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Draft genome sequence of Mycobacterium abscessus subsp. bolletii BD(T).

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2012, 194(10):2756. DOI: 10.1128/JB.00354-12.

J. Bacteriol.

Chun, Sang-Nae Cho and Sung Jae Shin

Go-Eun Choi, Yong-Joon Cho, Won-Jung Koh, Jongsik

T

abscessus subsp. bolletii BD

Draft Genome Sequence of Mycobacterium

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Draft Genome Sequence of Mycobacterium abscessus subsp.

bolletii BD

T

Go-Eun Choi,aYong-Joon Cho,b,cWon-Jung Koh,dJongsik Chun,b,c,eSang-Nae Cho,fand Sung Jae Shinf

Department of Microbiology and Research Institute for Medical Sciences, College of Medicine, Chungnam National University, Daejeon, Republic of Koreaa; Chunlab, Inc.,b

and School of Biological Sciences, Seoul National University,cSeoul, Republic of Korea; Division of Pulmonary and Critical Care Medicine, Department of Medicine,

Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Republic of Koread; A.I.C.T., Suwon, Gyeonggi-do, Republic of Koreae; and Department of

Microbiology, Yonsei University College of Medicine, Seoul, Republic of Koreaf

Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and

soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BDT.

M

ycobacterium abscessus subsp. bolletii belongs to a group of rapidly growing mycobacteria (RGM) (10). However, M. bolletii has been shown to be highly resistant to clarithromycin, unlike other RGM. Mycobacterium bolletii was first isolated in 2006 from the sputum of a patient with chronic pneumonia and later from a group of patients with cystic fibrosis (1). Consistent reports of human infections and several recent outbreaks indicate that M. bolletii is a highly pathogenic, emerging RGM species (5, 10). Historically, M. bolletii was recognized as separate from the Mycobacterium chelonae-Mycobacterium abscessus complex (1). However, the reclassification of M. bolletii as Mycobacterium ab-scessus subsp. bolletii was proposed in accordance with the rules of the Bacteriological Code (6).

To understand the genetics of M. bolletii in detail, the com-plete genome of the M. abscessus subsp. bolletii BDTtype strain

(⫽CIP108541) was obtained from the Collection of Institute Pasteur (Paris, France). The genome was sequenced and anno-tated.

The sequence data were obtained using Illumina GA IIx (San Diego, CA) with 100-bp single-end information (13,144,849 reads,⬃1,165.9 Mb). All reads were assembled into 22 contigs by de novo assembly. Reference mapping results for Mycobac-terium abscessus subsp. abscessus ATCC 19977Twere obtained

using CLC Genomics Workbench 4.6 (CLC bio, Aarhus, Den-mark). Coverage of the genome reached⬃231-fold; the N50

contig size was 462.2 kb. The functional annotation of pre-dicted coding regions was achieved using the RAST server (2) and BLASTP-based comparisons with the KEGG (4) and COG (9) databases.

The draft genome of M. bolletii BDTincludes 5,048,007 bp with

a 64.0% G⫹C content. It contains 4,923 protein-coding genes and 47 tRNA-encoding genes. Judging from coverage, two rRNA operons exist in the genome. Functions were assigned to 56.1% (2,782) of the total coding sequences; 8.7% (428) were found to be hypothetical proteins that are unique to this strain.

The average nucleotide identity (ANI) values between strain BDTand ATCC 19977Twere 96.64 and 96.7%, respectively, from comparisons in each direction. These correspond to DNA-DNA hybridization values of over 70% and agree with the classical spe-cies cutoff point (3).

We also detected the presence of a 63-kb prophage, but functional genes were not found. Comparative genomic analysis with M.

absces-sus ATCC 19977Trevealed that M. bolletii BDTcontains more viru-lence factor mammalian cell entry (MCE) operons. These proteins have high similarity to those from Mycobacterium sp. strain KMS, which supports the possibility of horizontal gene transfer between mycobacteria (8). In addition, several methyltransferases, glycosyl-transferases, and dehydrogenases, which participate in cell wall syn-thesis and modification (7), were detected in insertion regions. We expect that the complete, annotated genomic sequence of M. bolletii will facilitate the future understanding of this bacterium’s pathogenic properties.

Nucleotide sequence accession number. The draft genome

se-quence of M. abscessus subsp. bolletii BDThas been deposited in

the GenBank database under accession numberAHAS00000000.

ACKNOWLEDGMENT

This study was supported by a grant of the Korea Health Technology R&D Project, Ministry of Health & Welfare, Republic of Korea (A101750).

REFERENCES

1. Adekambi T, Berger P, Raoult D, Drancourt M. 2006. rpoB gene se-quence-based characterization of emerging non-tuberculous mycobacte-ria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov. Int. J. Syst. Evol. Microbiol. 56:133–143.

2. Aziz RK, et al. 2008. The RAST server: rapid annotations using subsys-tems technology. BMC Genomics 9:75.

3. Goris J, et al. 2007. DNA-DNA hybridization values and their relation-ship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol.

57:81–91.

4. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:D277– D280.

5. Koh WJ, et al. 2009. First case of disseminated Mycobacterium bolletii infection in a young adult patient. J. Clin. Microbiol. 47:3362–3366. 6. Leao SC, Tortoli E, Euzéby JP, Garcia MJ. 2011. Proposal that the two

species Mycobacterium massiliense and Mycobacterium bolletii be reclassi-fied as Mycobacterium abscessus subsp. bolletii comb. nov., designation of

Received 5 March 2012 Accepted 7 March 2012

Address correspondence to Sung Jae Shin, sjshin05@gmail.com. G.-E.C. and Y.-J.C. contributed equally to this article.

Copyright © 2012, American Society for Microbiology. All Rights Reserved.

doi:10.1128/JB.00354-12

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Mycobacterium abscessus subsp. abscessus subsp. nov., and emended de-scription of Mycobacterium abscessus. Int. J. Syst. Evol. Microbiol. 61: 2311–2313.

7. Perez E, et al. 2004. Characterization of three glycosyltransferases involved in the biosynthesis of the phenolic glycolipid antigens from the Mycobacterium tuberculosis complex. J. Biol. Chem. 279:42574 – 42583.

8. Ripoll F, et al. 2009. Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS One 4:e5660. 9. Tatusov RL, et al. 2003. The COG database: an updated version includes

eukaryotes. BMC Bioinformatics 4:41.

10. Zelazny AM, et al. 2009. Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Myco-bacterium bolletii. J. Clin. Microbiol. 47:1985–1995.

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