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. 2018 Jun 21;6(25):e00552-18. doi: 10.1128/genomeA.00552-18

Complete Genome Sequence of Mycobacterium shigaense

Mitsunori Yoshida a, Hanako Fukano a, Yoshitoshi Ogura b, Yuko Kazumi c, Satoshi Mitarai c, Tetsuya Hayashi b, Yoshihiko Hoshino a,✉
PMCID: PMC6013605  PMID: 29930060

ABSTRACT

Mycobacterium shigaense is a slowly growing scotochromogenic species and a member of the Mycobacterium simiae complex group. Here, we report the complete sequence of its genome, comprising a 5.2-Mb chromosome. The sequence will represent the essential data for future phylogenetic and comparative genome studies of the Mycobacterium simiae complex group.

GENOME ANNOUNCEMENT

Mycobacterium shigaense was reported by Nakanaga et al. in 2012 as a causative agent of skin lesions in an immune-suppressed patient (1). After that, a total of six patients were diagnosed and another three cases have already been reported, and we recently summarized the characteristics of M. shigaense (2–5). Notably, among four out of six patients (66.7%), the place they live is the Shiga prefecture, for which this strain is named. The first clinical isolate (JCM 32072T) is a reference strain of “M. shigaense.” Here, we report the complete genome sequence of JCM 32072T.

The strain was grown with Middlebrook 7H9 medium. DNA was purified with the standard phenol-chloroform method. The genome sequence was determined using PacBio reads (149,374 subreads) obtained with an RS II system (Menlo Park, CA, USA), and Illumina 150 × 2 paired-end reads (692,827 reads) obtained with a MiSeq sequencer (Illumina, San Diego, USA) were used for correction of sequence and assembly errors (6–10). The reads were assembled into one contig by using the HGAP/Quiver assembly approach (11) and circularized using Circlator (12). Alignments produced by mapping Illumina reads to the assembly using the Burrows–Wheeler aligner (13) were used for correction of sequence and assembly errors with Pilon (14). Automated annotation was carried out with the DDBJ Fast Annotation and Submission Tool (DFAST) (https://dfast.nig.ac.jp) (8, 9, 15, 16). Average nucleotide identity (ANI) was calculated by JSpeciesWS (17).

The chromosome of JCM 32072T is 5,232,660 bp in length with 67.3% G+C content. The average nucleotide identities for this strain were between 76 and 81% of those for the M. simiae complex group (3). The chromosome contains 4,920 predicted protein-coding sequences (CDS), which is much fewer than those of the M. simiae strain MO323 (5,664 CDS). The genome sequence of M. shigaense JCM 32072T will represent the essential data for future phylogenetic and comparative genome studies and will be useful for better understanding the evolution of the M. simiae complex group.

Accession number(s).

This complete genome sequence has been deposited at DDBJ/ENA/GenBank under the accession no. AP018164.

ACKNOWLEDGMENTS

This work was supported in part by a grant from the Japan Agency for Medical Research and Development/Japan International Cooperation Agency (AMED) to Y. Hoshino (jp18fk0108043, jp18fk0108064, jp18fk0108075, and jp18jm0510004), by a Grant-in-Aid for Scientific Research (C) from the Japan Society for the Promotion of Science (JSPS) to Y. Hoshino (jp18K08312), by a Grant-in-Aid for Young Scientists (B) to M. Yoshida (jp17K16066), and by a Grant-in-Aid for Early-Career Scientists to H. Fukano (jp18K15966). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Footnotes

Citation Yoshida M, Fukano H, Ogura Y, Kazumi Y, Mitarai S, Hayashi T, Hoshino Y. 2018. Complete genome sequence of Mycobacterium shigaense. Genome Announc 6:e00552-18. https://doi.org/10.1128/genomeA.00552-18.

REFERENCES

  • 1.Nakanaga K, Hoshino Y, Wakabayashi M, Fujimoto N, Tortoli E, Makino M, Tanaka T, Ishii N. 2012. 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 39:389–396. doi: 10.1111/j.1346-8138.2011.01355.x. [DOI] [PubMed] [Google Scholar]
  • 2.Cui P, Vissa V, Li W, Zhang X, Lin L, Wang H, Liu X, Wu Q, Zong W. 2013. Cutaneous Mycobacterium shigaense infection in immunocompetent woman, China. Emerg Infect Dis 19:819–820. doi: 10.3201/eid1905.121022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Fukano H, Yoshida M, Kazumi Y, Fujiwara N, Ogura Y, Hayashi T, Miyamoto Y, Fujimoto N, Hongsheng W, Mizumoto C, Koizumi Y, Maeda H, Hiranuma O, Mitarai S, Ishii N, Hoshino Y. 2018. Mycobacterium shigaense sp. nov., a slow-growing, scotochromogenic species, is a member of the Mycobacterium simiae complex. Int J Syst Evol Microbiol, in press. [DOI] [PubMed] [Google Scholar]
  • 4.Koizumi Y, Shimizu K, Shigeta M, Minamiguchi H, Hodohara K, Andoh A, Tanaka T, Chikamatsu K, Mitarai S, Mikamo H. 2016. 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 55:3375–3381. doi: 10.2169/internalmedicine.55.6996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Naito D, Mizumoto C, Takeoka T, Tsuji M, Tomo K, Kazumi Y, Hoshino Y, Sakai N, Ohno T. 2016. Case report: a case of disseminated Mycobacterium shigaense infection. J Jpn Soc Intern Med 105:717–722. (In Japanese.) doi: 10.2169/naika.105.717. [DOI] [PubMed] [Google Scholar]
  • 6.Fukano H, Wada S, Kurata O, Katayama K, Fujiwara N, Hoshino Y. 2017. Mycobacterium stephanolepidis sp. nov., a rapidly growing species related to Mycobacterium chelonae, isolated from marine teleost fish, Stephanolepis cirrhifer. Int J Syst Evol Microbiol 67:2811–2817. doi: 10.1099/ijsem.0.002028. [DOI] [PubMed] [Google Scholar]
  • 7.Yoshida M, Fukano H, Miyamoto Y, Shibayama K, Suzuki M, Hoshino Y. 2018. Complete genome sequence of a type strain of Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus complex. Genome Announc 6:e01530-17. doi: 10.1128/genomeA.01530-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Yoshida M, Izumiyama S, Fukano H, Sugiyama K, Suzuki M, Shibayama K, Hoshino Y. 2017. Draft genome sequence of Mycobacterium sp. strain shizuoka-1, a novel mycobacterium isolated from groundwater of a bathing facility in Shizuoka, Japan. Genome Announc 5:e01309-17. doi: 10.1128/genomeA.01309-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Yoshida M, Miyamoto Y, Ogura Y, Hayashi T, Hoshino Y. 2017. Complete chromosome sequence of a mycolactone-producing mycobacterium, Mycobacterium pseudoshottsii. Genome Announc 5:e01363-17. doi: 10.1128/genomeA.01363-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Yoshida M, Nakanaga K, Ogura Y, Toyoda A, Ooka T, Kazumi Y, Mitarai S, Ishii N, Hayashi T, Hoshino Y. 2016. Complete genome sequence of Mycobacterium ulcerans subsp. shinshuense. Genome Annouc 4:e01050-16. doi: 10.1128/genomeA.01050-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
  • 12.Hunt M, De Silva N, Otto TD, Parkhill J, Keane JA, Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 16:294. doi: 10.1186/s13059-015-0849-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. doi: 10.1093/bioinformatics/btp324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Fukano H, Yoshida M, Shimizu A, Iwao H, Katayama Y, Omatsu T, Mizutani T, Kurata O, Wada S, Hoshino Y. 2018. Draft genome sequence of Mycobacterium montefiorense isolated from Japanese black salamander (Hynobius nigrescens). Genome Announc 6:e00448-18. doi: 10.1128/genomeA.00448-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Yoshida M, Fukano H, Miyamoto Y, Shibayama K, Suzumi M, Hoshino Y. 2018. Complete genome sequence of Mycobacterium marinum ATCC 927T, obtained using Nanopore and Illumina sequencing technologies. Genome Announc 6:e00397-18. doi: 10.1128/genomeA.00397-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Richter M, Rosselló-Móra R, Glöckner FO, Peplies J. 2016. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. doi: 10.1093/bioinformatics/btv681. [DOI] [PMC free article] [PubMed] [Google Scholar]

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