Volume 26, Number 11—November 2020
Two New Cases of Pulmonary Infection by Mycobacterium shigaense, Japan
||Mapped region to reference genome†
||Pseudogenome by BactSNP, bases
|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).
- 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;175:367–416.
- 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;42:1604–13.
- 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:
- 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;39:389–96.
- 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;68:2437–42.
- 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:
- 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.
- 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;32:929–31.
- 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:
- Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3.
- 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.
- 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;189:467–74.
- Aksamit TR, Philley JV, Griffith DE. Nontuberculous mycobacterial (NTM) lung disease: the top ten essentials. Respir Med. 2014;108:417–25.
- Griffith DE, Philley JV. The new “Hesitation Blues”: initiating Mycobacterium avium complex lung disease therapy. Eur Respir J. 2017;49:
- 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;55:3375–81.
1These authors contributed equally to this article.
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