Draft Genome Sequence of Mycobacterium boenickei CIP 107829

ABSTRACT

Mycobacterium boenickei is a rapidly growing mycobacterium isolated for the first time from a leg wound in the United States. Its 6,506,908-bp draft genome exhibits a 66.77% G+C content, 6,279 protein-coding genes, and 59 predicted RNA genes. In silico DNA-DNA hybridization confirms its assignment to the Mycobacterium fortuitum complex.

GENOME ANNOUNCEMENT

Mycobacterium boenickei has been characterized as one of the members of the former M. fortuitum third biovariant complex sorbitol-negative (1). It is an acid-fast, Gram-positive, pleomorphic bacterium, forming white to slightly beige colonies in less than 7 days. It was initially isolated from a leg wound in the United States (1). M. boenickei encodes the intrinsic macrolide resistance gene erm (2), rendering it resistant to clarithromycin (3).

We performed the whole-genome sequencing of M. boenickei in order to describe its genomic content and to determine its phylogenetic relationships for facilitating the detection and identification of this species.

M. boenickei CIP 107829 (and Collection de Souches de l’Unité des Rickettsies, CSUR 25) was cultured in MGIT Middlebrook liquid culture (Becton Dickinson, Le Pont-de-Claix, France) at 37°C. M. boenickei CIP 107829 genomic DNA was sequenced by Illumina MiSeq runs (Illumina Inc, San Diego, CA, USA) with the mate-pair strategy using the Nextera mate-pair sample prep kit (Illumina). The index representation for M. boenickei CIP 107829 was determined to be 8.67%. A total of 1,391,382 paired-end reads were filtered per the read qualities. These reads were trimmed using Trimmomatic (4) and then assembled into scaffolds using SPAdes version 3.5 (5, 6) before manual finishing. SSPACE version 2 (7) and Opera version 2 (8) were used to combine the contigs, and GapFiller version 1.10 (9) was used to close gaps in the scaffolds. This yielded a draft genome comprising 14 scaffolds composed of 14 contigs, for a total of 6,506,908 bp with a 66.77% G+C content. Noncoding genes and miscellaneous features were predicted using RNAmmer (10), ARAGORN (11), Rfam (12), Pfam (13), and Infernal (14). Coding DNA sequences were predicted using Prodigal (15), and functional annotation was achieved using BLASTp against the GenBank database (16) and the Clusters of Orthologous Groups (COGs) database (17, 18). The genome was shown to encode 59 predicted RNAs, including 3 complete ribosomal operons (5S rRNA, 16S rRNA, and 23S rRNA genes) and 50 tRNAs. A total of 4,828 genes (76.89%) were assigned a putative function, 116 genes (1.85%) were identified as ORFans (open reading frames with no matches in the databases), and the remaining 1.035 genes (16.48%) were annotated as hypothetical proteins. The M. boenickei CIP 107829 genome was further incorporated into in silico DNA-DNA hybridization (DDH) (19) with reference genomes selected based on 16S rRNA gene proximity; DDH values were estimated using the GGDC version 2.0 online tool (20). This analysis yielded 36.35% ± 3.46 with M. septicum DSM 44393, 31.55% ± 3.46 with M. fortuitum strain CT6, 21.55% ± 3.32 with M. cosmeticum strain DSM 44829, 20.95% ± 3.32 with M. neoaurum VKM, 20% ± 3.25 with M. abscessus subsp. bolletii strain MA 1948, and 19.9% ± 3.25 with M. chelonae CCUG 47445, confirming at the genome level the taxonomic assignment of M. boenickei to the M. fortuitum complex.

Accession number(s).

The M. boenickei CIP 107829 genome sequence has been deposited at EMBL under the accession number FUWC00000000.