Abstract
Mycobacterium abscessus is a species of rapidly growing nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. Here, we report the annotated genome sequence of M. abscessus strain M94, which showed an unusual cluster of tRNAs.
GENOME ANNOUNCEMENT
Mycobacterium abscessus is an environmental bacterium that is also an important pathogen in immunocompromised individuals (9). The infections caused by this organism are often difficult to treat because of resistance to antimicrobial agents (8). The genome of the M. abscessus type strain ATCC 19977 was first sequenced in 2009 (7). Since then, more DNA sequence information has become available, resulting in the discovery of increasing numbers of subspecies that are mostly identified by the sequences of rpoB, hsp65, and other genes (1, 2). These subspecies are now being examined for their genetic determinants of environmental survival and pathogenicity in the human host.
M. abscessus strain M94 is an isolate from a sputum sample of a Malaysian patient with a persistent cough and fever and consolidation in the chest radiograph. It was identified as M. abscessus subspecies abscessus (5) by its clustering with the reference strain Mycobacterium abscessus ATCC 19977 in a phylogenetic analysis based on multilocus sequencing with 7 housekeeping genes (10).
The genome of strain M94 (AJGG00000000) was shotgun sequenced using Illumina GA 2× technology. From the 2,352,350 reads generated, 83 contigs were obtained after assembly with Genomics Workbench 4.9. The N50 contig size was 145,063 bp. The genome is composed of a single circular chromosome of 5,095,496 bp with an average G/C content of 64%. Genome sequence annotation was carried out using the Rapid Annotation Subsystem Technology (RAST) Pipeline (3). The results showed 5,146 predicted coding sequences and 3 rRNA loci. Using tRNAscan-SE analysis (6), 62 tRNA were predicted throughout the genome, with a cluster of 16 tRNAs plus 1 pseudo-tRNA spanning the region from 51150 to 57394 in contig 33. This cluster was again observed when we reextracted DNA from M94 and repeated the sequencing using PacBio technology. Large tRNA gene clusters have been previously reported to be widespread in low-G+C-content Gram-positive bacteria (4) and could be associated with elevated levels of protein synthesis. We are conducting further investigations to examine the association of this cluster of tRNAs with the organism's pathogenicity.
Nucleotide sequence accession number.
The M. abscessus strain M94 genome sequence and annotation data can be accessed under NCBI GenBank accession number AJGG00000000.
ACKNOWLEDGMENTS
This work was supported by research grants UM.C/625/1/HIR/004 and UM.C/HIR/MOHE/08 from the University of Malaya, Kuala Lumpur, Malaysia.
REFERENCES
- 1. Adékambi T, Colson P, Drancourt M. 2003. rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J. Clin. Microbiol. 41: 5699–5708 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Adékambi T, Drancourt M. 2004. Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int. J. Syst. Evol. Microbiol. 54: 2095–2105 [DOI] [PubMed] [Google Scholar]
- 3. Aziz RK, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 8: 75 doi:10.1186/1471-2164-9-75.3 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Green CJ, Vold BS. 1993. Staphylococcus aureus has clustered tRNA genes. J. Bacteriol 175:5091–5096 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Leão SC, Tortoli E, Euzéby JP, Garcia MJ. 2011. Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. bolletii comb. nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus. Int. J. Syst. Evol. Microbiol. 61(Pt 9):2311–2313 [DOI] [PubMed] [Google Scholar]
- 6. 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]
- 7. Ripoll F, et al. 2009. Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus ATCC 19977. PLoS One 4: E5660 doi:10.1371/journal.pone.0005660 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Swenson JM, Wallace RJ, Jr, Silcox VA, Thornsberry C. 1985. Antimicrobial susceptibility of five subgroups of Mycobacterium fortuitum and Mycobacterium chelonae. Antimicrob. Agents Chemother. 28:807–811 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Wallace RJ, Jr, Brown BA, Griffith DE. 1998. Nosocomial outbreaks/pseudo-outbreaks caused by nontuberculous mycobacteria. Annu. Rev. Microbiol. 52: 453–490 [DOI] [PubMed] [Google Scholar]
- 10. Wong YL, Ong CS, Ngeow YF. 2012. Molecular typing of Mycobacterium abscessus based on tandem-repeat polymorphism. J. Clin. Microbiol. 50: 3084–3088 [DOI] [PMC free article] [PubMed] [Google Scholar]