title: Phylogenetic assignment of Mycobacterium tuberculosis Beijing clinical isolates in Japan by maximum a posteriori estimation.
abstract: Intra-species phylogeny of Mycobacterium tuberculosis has been regarded as a clue to estimate its potential risk to develop drug-resistance and various epidemiological tendencies. Genotypic characterization of variable number of tandem repeats (VNTR), a standard tool to ascertain transmission routes, has been improving as a public health effort, but determining phylogenetic information from those efforts alone is difficult. We present a platform based on maximum a posteriori (MAP) estimation to estimate phylogenetic information for M. tuberculosis clinical isolates from individual profiles of VNTR types. This study used 1245 M. tuberculosis clinical isolates obtained throughout Japan for construction of an MAP estimation formula. Two MAP estimation formulae, classification of Beijing family and other lineages, and classification of five Beijing sublineages (ST11/26, STK, ST3, and ST25/19 belonging to the ancient Beijing subfamily and modern Beijing subfamily), were created based on 24 loci VNTR (24Beijing-VNTR) profiles and phylogenetic information of the isolates. Recursive estimation based on the formulae showed high concordance with their authentic phylogeny by multi-locus sequence typing (MLST) of the isolates. The formulae might further support phylogenetic estimation of the Beijing lineage M. tuberculosis from the VNTR genotype with various geographic backgrounds. These results suggest that MAP estimation can function as a reliable probabilistic process to append phylogenetic information to VNTR genotypes of M. tuberculosis independently, which might improve the usage of genotyping data for control, understanding, prevention, and treatment of TB.
authors.affiliation: Department of Microbiology, Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan. Electronic address: setoj@pref.yamagata.jp.
authors.forename: Junji
authors.initials: J
authors.lastname: Seto
authors.affiliation: Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan. Electronic address: twada@nagasaki-u.ac.jp.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Wada
authors.affiliation: Department of Microbiology, Kobe Institute of Health, 4-6 Minatojima-nakamachi, Chuo-ku, Kobe 650-0046, Japan.
authors.forename: Tomotada
authors.initials: T
authors.lastname: Iwamoto
authors.affiliation: Department of Microbiology, Osaka Prefectural Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
authors.forename: Aki
authors.initials: A
authors.lastname: Tamaru
authors.affiliation: School of Pharmacy, Hokkaido Pharmaceutical University, 7-15-4-1 Maeda, Teine-ku, Sapporo, Hokkaido 006-8590, Japan.
authors.forename: Shinji
authors.initials: S
authors.lastname: Maeda
authors.affiliation: Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan; Department of International Health, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Yamamoto
authors.affiliation: Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Hase
authors.affiliation: Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Murakami
authors.affiliation: Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan.
authors.forename: Eriko
authors.initials: E
authors.lastname: Maeda
authors.affiliation: Department of Health Science, Fukuoka Institute of Health and Environmental Sciences, 39 Mukaizano, Dazaifu, Fukuoka 818-0135, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Oishi
authors.affiliation: Department of Microbiology, Nagasaki Prefectural Institute for Environmental Research and Public Health, 2-1306-11 Ikeda, Ohmura, Nagasaki 856-0026, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Migita
authors.affiliation: Department of International Health, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; Department of International Health, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
authors.forename: Taro
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: Department of Microbiology, Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan.
authors.forename: Tadayuki
authors.initials: T
authors.lastname: Ahiko
mesh_terms: D000465:Algorithms; D015373:Bacterial Typing Techniques; D000068476:Beijing; D004269:DNA, Bacterial / Q000032:analysis; D005838:Genotype; D006801:Humans; D007564:Japan; D018598:Minisatellite Repeats; D008957:Models, Genetic; D058885:Multilocus Sequence Typing / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D010802:Phylogeny; D058974:Phylogeography; D014376:Tuberculosis / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial
keywords: Genotype; Maximum a posteriori; Mycobacterium tuberculosis; Phylogeny; VNTR