Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 26, Number 11—November 2020

Two New Cases of Pulmonary Infection by Mycobacterium shigaense, Japan

Shiomi Yoshida1Comments to Author , Tomotada Iwamoto1, Takehiko Kobayashi1, Ryohei Nomoto, Yoshikazu Inoue, Kazunari Tsuyuguchi, and Katsuhiro Suzuki
Author affiliations: National Hospital Organization Kinki-chuo Chest Medical Center, Sakai, Osaka, Japan (S. Yoshida, T. Kobayashi, Y. Inoue, K. Tsuyuguchi, K. Suzuki); Kobe Institute of Health, Kobe, Japan (T. Iwamoto, R. Nomoto)

Main Article

Table 2

SNP detection using Mycobacterium shigaense JCM 32072T as reference genome for 2 strains isolated*

Strain no.
No. SNPs
Mapped region to reference genome†
Pseudogenome by BactSNP, bases
Length, bases
Coverage ratio
Case 2, NB-type, KC354 19 5,232,622 0.99999 5,182,569
Case 1, FC-type, KC8 6,826 5,200,032 0.99376 5,138,016

*SNPs called by BactSNP pipeline (9). FC, fibrocavitary; NB, nodular bronchiectasis; SNP, single-nucleotide polymorphism.
†Coverage depth is >5 at each position of the reference genome (5,232,660).

Main Article

  1. Griffith  DE, Aksamit  T, Brown-Elliott  BA, Catanzaro  A, Daley  C, Gordin  F, et al.; ATS Mycobacterial Diseases Subcommittee; American Thoracic Society; Infectious Disease Society of America. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med. 2007;175:367416. DOIPubMedGoogle Scholar
  2. Hoefsloot  W, van Ingen  J, Andrejak  C, Ängeby  K, Bauriaud  R, Bemer  P, et al.; Nontuberculous Mycobacteria Network European Trials Group. The geographic diversity of nontuberculous mycobacteria isolated from pulmonary samples: an NTM-NET collaborative study. Eur Respir J. 2013;42:160413. DOIPubMedGoogle Scholar
  3. Hwang  JA, Kim  S, Jo  KW, Shim  TS. Natural history of Mycobacterium avium complex lung disease in untreated patients with stable course. Eur Respir J. 2017;49:1600537. DOIPubMedGoogle Scholar
  4. Nakanaga  K, Hoshino  Y, Wakabayashi  M, Fujimoto  N, Tortoli  E, Makino  M, et al. Mycobacterium shigaense sp. nov., a novel slowly growing scotochromogenic mycobacterium that produced nodules in an erythroderma patient with severe cellular immunodeficiency and a history of Hodgkin’s disease. J Dermatol. 2012;39:38996. DOIPubMedGoogle Scholar
  5. Fukano  H, Yoshida  M, Kazumi  Y, Fujiwara  N, Katayama  K, Ogura  Y, et al. Mycobacterium shigaense sp. nov., a slow-growing, scotochromogenic species, is a member of the Mycobacterium simiae complex. Int J Syst Evol Microbiol. 2018;68:243742. DOIPubMedGoogle Scholar
  6. Fukano  H, Hiranuma  O, Matsui  Y, Tanaka  S, Hoshino  Y. The first case of chronic pulmonary Mycobacterium shigaense infection in an immunocompetent patient. New Microbes New Infect. 2019;33:100630. DOIPubMedGoogle Scholar
  7. Clinical and Laboratory Standards Institute. Woods GL, Wengenack NL, Lin G, Brown-Elliott BA, Cirillo DM, Conville PS, et al. Performance standards for susceptibility testing of Mycobacteria, Nocardia spp., and other aerobic Actinomycetes, 2018. M62, 1st ed. Wayne (PA): The Institute, 2018.
  8. Richter  M, Rosselló-Móra  R, Oliver Glöckner  F, Peplies  J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics. 2016;32:92931. DOIPubMedGoogle Scholar
  9. Yoshimura  D, Kajitani  R, Gotoh  Y, Katahira  K, Okuno  M, Ogura  Y, et al. Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP. Microb Genom. 2019;5:e000261. DOIPubMedGoogle Scholar
  10. Page  AJ, Cummins  CA, Hunt  M, Wong  VK, Reuter  S, Holden  MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:36913. DOIPubMedGoogle Scholar
  11. Bouam  A, Armstrong  N, Levasseur  A, Drancourt  M. Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots. Sci Rep. 2018;8:9309. DOIPubMedGoogle Scholar
  12. Shu  C-C, Lee  C-H, Hsu  C-L, Wang  J-T, Wang  J-Y, Yu  C-J, et al.; TAMI Group. Clinical characteristics and prognosis of nontuberculous mycobacterial lung disease with different radiographic patterns. Hai. 2011;189:46774. DOIPubMedGoogle Scholar
  13. Aksamit  TR, Philley  JV, Griffith  DE. Nontuberculous mycobacterial (NTM) lung disease: the top ten essentials. Respir Med. 2014;108:41725. DOIPubMedGoogle Scholar
  14. Griffith  DE, Philley  JV. The new “Hesitation Blues”: initiating Mycobacterium avium complex lung disease therapy. Eur Respir J. 2017;49:1700110. DOIPubMedGoogle Scholar
  15. Koizumi  Y, Shimizu  K, Shigeta  M, Minamiguchi  H, Hodohara  K, Andoh  A, et al. Mycobacterium shigaense causes lymph node and cutaneous lesions as immune reconstitution syndrome in an AIDS patient: the third case report of a novel strain non-tuberculous Mycobacterium. Intern Med. 2016;55:337581. DOIPubMedGoogle Scholar

Main Article

1These authors contributed equally to this article.

Page created: July 16, 2020
Page updated: October 19, 2020
Page reviewed: October 19, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.