title: Genetic diversity of Mycobacterium tuberculosis isolates from foreign-born and Japan-born residents in Tokyo.
abstract: Sequences of the full genomes of 259 clinical isolates of Mycobacterium tuberculosis, obtained from foreign-born and Japan-born patients in Tokyo, Japan, were determined, and a phylogenetic tree constructed by concatenated single-nucleotide polymorphism (SNP) sequences. The 259 isolates were clustered into four clades: Lineage 2 (East Asian or "Beijing" genotype; n = 182, 70.3%), Lineage 4 (Euro-American, n = 46, 17.8%), Lineage 1 (Indo-Oceanic, n = 23, 8.9%), and Lineage 3 (East African-Indian, n = 8, 3.1%). Of the 259, 36 (13.9%) were resistant to at least one drug. There was no multi-drug-resistant isolate. Drug resistance was greater for the strains in Lineage 2 than the non-Lineage 2. The proportion of Lineage 2 isolates was significantly smaller in foreign-born (n = 43/91, 47.3%) than in Japan-born (n = 139/168, 82.7%) patients, whereas the proportion of Lineage 1 isolates was significantly larger in foreign-born (n = 19/91, 20.9%) than in Japan-born (n = 4/168, 2.4%) patients. We also found eight SNPs specific to the typical Beijing sub-genotype in Lineage 2, including 4 non-synonymous SNPs. Of the 259 isolates, 244 had strain-specific SNP(s) and small (1-30-bp) insertions and deletions (indels). The numbers of strain-specific SNPs and indels per isolate were significantly larger from foreign-born (median 89, range 0-520) than from Japan-born (median 23, range 0-415) (p 3.66E-15) patients. These results suggested that M. tuberculosis isolates from foreign-born patients had more genetic diversity than those from Japan-born patients.
authors.affiliation: Department of Infectious Diseases, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Kato-Miyazawa
authors.affiliation: Department of Infectious Diseases, Japan; Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Miyoshi-Akiyama
authors.affiliation: Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Kanno
authors.affiliation: Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Takasaki
authors.affiliation: Department of Infectious Diseases, Japan. Electronic address: tkirikae@ri.ncgm.go.jp.
authors.forename: T
authors.initials: T
authors.lastname: Kirikae
authors.affiliation: Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan; National Hospital Organization Tokyo National Hospital, Tokyo, Japan.
authors.forename: N
authors.initials: N
authors.lastname: Kobayashi
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000995:Antitubercular Agents / Q000494:pharmacology; D044466:Asian People; D024881:Drug Resistance, Bacterial; D054242:Emigrants and Immigrants; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014041:Tokyo / Q000453:epidemiology; D014376:Tuberculosis / Q000453:epidemiology* / Q000382:microbiology*; D055815:Young Adult
chemical_list: D000995:Antitubercular Agents
keywords: Epidemiology; Mycobacterium tuberculosis; foreign-born; lineage; whole genome sequencing