Ryoo, Sungweon
(Clinical Research Centre, Masan National Tuberculosis Hospital)
,
Lee, Jeongsoo
(LAS Inc.)
,
Oh, Jee Youn
(Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine)
,
Kim, Byeong Ki
(Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine)
,
Kim, Young
(Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine)
,
Kim, Je Hyeong
(Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine)
,
Shin, Chol
(Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Korea University College of Medicine)
,
Lee, Seung Heon
(Division of Pulmonary, Sleep, and Critical Care Medicine, Department of Internal Medicine, Korea University An)
Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank acce...
Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. Results: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. Conclusion: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.
Background: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. Methods: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. Results: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: strains from Chinese individuals and strains from Korean individuals. Conclusion: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
문제 정의
The aims of this study are to characterize TB strains isolated from immigrants from China based on molecular and bio-informatics as well as to compare them with clinical isolates from native Chinese and Korean individuals.
제안 방법
Then, a progressive genome alignment according to a guide tree was built up after computing a pairwise genome content distance using the neighbor joining method and a pairwise breakpoint distance matrix. During progressive alignment, the breakpoint penalty according to the expected level of sequence divergence and the number of well-supported genomic rearrangements among the pair of input genomes were scaled. Anchor alignment using a global genome alignment algorithm was performed, and alignments that had unrelated sequences were ultimately rejected.
Initially, local multiple alignments that had unique subsequences shared by two or more input genomes were selected, and ungapped extension was performed until the seed pattern no longer matched. Then, a progressive genome alignment according to a guide tree was built up after computing a pairwise genome content distance using the neighbor joining method and a pairwise breakpoint distance matrix. During progressive alignment, the breakpoint penalty according to the expected level of sequence divergence and the number of well-supported genomic rearrangements among the pair of input genomes were scaled.
대상 데이터
In total, 4,290 genes comprising 4,239 CDS, 117 pseudo genes, three rRNA genes (5S, 16S, and 23S), 45 tRNAs, and three ncRNAs were annotated. The patient with MTB_2 strain was a 33-year-old man. He had moved to South Korea from the Yanbian Korean autonomous prefecture where most Korean-Chinese (Chosun race) reside, 2 years before the TB diagnosis was confirmed.
gov/ genome/annotation_prok). The patient with the MTB_1 strain was a 39-year-old woman. She had recently emigrated from Shandong Province in China to South Korea to marry a Korean.
이론/모형
We compared the genome topology network (GTN) of each strain using a bootstrap topology tree and detected the locally collinear blocks of the conserved segments using a modified MUSCLE (multiple sequence alignment method with reduced time and space complexity) global alignment algorithm. We used the Mauve package for the identification and alignment of the conserved genomic DNA sequences of the nine M.
성능/효과
In conclusion, phylogenetic trees based on Mauve alignments supposed to reveal the dynamics of TB transmission from immigrants to South Korea, providing important information for the scaling up of the TB screening policy for immigrants, especially from China.
tuberculosis MTB2 genome comprises one chromosome of 4,417,716 bp. In total, 4,290 genes comprising 4,239 CDS, 117 pseudo genes, three rRNA genes (5S, 16S, and 23S), 45 tRNAs, and three ncRNAs were annotated. The patient with MTB_2 strain was a 33-year-old man.
후속연구
Otherwise, another plausible explanation is that the strains from Yanbian Province, where Chosun race live because of the geographical proximity to the Korean Peninsula, may have the same lineage as the native Korean K strains. Therefore, additional molecular epidemiology studies with large numbers of samples must be conducted to characterize the strains from Korean-Chinese (Chosun race) individuals.
참고문헌 (18)
1 World Health Organization Global tuberculosis report 2016 [Internet] Geneva World Health Organization 2016 cited 2018 Jan 5 Available from: http://apps.who.int/iris/bitstream/10665/250441/1/9789241565394-eng.pdf?ua=1
2 Lee YK Kwon YH Lee SC Sohn HJ Koh YW Overview of tuberculosis control and prevention polices in Korea Public Health Wkly Rep 2015 8 651 656
3 Korea Centers for Disease Control and Prevention Annual report on the notified tuberculosis in Korea Cheongwon Korea Centers for Disease Control and Prevention 2015
4 Min GH Kim Y Lee JS Oh JY Hur GY Lee YS Social and clinical characteristics of Immigrants with tuberculosis in South Korea Yonsei Med J 2017 58 592 597 28332365
5 Kim SJ Bai GH Lee H Kim HJ Lew WJ Park YK Transmission of Mycobacterium tuberculosis among high school students in Korea Int J Tuberc Lung Dis 2001 5 824 830 11573893
6 Jeon CY Kang H Kim M Murray MB Kim H Cho EH Clustering of Mycobacterium tuberculosis strains from foreign-born patients in Korea J Med Microbiol 2011 60 Pt 12 1835 1840 21799194
7 Jiang J Gu J Zhang L Zhang C Deng X Dou T Comparing Mycobacterium tuberculosis genomes using genome topology networks BMC Genomics 2015 16 85 25766780
8 Darling AC Mau B Blattner FR Perna NT Mauve: multiple alignment of conserved genomic sequence with rearrangements Genome Res 2004 14 1394 1403 15231754
11 Chin CS Alexander DH Marks P Klammer AA Drake J Heiner C Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Nat Methods 2013 10 563 569 23644548
12 Koren S Schatz MC Walenz BP Martin J Howard JT Ganapathy G Hybrid error correction and de novo assembly of single-molecule sequencing reads Nat Biotechnol 2012 30 693 700 22750884
13 Park YK Kang H Yoo H Lee SH Roh H Kim HJ Whole-genome sequence of Mycobacterium tuberculosis Korean strain KIT87190 Genome Announc 2014 2 e01103 e01114 25359915
14 Han SJ Song T Cho YJ Kim JS Choi SY Bang HE Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family Stand Genomic Sci 2015 10 78 26473025
15 Chen L Zhang DT Zhang J Su YA Zhang H Whole-genome sequences of two clinical isolates of extensively drug-resistant Mycobacterium tuberculosis from Zunyi, China Genome Announc 2014 2 e00910 e00914 25237021
16 Zhang Y Chen C Liu J Deng H Pan A Zhang L Complete genome sequences of Mycobacterium tuberculosis strains CCDC5079 and CCDC5080, which belong to the Beijing family J Bacteriol 2011 193 5591 5592 21914894
17 Wan X Qian L Hou S Drees KP Foster JT Douglas JT Complete genome sequences of Beijing and Manila family strains of Mycobacterium tuberculosis Genome Announc 2014 2 e01135 e01114
18 Niemann S Koser CU Gagneux S Plinke C Homolka S Bignell H Genomic diversity among drug sensitive and multidrug resistant isolates of Mycobacterium tuberculosis with identical DNA fingerprints PLoS One 2009 4 e7407 19823582
AI-Helper
※ AI-Helper는 부적절한 답변을 할 수 있습니다.