Genomics Study of Mycobacterium tuberculosis Strains from Different Ethnic Populations in Taiwan

Abstract

To better understand the transmission and evolution of Mycobacterium tuberculosis (MTB) in Taiwan, six different MTB isolates (representatives of the Beijing ancient sublineage, Beijing modern sublineage, Haarlem, East-African Indian, T1, and Latin-American Mediterranean (LAM)) were characterized and their genomes were sequenced. Discriminating among large sequence polymorphisms (LSPs) that occur once versus those that occur repeatedly in a genomic region may help to elucidate the biological roles of LSPs and to identify the useful phylogenetic relationships. In contrast to our previous LSP-based phylogeny, the sequencing data allowed us to determine actual genetic distances and to define precisely the phylogenetic relationships between the main lineages of the MTB complex. Comparative genomics analyses revealed more nonsynonymous substitutions than synonymous changes in the coding sequences. Furthermore, MTB isolate M7, a LAM-3 clinical strain isolated from a patient of Taiwanese aboriginal origin, is closely related to F11 (LAM), an epidemic tuberculosis strain isolated in the Western Cape of South Africa. The PE/PPE protein family showed a higher dn/ds ratio compared to that for all protein-coding genes. Finally, we found Haarlem-3 and LAM-3 isolates to be circulating in the aboriginal community in Taiwan, suggesting that they may have originated with post-Columbus Europeans. Taken together, our results revealed an interesting association with historical migrations of different ethnic populations, thus providing a good model to explore the global evolution and spread of MTB.

Experiments Investigating the Competitive Growth Advantage of Two Different Genotypes of Human Metapneumovirus: Implications for the Alternation of Genotype Prevalence

“…This is inconsistent with the conclusion that subtype A is the dominant strain in human 52,53 . It may be that the hMPV dominant strain is different in different populations, or that our experiment time is too short 54,55 . In a word, our experiments showed that the competition exist between the two subtypes and this competition could affect the alternation of genotype prevalence.…”

Lineage-specific SNPs for genotyping of Mycobacterium tuberculosis clinical isolates

“…After performing the de-multiplexing procedure, the average sequence size of each sample was 3.38 Gb, and the depths of these samples ranged from 568- to 1068-fold when mapped to the H37Rv reference sequence, resulting in a reference coverage of these samples of 99.44% to 99.82%. The detailed information was described in our recent article 29 .…”