Draft Genome Sequence of a Mycobacterium avium Complex Isolate from a Broadbill Bird.

We report the draft genome sequence of a Mycobacterium avium complex isolate. This isolate has an estimated genome size of 5.1 Mb with an average GC content of 68.9% and is predicted to carry 4,497 protein-encoding genes and 317 pseudogenes.

GENOME ANNOUNCEMENT

Mycobacterium avium complex (MAC) organisms cause opportunistic infections in humans, yet their epidemiology remains poorly understood. They are slowly growing environmental and animal-associated mycobacteria that have little notoriety except for the strains that cause disseminated infections in HIV-infected humans (1). Most MAC organisms are classified taxonomically as a single species, M. avium, which is divided into at least four subspecies, M. avium subsp. avium, M. avium subsp. hominissuis, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum (2). The only other species in this group is M. intracellulare. Genotyping of this diverse bacterial group has been achieved using intergenic spacers (3) and rpoB sequence analysis (4, 5).

The genome sequences of M. avium subsp. hominissuis strain 104 and M. avium subsp. avium ATCC 25291 have been made publically available, but neither has yet been formally published. Strain 104 was isolated from an immunocompromised human and ATCC 25291 was obtained from a bird. Here we present the draft genome sequence of another M. avium subspecies. This isolate was obtained from a broadbill bird (family Eurylaimidae; species not specified) from a Texas zoo in 2005. Analysis of the rpoB gene sequence using the method of Ben Salah et al. (4) shows that this isolate clusters with M. avium subsp. hominissuis.

Purified genomic DNA obtained from this isolate was subjected to whole-genome shotgun sequencing using the Ion PGM sequencing system (Ion Torrent) with 200-bp read chemistry (Life Technologies). Sequence coverage was 81.0×. A de novo assembly of the ~5.15-Mbp sequence using MIRA assembly software version 3.2.0 yielded 190 contigs. The sequence was annotated with the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok/). A total of 5 rRNA operons and 46 tRNA genes were identified.

Nucleotide sequence accession numbers.

This whole-genome shotgun project was deposited at DDBJ/EMBL/GenBank under the accession number AYLW00000000. The version described in this paper is AYLW01000000.