• Fisheries and Aquatic Sciences
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• 제22권8호
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• pp.17.1-17.9
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• 2019

Bacillus is a diverse genus consisting of more than 200 species with extensive genetic diversity. Their beneficial effects in industrial shrimp farming have been well documented. However, little is known about the biodiversity of the Bacillus spp. in this aquaculture system. Taxonomic analysis by 16S rRNA sequencing does not always allow species-level identification of Bacillus spp. In this study, 26 Bacillus isolates from two industrial Litopenaeus vannamei shrimp ponds in Bac Lieu Province, Vietnam, were analyzed for their genetic diversity by multi-locus sequence typing (MLST). A total of 22 sequence types were identified and segregated into four distinct clusters, corresponding to B. subtilis, B. velezensis, B. siamensis, and B. licheniformis. Bacillus subtilis and B. velezensis accounted for more than 73% of the Bacillus isolates. Notably, the MLST scheme exhibited high discriminatory power and might be further simplified to be a convenient method to identify species of the genus Bacillus.

• 생명과학회지
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• 제30권2호
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• pp.122-128
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• 2020

Candida albicans가 칸디다 혈증의 주요 원인 균으로 알려져 있지만, 최근에는 non-albicans Candida (NAC)에 의한 심각한 감염이 증가하고 있다. NAC 중에서 C. glabrata는 두 번째로 병원성을 나타내는 원인 균이지만 C. glabrata의 구조, 역학 등의 기본적인 연구는 거의 없는 실정이다. 따라서 본 연구에서는 다양한 유형의 임상 표본으로부터 분리된 총 102개의 C. glabrata균주로 multi-locus sequence typing (MLST)을 수행하였다. FKS, LEU2, NMT1, TRP1, UGP1 및 URA3을 포함한 6개의 하우스키핑 유전자를 증폭하여 염기서열을 분석하였다. 총 3,345개의 DNA 염기서열 중 49개의 가변 염기서열 부위가 발견되었으며, 그 결과 102개의 균주에서 총 12개의 상이한 서열 유형을 확인하였고, 알려지지 않은 서열 유형(USTs) 중 UST1이 가장 많이 나타났다. 이 연구의 결과는 국내 C. glabrata 항생제 처방에 도움이 될 것으로 사료되며, 한국에서 유행하는 C. glabrata에 대한 추가 연구를 위한 기본 역학자료로 사용될 것으로 기대한다.

• Parasites, Hosts and Diseases
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• 제52권3호
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• pp.299-304
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• 2014

This study aimed to identify the assemblages (or subassemblages) of Giardia duodenalis by using normal or nested PCR based on 4 genetic loci: glutamate dehydrogenase (gdh), triose phosphate isomerase (tpi), ${\beta}$-giardin (bg), and small subunit ribosomal DNA (18S rRNA) genes. For this work, a total of 216 dogs' fecal samples were collected in Guangdong, China. The phylogenetic trees were constructed with MEGA5.2 by using the neighbor-joining method. Results showed that 9.7% (21/216) samples were found to be positive; moreover, 10 samples were single infection (7 isolates assemblage A, 2 isolates assemblage C, and 1 isolate assemblage D) and 11 samples were mixed infections where assemblage A was predominant, which was potentially zoonotic. These findings showed that most of the dogs in Guangdong were infected or mixed-infected with assemblage A, and multi-locus sequence typing could be the best selection for the genotype analysis of dog-derived Giardia isolates.

• 대한의생명과학회지
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• 제23권3호
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• pp.223-229
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• 2017

Fungal infections by human pathogenic fungi are increasing globally in elderly, children and immune suppressed or deficient patients. Aspergillus fumigatus is one of the well-known pathogenic fungi and causes aspergilloses in human world widely. However, current identification and classification methods based on its phenotypic characteristics still have limitations. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to analyze genetic variations of A. fumigatus clinical isolates, a total of six housekeeping genes were amplified by PCR using specific primer pairs and multi-locus sequence typing (MLST) assay. Results from phylogenetic tree analysis showed that most A. fumigatus strains (88.9%) from respiratory specimens were classified into cluster A and B, and approximately half of A. fumigatus strains (46%) from non-respiratory specimens were classified into cluster C and D. Although the sample size was limited, genetic characteristics of A. fumigatus clinical isolates according to their origins were very similar and well-correlated with other clinical data.

• 대한수의학회지
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• 제55권1호
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• pp.31-39
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• 2015

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.

• Journal of Microbiology and Biotechnology
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• 제32권12호
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• pp.1605-1614
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• 2022

The strains associated with foodborne Salmonella enterica Thompson outbreaks in Korea have not been identified. Therefore, we characterized S. Thompson strains isolated from chocolate cakes linked to foodborne outbreaks in Korea. A total of 56 strains were isolated from preserved cake products, products in the supply chain distribution, the manufacturer's apparatus, and egg white liquid products used for cream preparation. Subsequently, serological typing, pathogenic gene-targeted polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE), and whole-genome multi-locus sequence typing (wgMLST) were performed to characterize these isolates. The antigen formula of all isolates was 7:k:1,5, namely Salmonella enterica subsp. enterica Serovar Thompson. All 56 isolates harbored invA, his, hin, and stn, and were negative for sefA and spvC based on gene-targeted PCR analyses. Based on PFGE results, these isolates were classified into one group based on the same SP6X01.011 pattern with 100% similarity. We selected 19 strains based on the region and sample type, which were subjected to wgMLST. Although the examined strains showed 100% similarity, they were classified into seven clusters based on allelic differences. According to our findings, the cause of these outbreaks was chocolate cake manufactured with egg white liquid contaminated with the same Salmonella Thompson. Additionally, comparative analysis of wgMLST on domestic isolates of S. Thompson from the three outbreaks showed genetic similarities of over 99.6%. Based on the results, the PFGE and wgMLST combination can provide highly resolved phylogeny and reliable evidence during Salmonella outbreak investigations.

• Mycobiology
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• 제45권4호
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• pp.401-408
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• 2017

Colletotrichum gloeosporioides is an economically important fungal pathogen causing substantial yield losses indifferent host plants. To understand the genetic diversity and molecular epidemiology of this fungus, we have developed a novel, high-resolution multi-locus microsatellite typing (MLMT) method. Bioinformatic analysis of C. gloeosporioides unannotated genome sequence yielded eight potential microsatellite loci, of which five, CG1 $(GT)_n$, CG2 $(GT1)_n$, CG3 $(TC)_n$, CG4 $(CT)_n$, and CG5 $(CT1)_n$ were selected for further study based on their universal amplification potential, reproducibility, and repeat number polymorphism. The selected microsatellites were used to analyze 31 strains of C. gloeosporioides isolated from 20 different host plants from India. All microsatellite loci were found to be polymorphic, and the approximate fragment sizes of microsatellite loci CG1, CG2, CG3, CG4, and CG5 were in ranges of 213-241, 197-227, 231-265, 209-275, and 132-188, respectively. Among the 31 isolates, 55 different genotypes were identified. The Simpson's index of diversity (D) values for the individual locus ranged from 0.79 to 0.92, with the D value of all combined five microsatellite loci being 0.99. Microsatellite data analysis revealed that isolates from Ocimum sanctum, Capsicum annuum (chili pepper), and Mangifera indica (mango) formed distinct clusters, therefore exhibited some level of correlation between certain genotypes and host. The developed MLMT method would be a powerful tool for studying the genetic diversity and any possible genotype-host correlation in C. gloeosporioides.

• 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.

• 대한임상검사과학회지
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• 제50권3호
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• pp.331-336
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• 2018

본 연구에서는 국내 대전 소재 3차 병원 임상에서 분리된 Candida albicans 40 균주를 대상으로 균주 분리원에 따라 7종류의 housekeeping gene에 대한 염기서열 변이를 확인하고 MLST 분석을 통해 균주간의 계통학적 연관성에 대한 연구를 수행하여 다음과 같은 결과를 얻었다. Phylogenetic tree 분석 결과 sub-cluster 1로 central line blood (2), others (5), sputum (4), urine (7)을 포함해 총 18개가 분류되었으며, sub-cluster 2로는 central line blood (1), others (5), peripheral blood (6), sputum (1), urine (1)을 포함해 총 14개가 분류되어 동일 채취 부위에서 분리된 균주는 유전학적으로 유사성을 가지고 있을 가능성이 있음을 확인하였다. 앞으로 분리지역과 상병 등에 따른 C. albicans 유전자들의 변이 추세에 대한 자료의 축적과 임상 검체에 따른 계통학적 관계를 추정하여 감염병 연구 및 역학적 감시체계 구축에 도움이 될 것으로 생각된다.

• Mycobiology
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• 제48권2호
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• pp.133-138
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• 2020

Talaromyces halophytorum sp. nov. was isolated from the roots of halophyte Limonium tetragonum collected from Seocheon-gun, Korea in November 2015. It showed a slow growth on yeast extract sucrose agar at 25 ℃, no growth at 4 ℃ or 37 ℃ and produced smooth-walled and globose to sub-globose conidia. T. halophytorum is phylogenetically distinct from the other reported Talaromyces species of section Trachyspermi based on multi-locus sequence typing results using partial fragments of β-tubulin, calmodulin, ITS, and RNA polymerase II genes.