Draft Genome Sequence of Mycobacterium abscessus subsp. bolletii BD^T

Abstract

Mycobacterium abscessus subsp. bolletii is an increasing cause of human pulmonary disease and infections of the skin and soft tissues. Consistent reports of human infections indicate that M. bolletii is a highly pathogenic, emerging species of rapidly growing mycobacteria (RGM). Here we report the first whole-genome sequence of M. abscessus subsp. bolletii BD^T.

GENOME ANNOUNCEMENT

Mycobacterium abscessus subsp. bolletii belongs to a group of rapidly growing mycobacteria (RGM) (10). However, M. bolletii has been shown to be highly resistant to clarithromycin, unlike other RGM. Mycobacterium bolletii was first isolated in 2006 from the sputum of a patient with chronic pneumonia and later from a group of patients with cystic fibrosis (1). Consistent reports of human infections and several recent outbreaks indicate that M. bolletii is a highly pathogenic, emerging RGM species (5, 10). Historically, M. bolletii was recognized as separate from the Mycobacterium chelonae-Mycobacterium abscessus complex (1). However, the reclassification of M. bolletii as Mycobacterium abscessus subsp. bolletii was proposed in accordance with the rules of the Bacteriological Code (6).

To understand the genetics of M. bolletii in detail, the complete genome of the M. abscessus subsp. bolletii BD^T type strain (=CIP108541) was obtained from the Collection of Institute Pasteur (Paris, France). The genome was sequenced and annotated.

The sequence data were obtained using Illumina GA IIx (San Diego, CA) with 100-bp single-end information (13,144,849 reads, ∼1,165.9 Mb). All reads were assembled into 22 contigs by de novo assembly. Reference mapping results for Mycobacterium abscessus subsp. abscessus ATCC 19977^T were obtained using CLC Genomics Workbench 4.6 (CLC bio, Aarhus, Denmark). Coverage of the genome reached ∼231-fold; the N₅₀ contig size was 462.2 kb. The functional annotation of predicted coding regions was achieved using the RAST server (2) and BLASTP-based comparisons with the KEGG (4) and COG (9) databases.

The draft genome of M. bolletii BD^T includes 5,048,007 bp with a 64.0% G+C content. It contains 4,923 protein-coding genes and 47 tRNA-encoding genes. Judging from coverage, two rRNA operons exist in the genome. Functions were assigned to 56.1% (2,782) of the total coding sequences; 8.7% (428) were found to be hypothetical proteins that are unique to this strain.

The average nucleotide identity (ANI) values between strain BD^T and ATCC 19977^T were 96.64 and 96.7%, respectively, from comparisons in each direction. These correspond to DNA-DNA hybridization values of over 70% and agree with the classical species cutoff point (3).

We also detected the presence of a 63-kb prophage, but functional genes were not found. Comparative genomic analysis with M. abscessus ATCC 19977^T revealed that M. bolletii BD^T contains more virulence factor mammalian cell entry (MCE) operons. These proteins have high similarity to those from Mycobacterium sp. strain KMS, which supports the possibility of horizontal gene transfer between mycobacteria (8). In addition, several methyltransferases, glycosyltransferases, and dehydrogenases, which participate in cell wall synthesis and modification (7), were detected in insertion regions. We expect that the complete, annotated genomic sequence of M. bolletii will facilitate the future understanding of this bacterium's pathogenic properties.

Nucleotide sequence accession number.

The draft genome sequence of M. abscessus subsp. bolletii BD^T has been deposited in the GenBank database under accession number AHAS00000000.