Comparing two mycobacterium tuberculosis genomes from Chinese immigrants with native genomes using mauve alignments

Sungweon Ryoo, Jeongsoo Lee, Jee Youn Oh, Byeong Ki Kim, Young Kim, Je Hyeong Kim, Chol Shin, Seung Heon Lee

Research output: Contribution to journalArticle

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: 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.

Original languageEnglish
Pages (from-to)216-221
Number of pages6
JournalTuberculosis and Respiratory Diseases
Volume81
Issue number3
DOIs
Publication statusPublished - 2018 Jul 1

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Mycobacterium tuberculosis
Tuberculosis
Genome
Republic of Korea
Conserved Sequence
Nucleic Acid Databases

Keywords

  • Immigrants
  • Mycobacterium tuberculosis
  • Strains
  • Whole genome sequencing

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine
  • Infectious Diseases

Cite this

Comparing two mycobacterium tuberculosis genomes from Chinese immigrants with native genomes using mauve alignments. / Ryoo, Sungweon; Lee, Jeongsoo; Oh, Jee Youn; Kim, Byeong Ki; Kim, Young; Kim, Je Hyeong; Shin, Chol; Lee, Seung Heon.

In: Tuberculosis and Respiratory Diseases, Vol. 81, No. 3, 01.07.2018, p. 216-221.

Research output: Contribution to journalArticle

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AU - Kim, Je Hyeong

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