• 제목/요약/키워드: genetic typing

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Discrimination of Listeria monocytogenes by Sequence Typing Based on Two Housekeeping Genes and Its Comparison to PFGE Patterns

  • Suh, Dong-Kyun
    • 대한의생명과학회지
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    • 제11권3호
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    • pp.289-293
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    • 2005
  • Two housekeeping genes, of Listeria monocytogenes dat and hlyA, were analyzed in a set of 28 isolates from different sources to estimate their genetic diversities. These strains were previously characterized by pulsed-field gel electrophoresis. Complete gene sequences for dat (465 bp) and hlyA (584 bp) had sequence similarity of $99.87-100\%$ S and $99.96-100\%$ S among isolates, respectively. Also, we found that the numbers of sequence types (ST) were about 3-fold less than those of PFGE types (3 STs versus 11 PFGE types). There was, however, a good correlation between the PFGE patterns and phylogenetic grouping of two gene sequences among the isolates. Further studies on analyzing additional loci would increase the discriminatory power of sequence typing for L. monocytogenes strains.

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Microsatellite DNA형 분석을 이용한 더러브렛 말의 친자감정 (Parentage Testing for Thoroughbred Horse by Microsatellite DNA Typing)

  • 조길재
    • Journal of Animal Science and Technology
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    • 제46권2호
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    • pp.129-136
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    • 2004
  • The objective of present study was to ascertain parentage of Thoroughbred(TB) horses in Korea. A total of 2,029 TB horse samples including 993 foal samples for parentage testing were genotyped for nine international minimum standard markers(AHT4, 5, ASB2, HMS3, 6, 7, HTG4, 10, and VHL20). This method consisted of multiplexing PCR procedure, and showed reasonable amplification of all PCR products. Genotyping was performed with an ABI 310 genetic analyzer. The number of alleles per locus varied from 5 to 11 with a mean value of 7.33 in TB. Expected heterozygosity was ranged from 0.544 to 0.837(mean 0.709) and the total exclusion probability of 9 microsatellites loci was 0.9978. Of the 9 markers, ASB2, HMS7 and HTG10 loci have relatively high PIC value(>0.7). All of the 993 foals were qualified by compatibility according to Mendelian fashion in the present DNA typing for parentage testing. These results suggest that the present DNA typing has high potential for parentage verification of TB horses.

Analysis of Leuconostoc citreum strains using multilocus sequence typing

  • Sharma, Anshul;Kaur, Jasmine;Lee, Sulhee;Park, Young-Seo
    • Food Science and Biotechnology
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    • 제27권6호
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    • pp.1755-1760
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    • 2018
  • The objective of this study was to perform genetic diversity analysis of 13 strains isolated from South Korean foods by multilocus sequence typing (MLST). For typing, seven housekeeping loci (atpA, dnaA, dnaK, gyrB, pheS, pyrG, and rpoA) were selected, amplified and analyzed. Fifty-one polymorphic sites varying from 1 to 22 in each species were identified. Thirteen sequence types were generated with allele numbers ranged from 2 to 10. The overall relationship between strains was assessed by unweighted pair group method with arithmetic mean dendrogram and minimum spanning tree. In addition, combined spits tree analysis revealed intragenic recombination. No clear relationship was observed between the isolation sources and strains. The developed MLST scheme enhanced our knowledge of the population diversity of Leu. citreum strains and will be used further for the selection of industrially important strain.

Genetic Diversity and Antibiotic Resistance of Enterococcus faecalis Isolates from Traditional Korean Fermented Soybean Foods

  • Lee, Jong-Hoon;Shin, Donghun;Lee, Bitnara;Lee, Hyundong;Lee, Inhyung;Jeong, Do-Won
    • Journal of Microbiology and Biotechnology
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    • 제27권5호
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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.

Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing

  • Choi, Jaehyuk;Kim, Hyojung;Lee, Yong-Hwan
    • 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.

Molecular prophage typing of Staphylococcus aureus isolates from bovine mastitis

  • Ko, Dae-Sung;Seong, Won-Jin;Kim, Danil;Kim, Eun-Kyung;Kim, Nam-Hyung;Lee, Chung-Young;Kim, Jae-Hong;Kwon, Hyuk-Joon
    • Journal of Veterinary Science
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    • 제19권6호
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    • pp.771-781
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    • 2018
  • Staphylococcus aureus is one of the major pathogens causing bovine mastitis and foodborne diseases associated with dairy products. To determine the genetic relationships between human and bovine or bovine isolates of S. aureus, various molecular methods have been used. Previously we developed an rpoB sequence typing (RSTing) method for molecular differentiation of S. aureus isolates and identification of RpoB-related antibiotic resistance. In this study, we performed spa typing and RSTing with 84 isolates from mastitic cows (22 farms, 72 cows, and 84 udders) and developed a molecular prophage typing (mPPTing) method for molecular epidemiological analysis of bovine mastitis. To compare the results, human isolates from patients (n = 14) and GenBank (n = 166) were used for real and in silico RSTing and mPPTing, respectively. Based on the results, RST10-2 and RST4-1 were the most common rpoB sequence types (RSTs) in cows and humans, respectively, and most isolates from cows and humans clearly differed. Antibiotic resistance-related RSTs were not detected in the cow isolates. A single dominant prophage type and gradual evolution through prophage acquisition were apparent in most of the tested farms. Thus, RSTing and mPPTing are informative, simple, and economic methods for molecular epidemiological analysis of S. aureus infections.

Genetic Variations of Trichophyton rubrum Clinical Isolates from Korea

  • Yoon, Nam-Sup;Kim, Hyunjung;Park, Sung-Bae;Park, Min;Kim, Sunghyun;Kim, Young-Kwon
    • 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.

High Resolution Whole Genome Multilocus Sequence Typing (wgMLST) Schemes for Salmonella enterica Weltevreden Epidemiologic Investigations

  • Tadee, Pakpoom;Tadee, Phacharaporn;Hitchings, Matthew D.;Pascoe, Ben;Sheppard, Samuel K.;Patchanee, Prapas
    • 한국미생물·생명공학회지
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    • 제46권2호
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    • pp.162-170
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    • 2018
  • Non-typhoidal Salmonella is one of the main pathogens causing food-borne illness in humans, with up to 20% of cases resulting from consumption of pork products. Over the gastroenteritis signs, multidrug resistant Salmonella has arisen. In this study, pan-susceptible phenotypic strains of Salmonella enterica serotype Weltevreden recovered from pig production chain in Chiang Mai, Thailand during 2012-2014 were chosen for analysis. The aim of this study was to use whole genome sequencing (WGS) data with an emphasis on antimicrobial resistance gene investigation to assess their pathogenic potential and genetic diversity determination based on whole genome Multilocus Sequence Typing (wgMLST) to expand epidemiological knowledge and to provide additional guidance for disease control. Analyis using ResFinder 3.0 for WGS database tracing found that one of pan-susceptible phenotypic strain carried five classes of resistance genes: aminoglycoside, beta-lactam, phenicol, sulfonamide, and tetracycline associated genes. Twenty four and 36 loci differences were detected by core genome Multilocus Sequence Typing (cgMLST) and pan genome Multilocus Sequence Typing (pgMLST), respectively, in two matching strains (44/13 vs A543057 and A543056 vs 204/13) initially assigned by conventional MLST and Pulsed-field Gel Electrophoresis (PFGE). One hundread percent discriminant ability can be achieved using the wgMLST technique. WGS is currently the ultimate molecular technique for various in-depth studies. As the findings stated above, a new of "gold standard typing method era" for routine works in genome study is being set.

Multi-locus sequence typing을 이용한 한국에서 분리한 Candida glabrata 임상균주의 유전자 유형 분석 (Genetic Variations of Candida glabrata Clinical Isolates from Korea using Multi-locus Sequence Typing)

  • 강민지;이경은;진현우
    • 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.

Comparison of Multilocus Sequence Typing (MLST) and Repetitive Sequence-Based PCR (rep-PCR) Fingerprinting for Differentiation of Campylobacter jejuni Isolated from Broiler in Chiang Mai, Thailand

  • Patchanee, Prapas;Chokboonmongkol, Chomporn;Zessin, Karl-Hans;Alter, Thomas;Pornaem, Sarinya;Chokesajjawatee, Nipa
    • Journal of Microbiology and Biotechnology
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    • 제22권11호
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    • pp.1467-1470
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    • 2012
  • We compared rapid fingerprinting using repetitive sequencebased PCR (rep-PCR) for subtyping Campylobacter jejuni isolates to the widely used multilocus sequence typing (MLST). Representative C. jejuni isolates (n = 16) from broilers were analyzed using MLST and rep-PCR. Both techniques demonstrated an equal discriminatory power of 0.8917, and 9 subgroups were identified. Clonal identification of all 16 isolates was identical for both techniques. The rep-PCR as described in this study may be used as a rapid and cost-effective alternative for subtyping of C. jejuni isolates, or as an effective screening tool in large epidemiological studies.