Phylogeographical particularity of the Mycobacterium tuberculosis Beijing family in South Korea based on international comparison with surrounding countries

Abstract

To understand the domestic population structure of Mycobacterium tuberculosis clinical isolates in the Republic of Korea, we genotypically analysed 80 isolates obtained from various geographical origins in the country. Of these, 64 (80.0 %) isolates were identified as Beijing family strains. It is particularly interesting that their phylogenetic classification, based on the ancient/ modern separation and the presence/absence of the genomic region RD181, revealed a majority of the ancient (RD181+) subfamily in the population. The 15 loci of variable number of tandem repeat(s) of mycobacterial interspersed repetitive units (15-MIRU-VNTR) were also analysed. Combination with the previous VNTR data reported from surrounding countries revealed that the topology of the minimum spanning tree was linked tightly not to the geographical origins of the patients but to the phylogenetic characteristics of the isolates. These results show that the phylogeographical distribution of the M. tuberculosis Beijing family around far-eastern Asia could be estimated using international accumulation and comparison of VNTR genotyping data. INTRODUCTIONThe Beijing family, a lineage of Mycobacterium tuberculosis, is well known for its highly endemic prevalence around East Asian countries and as a causative agent of tuberculosis (TB) (van Soolingen et al., 1995). In the Republic of Korea (South Korea), TB is still a major public health concern, with 34 157 (70.3 per 100 000) registered new TB patients in 2008 and 2376 deaths attributable to TB in 2007 (Korea Centers for Disease Control & Prevention, 2008). More than 70 % of M. tuberculosis strains isolated from Korean pulmonary TB patients belong to the Beijing family. 'K strain' (Park et al., 2000), one of the Beijing family strains, has been reported as the cause of a severe outbreak of TB in South Korea (Kim et al., 2001). Although their phylogenetic position in the Beijing family lineage has been unclear, Shamputa et al. (2010) reported recently that K strains show genetic diversity by some genotyping methods, even in isolates obtained from a single hospital.The detailed phylogenetic variation of the Beijing family has been unveiled by various genetic markers such as single nucleotide polymorphisms, regions of difference and variable number of tandem repeat (VNTR) loci (Filliol et al., 2006;Tsolaki et al., 2005;. A notable characteristic of the lineage is the insertion of IS6110 in a genomic region named NTF (Mokrousov et al., 2005;Plikaytis et al., 1994). This phylogenetic marker can classify the Beijing family into two distinct sublineages: ancient and modern. The modern Beijing sublineage has been more predominant than the ancient sublineage throughout the world, including countries surrounding South Korea (Bifani et al., 2002;Dou et al., 2008; Kremer et al., 2009; Mokrousov et al., 2005Mokrousov et al., , 2006 van Soolingen & Kremer, 2009). However, reported that the ancient Beijing sublineage has been observed to be exceptionally predominant in Japan.Abbreviations: MIRU-VNTR, ...

Novel DNA Chip Based on a Modified DigiTag2 Assay for High-Throughput Species Identification and Genotyping of Mycobacterium tuberculosis Complex Isolates

“…The correlations of genotypes based on 45 SNPs were analyzed across the other acceptable genotypic markers for M. tuberculosis. Previously published data and the genotyping results of 183 M. tuberculosis isolates revealed results concordant with spoligotyping and PGG results and were related to the presence or absence of TbD1, RD105, and RD181 and the orientation of IS6110 at the NTF region (24,(32)(33)(34)(35) (Table 3). The investigation of known spoligotype isolates, along with the previously published results, revealed that this SNP set was more informative for subgenotyping the BJ family (SCG2) ( Table 4).…”

Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation

“…Supply et al reported that M. tuberculosis lineages are distinguished by a minimum spanning tree (MST) of 24-MIRU-VNTR profiles of cosmopolitan isolates (Supply et al, 2006). Moreover, previous reports describe that VNTR clustering of detailed sublineages of the Beijing family was observed according to the phylogenetic classification (Kang et al, 2010;Maeda et al, 2010;Merker et al, 2015). These findings indicate that the phylogeny of M. tuberculosis can be estimated properly from VNTR genotypes that were originally improved to trace transmission routes.…”

“…These two subfamilies are classifiable further into refined types of sequences (STs) using the patterns of 10 single-nucleotide polymorphisms (SNPs) identified by genomic comparison among referential strains (Filliol et al, 2006;Iwamoto et al, 2008;Nakanishi et al, 2013). Such detailed subdivisions reflect the phylogeographical variation of the Beijing family in countries of eastern Asia (Kang et al, 2010;Wada et al, 2009b). The most outstanding features of the genetic population structure are found in Japan, located at the far eastern edge of Asia.…”

Genetic Diversity and Dynamic Distribution of Mycobacterium tuberculosis Isolates Causing Pulmonary and Extrapulmonary Tuberculosis in Thailand

“…In other high-BJ-burden countries, such as China, a high prevalence of modern BJ strains has also been reported; however, in other countries, such as Japan and South Korea, more strains from ancestral BJ genotypes (ST3 and ST19 in Japan and ST11 or ST26 in South Korea) have been found. Modern BJ genotypes (ST10 and ST22) are also predominant in Taiwan and Peru (17,18,29). The close historical relationship between China (39) and Japan (17) might be responsible for the BJ sublineages in Thailand.…”