Kikuchi Takashi, Nakamura Masaki, Hachisu Yushi, Hirai Shinichiro, Yokoyama Eiji
Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan.
Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan.
J Infect Chemother. 2022 Apr;28(4):521-525. doi: 10.1016/j.jiac.2021.12.020. Epub 2022 Jan 10.
The prevalence of the phylogenetic groups of Mycobacterium tuberculosis Beijing genotype has been reported to be similar in different areas of Japan. However, recent reports from rural areas of Japan show a low prevalence of modern Beijing strains, suggesting that the distribution of modern Beijing strains may have changed recently. Therefore, multi-locus variable number of tandem repeats analysis (MLVA) and draft whole genome sequence (DWGS) analysis were carried out to investigate the prevalence of particular genotype strains.
Nine hundred and ninety modern Beijing strains were studied using minimum spanning tree (MST) analysis and neighbor-net analysis of MLVA and WGS data.
An MST of M. tuberculosis Beijing genotype strains reconstructed from 12 loci-MLVA data showed two large complexes with the J-0006 MLVA pattern. In one of the complexes, strains with the pECT07 pattern produced by 24 loci-MLVA and its SLVs were most prevalent. DWGS analysis was carried out for pECT07 and its SLV strains. Neighbor-net and MST analyses of the DWGS data showed that pECT07 and its SLV strains were grouped in separate clusters. When all the combinations of two of the tested strains were analyzed, MST analysis showed that only 9 (1.7%) of the 528 pairs of tested strains had 5 or less SNPs.
The results of this study suggested that pECT07 and its variants were prevalent among M. tuberculosis modern Beijing strains in Chiba Prefecture, but the prevalence of those strains may not have been due to an earlier large-scale latent outbreak.
据报道，结核分枝杆菌北京基因型的系统发育群在日本不同地区的流行率相似。然而，日本农村地区最近的报告显示现代北京菌株的流行率较低，这表明现代北京菌株的分布可能最近发生了变化。因此，开展了多位点可变数目串联重复序列分析（MLVA）和全基因组草图序列（DWGS）分析，以调查特定基因型菌株的流行情况。
使用最小生成树（MST）分析以及MLVA和WGS数据的邻接网分析，对990株现代北京菌株进行了研究。
根据12个位点的MLVA数据重建的结核分枝杆菌北京基因型菌株的MST显示，有两个大的复合体具有J-0006 MLVA模式。在其中一个复合体中，由24个位点的MLVA产生的具有pECT07模式的菌株及其单核苷酸多态性（SNP）侧翼变异株最为普遍。对pECT07及其SNP侧翼变异株进行了DWGS分析。DWGS数据的邻接网和MST分析表明，pECT07及其SNP侧翼变异株被归为不同的簇。当对所测试菌株的两两组合进行所有分析时，MST分析显示，在528对测试菌株中，只有9对（1.7%）的SNP数量为5个或更少。
本研究结果表明，pECT07及其变异株在千叶县的结核分枝杆菌现代北京菌株中很普遍，但这些菌株的流行可能并非由于早期大规模的潜伏性暴发。
