September 22, 2019  |  

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

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

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.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.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.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. Copyright©2018. The Korean Academy of Tuberculosis and Respiratory Diseases.

Journal: Tuberculosis and respiratory diseases
DOI: 10.4046/trd.2017.0091
Year: 2018

Read publication

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.