Abstract
We report the complete genome sequence of the Mycobacterium massiliense clinical strain Asan 50594, which was grouped into the M. massiliense type II genotype, isolated from a Korean patient. This genome sequence will serve as a valuable reference for understanding the disparity in virulence and epidemiological traits between strains belonging to the Mycobacterium abscessus complex.
GENOME ANNOUNCEMENT
Globally, Mycobacterium abscessus is the most commonly encountered pathogen among rapidly growing mycobacteria (RGM) (1). In South Korea, infection from M. abscessus is also the most prevalent RGM infection, second only to the Mycobacterium avium complex for nontuberculous mycobacterium (NTM) (2, 3). The recent application of multilocus sequencing has broadened our knowledge about the diversity of the strains in the M. abscessus complex (4, 5). Of these, Mycobacterium massiliense infections have gained importance since they cause soft tissue infection outbreaks (6) and pulmonary infections (7, 8). Recently, our group has introduced a novel hsp65 genotype (type II) of M. massiliense, related to the rough colony morphotype, from Korean patients (9).
The aim of the present study is to introduce the complete genome sequence of M. massiliense clinical strain Asan 50594, belonging to the M. massiliense type II genotype (9). This strain was isolated from a patient with a pulmonary infection. The genome was sequenced by a standard shotgun strategy using GS FLX pyrosequencing technology. Sequencing analysis was performed at the National Instrumentation Center for Environmental Management (NICEM) (genome analysis unit) at Seoul National University. A total of 1,124,128 reads were generated, with an average read length of 342.7 bp, yielding 385,247,859 bp of total sequences. This represents ~77× coverage for the estimated 5.0-Mb chromosome size. The 61 contigs we obtained were compared for mapping to the whole-genome sequences of the reference strain using the BLASTz program (http://www.bx.psu.edu/miller_lab/). All the remaining gaps between contigs were completely filled by ~50-fold Solexa reads and PCR amplifications. The protein-coding genes (open reading frames [ORFs]) were predicted by Double ACT (http://www.hpa-bioinfotools.org.uk/pise/double_act.html) and the RAST server (10). The tRNAs and rRNAs were identified using tRNAscan-SE (11) and RNAmmer (12), respectively. Using the BLASTp program, each gene was identified by similarities and annotated. Finally, using Artemis (genome browser and annotation tool), the annotated ORFs were edited or corrected (13).
The M. massiliense type II (strain Asan 50594) genome has a circular DNA of 5,000,473 bp with two circular plasmids of 172,814 and 97,240 bp. It has a chromosomal size similar to those of M. abscessus CIP 104536T (5,067,172 bp) and M. massiliense strain GO 06 (5,068,807 bp). It carries more protein-coding genes (4,958 ORFs) than M. massiliense strain GO 06 (4,313 ORFs), but the number of ORFs is similar to that for M. abscessus CIP 104536T (4,920 ORFs). The M. massiliense type II genome includes 47 tRNA genes and one rRNA operon, comprising 5S, 16S, and 23S rRNA genes. The genome of M. massiliense type II and two plasmids have G+C contents of 64.22%, 64.18%, and 62.90%, respectively.
Nucleotide sequence accession numbers.
The whole-genome sequences of M. massiliense type II strain have been deposited at GenBank under the accession no. CP004374 to CP004376.
ACKNOWLEDGMENTS
This work was supported by a National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST, the Korean Ministry of Education, Science and Technology) (2013005810) and by a National Research Foundation of Korea (NRF) grant (no. 2012R1A1A2041449), Republic of Korea.
Footnotes
Citation Kim B-J, Kim B-R, Hong S-H, Seok S-H, Kook Y-H, Kim B-J. 2013. Complete genome sequence of Mycobacterium massiliense clinical strain Asan 50594, belonging to the type II genotype. Genome Announc. 1(4):e00429-13. doi:10.1128/genomeA.00429-13.
REFERENCES
- 1. Petrini B. 2006. Mycobacterium abscessus: an emerging rapid-growing potential pathogen. APMIS 114:319–328 [DOI] [PubMed] [Google Scholar]
- 2. Choi G-E, Jo Y, Shin SJ. 2012. Current understanding of Mycobacterium abscessus infection. J. Bacteriol. Virol. 42:17–28 [Google Scholar]
- 3. Koh WJ, Kwon OJ, Jeon K, Kim TS, Lee KS, Park YK, Bai GH. 2006. Clinical significance of nontuberculous mycobacteria isolated from respiratory specimens in Korea. Chest 129:341–348 [DOI] [PubMed] [Google Scholar]
- 4. Adekambi T, Berger P, Raoult D, Drancourt M. 2006. rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov. Int. J. Syst. Evol. Microbiol. 56:133–143 [DOI] [PubMed] [Google Scholar]
- 5. Adékambi T, Reynaud-Gaubert M, Greub G, Gevaudan MJ, La Scola B, Raoult D, Drancourt M. 2004. Amoebal coculture of “Mycobacterium massiliense” sp. nov. from the sputum of a patient with hemoptoic pneumonia. J. Clin. Microbiol. 42:5493–5501 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Kim HY, Yun YJ, Park CG, Lee DH, Cho YK, Park BJ, Joo SI, Kim EC, Hur YJ, Kim BJ, Kook YH. 2007. Outbreak of Mycobacterium massiliense infection associated with intramuscular injections. J. Clin. Microbiol. 45:3127–3130 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Kim HS, Lee KS, Koh WJ, Jeon K, Lee EJ, Kang H, Ahn J. 2012. Serial CT findings of Mycobacterium massiliense pulmonary disease compared with Mycobacterium abscessus disease after treatment with antibiotic therapy. Radiology 263:260–270 [DOI] [PubMed] [Google Scholar]
- 8. Mitra S, Tapadar SR, Banerjee D, Bhattacharjee S, Dey S, Kundu S. 2012. Pulmonary disease due to Mycobacterium massiliense. Indian J. Chest Dis. Allied Sci. 54:53–57 [PubMed] [Google Scholar]
- 9. Kim BJ, Yi SY, Shim TS, Do SY, Yu HK, Park YG, Kook YH, Kim BJ. 2012. Discovery of a novel hsp65 genotype within Mycobacterium massiliense associated with the rough colony morphology. PLoS One 7:e38420. 10.1371/journal.pone.0038420 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, Parkhill J, Rajandream MA. 2008. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24:2672–2676 [DOI] [PMC free article] [PubMed] [Google Scholar]