한주 동안 각각 3명의 환자가 발생하였다. 그러나 MLST 분석상 일정한 패턴이 없는, 다양한 sequence types (STs)들로 확인되었다. 2013년 이전의 5개의 균주들의 ST는 ST18, ST26, ST177, ST147-like type, ST219-like type이었고, 2013년도의 균주들의 ST는 ST18, ST73, ST90, ST427, ST784, ST34-like type, ST130-like type으로 확인되었다. 고찰: MLST 분석상 B. cereus 균주들의 다양한 ST 분포가 확인되었다. 이번 연구에서 단일 ST의 B. cereus 에 의한 균혈증 발생의 가능성은 낮아보인다.