論文

査読有り
2015年10月

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

INFECTION GENETICS AND EVOLUTION
  • Junji Seto
  • Takayuki Wada
  • Tomotada Iwamoto
  • Aki Tamaru
  • Shinji Maeda
  • Kaori Yamamoto
  • Atsushi Hase
  • Koichi Murakami
  • Eriko Maeda
  • Akira Oishi
  • Yuji Migita
  • Taro Yamamoto
  • Tadayuki Ahiko
  • 全て表示

35
開始ページ
82
終了ページ
88
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1016/j.meegid.2015.07.029
出版者・発行元
ELSEVIER SCIENCE BV

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 (24(Beijing)-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. (C) 2015 Elsevier B.V. All rights reserved.

リンク情報
DOI
https://doi.org/10.1016/j.meegid.2015.07.029
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/26220897
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000362607400012&DestApp=WOS_CPL
ID情報
  • DOI : 10.1016/j.meegid.2015.07.029
  • ISSN : 1567-1348
  • eISSN : 1567-7257
  • PubMed ID : 26220897
  • Web of Science ID : WOS:000362607400012

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