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Comparing two Mycobacterium tuberculosis genomes from Chinese immigrants with native genomes using Mauve alignments
File(s)
trd-81-e19.pdf (772.28 KB)
Published version
Author(s)
Ryu, Sungweon
Lee, Jeongsoo
Oh, Jee Youn
Kim, Byeong Ki
Kim, Young
Type
Journal Article
Abstract
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: (1) strains from Chinese individuals and (2) 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.
Date Issued
2018-07-01
Date Acceptance
2017-11-01
Citation
Tuberculosis and Respiratory Diseases, 2018, 81 (3), pp.216-221
URI
DOI
ISSN
0378-0066
Publisher
Korean National Tuberculosis Association
Start Page
216
End Page
221
Journal / Book Title
Tuberculosis and Respiratory Diseases
Volume
81
Issue
3
Copyright Statement
© 2018 The Korean Academy of Tuberculosis and Respiratory Diseases. It is identical to the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/)
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/29926541
PII: 81.e19
Subjects
Immigrants
Mycobacterium tuberculosis
Strains
Whole Genome Sequencing
Publication Status
Published online
Coverage Spatial
Korea (South)
Date Publish Online
2018-06-19