Takashi Kikuchi1, Masaki Nakamura2, Yushi Hachisu2, Shinichiro Hirai3, Eiji Yokoyama2. 1. Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan. Electronic address: t.kkch6@pref.chiba.lg.jp. 2. Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan. 3. Division of Bacteriology, Chiba Prefectural Institute of Public Health, 666-2, Nitona, Chuo, Chiba, 260-8715, Japan; Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashi-murayama, Tokyo, 208-0011, Japan.
Abstract
INTRODUCTION: 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. METHODS: Nine hundred and ninety modern Beijing strains were studied using minimum spanning tree (MST) analysis and neighbor-net analysis of MLVA and WGS data. RESULTS: An MST of M. tuberculosis Beijing genotype strains reconstructed from 12 loci-MLVA data showed two large complexes with the J12-0006 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. CONCLUSIONS: 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.
INTRODUCTION: 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. METHODS: Nine hundred and ninety modern Beijing strains were studied using minimum spanning tree (MST) analysis and neighbor-net analysis of MLVA and WGS data. RESULTS: An MST of M. tuberculosis Beijing genotype strains reconstructed from 12 loci-MLVA data showed two large complexes with the J12-0006 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. CONCLUSIONS: 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.
Keywords:
Draft whole genome sequence analysis; Modern Beijing genotype; Molecular epidemiology; Multi-locus variable number of tandem repeats analysis; Mycobacterium tuberculosis