Complete Genome Sequence of Mycobacterium intracellulare Clinical Strain MOTT-64, Belonging to the INT1 Genotype

Abstract

Here, we report the complete genome sequence of the Mycobacterium intracellulare clinical strain MOTT-64, previously grouped into the INT1 genotype among five genotypes of M. intracellulare. This genome sequence will serve as a valuable reference for understanding the disparity in the virulence and epidemiologic traits among M. intracellulare genotypes.

GENOME ANNOUNCEMENT

Members of the Mycobacterium avium complex (MAC) are the most frequently isolated nontuberculous mycobacteria (NTM) (1, 8). Mycobacterium intracellulare has been reported to be isolated more frequently than M. avium in South Korea (4, 5, 7). Previously, we reported that 94 M. intracellulare clinical isolates from Korean patients were divided into five genotypes (INT1, INT2, INT3, INT4, and INT5) (6). Recently, we have introduced the complete genome sequences of two M. intracellulare strains belonging to the INT2 genotype, M. intracellulare ATCC 13950^T (GenBank accession no. CP003322) (3) and MOTT-02 (GenBank accession no. CP003323) (2).

The aim of the present study is to introduce the complete genome sequence of M. intracellulare clinical strain MOTT-64, which belongs to INT1, the most frequently encountered genotype in South Korea (6). The MOTT-64 genome was sequenced by a standard shotgun strategy using GS FLX pyrosequencing technology. Sequencing analysis was performed in the National Instrumentation Center for Environmental Management (NICEM; genome analysis unit) at Seoul National University, Seoul, Republic of Korea. A total of 544,705 reads were generated, with an average read length of 435, yielding 236,979,211 bp of total sequence. This represents ∼43× coverage for the estimated 5.5-Mb genome. The obtained contigs were compared for mapping to the whole genome sequences of reference strains 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. Genome annotation was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP; http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).

Comparison of the MOTT-64 genome with those of two M. intracellulare strains, M. intracellulare ATCC 13950^T (GenBank accession no. CP003322) (3) and MOTT-02 (GenBank accession no. CP003323) (2), shows that it has a circular DNA molecule of 5,501,090 bp with no plasmid and is thus larger than the genome of M. intracellulare ATCC 13950^T (5,402,402 bp) or MOTT-02 (5,409,696 bp). MOTT-64 carries more protein-encoding genes (5,251 open reading frames [ORFs]) than M. intracellulare ATCC 13950^T (5,145 ORFs) or MOTT-02 (5,151 ORFs), but it has fewer tRNA genes (46 tRNA genes) than M. intracellulare ATCC 13950^T (47 tRNA genes) or MOTT-02 (47 tRNA genes). The genome of Mycobacterium strain MOTT-64 has a G+C content of 68.07%. Comparison of the predicted ORFs between ATCC 13950^T and MOTT-64 shows that 295 ORFs (5.7%) and 395 ORFs (7.5%) are specific to ATCC 13950^T and MOTT-64, respectively. Comparison of the predicted ORFs between MOTT-64 and MOTT-02 shows that 400 ORFs (7.6%) and 301 ORFs (5.8%) are specific to MOTT-64 and MOTT-02, respectively. Our phylogenetic analysis based on complete genome sequences from the NCBI microbial sequence databases also shows that MOTT-64, a member of the INT1 genotype, is phylogenetically separated from two strains of the INT2 genotype, M. intracellulare ATCC 13950^T and MOTT-02 (2, 3). This genome sequence will serve as a valuable reference for understanding the disparity in the virulence and epidemiologic traits among M. intracellulare genotypes.

Nucleotide sequence accession number.

The whole-genome sequence of Mycobacterium strain MOTT-64 has been deposited at GenBank under the accession number CP003324.