Analysis of the Genome of Mycobacterium abscessus Strain M94 Reveals an Uncommon Cluster of tRNAs

Siew Woh Choo, Yan Ling Wong, Mee Lian Leong, Hamed Heydari, Chia Sui Ong, Kee Peng Ng and Yun Fong Ngeow J. Bacteriol. 2012, 194(20):5724. DOI: 10.1128/JB.01407-12. Downloaded from http://jb.asm.org/ on September 30, 2013 by UNIVERSITY OF MALAYA

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GENOME ANNOUNCEMENT

Analysis of the Genome of Mycobacterium abscessus Strain M94 Reveals an Uncommon Cluster of tRNAs
Siew Woh Choo,b Yan Ling Wong,a Mee Lian Leong,b Hamed Heydari,b Chia Sui Ong,c Kee Peng Ng,a and Yun Fong Ngeowa
Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysiaa; Dental Research and Training Unit, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysiab; and Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysiac

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.

ycobacterium abscessus is an environmental bacterium that is also an important pathogen in immunocompromised individuals (9). The infections caused by this organism are often difcult to treat because of resistance to antimicrobial agents (8). The genome of the M. abscessus type strain ATCC 19977 was rst 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 identied 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 identied 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-GC-content Grampositive 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 organisms 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.

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Received 2 August 2012 Accepted 6 August 2012 Address correspondence to Yun Fong Ngeow, yunngeow@um.edu.my, or Siew Woh Choo, lchoo@um.edu.my. Copyright 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JB.01407-12

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