Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments.
- Author:
Sungweon RYOO
1
;
Jeongsoo LEE
;
Jee Youn OH
;
Byeong Ki KIM
;
Young KIM
;
Je Hyeong KIM
;
Chol SHIN
;
Seung Heon LEE
Author Information
- Publication Type:Original Article
- Keywords: Immigrants; Mycobacterium tuberculosis; Strains; Whole Genome Sequencing
- MeSH: Asian Continental Ancestry Group*; Databases, Nucleic Acid; Emigrants and Immigrants*; Genome*; Humans; Korea; Mass Screening; Mycobacterium tuberculosis*; Mycobacterium*; Trees; Tuberculosis
- From:Tuberculosis and Respiratory Diseases 2018;81(3):216-221
- CountryRepublic of Korea
- Language:English
- 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.
