Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain DSM46621

GENOME ANNOUNCEMENT

Mycobacterium fortuitum is a nonpigmented rapidly growing Mycobacterium classified in Runyon group IV (5), first isolated from an amphibian source in 1905 and subsequently identified as the cause of a human cutaneous infection in a patient in 1938 (3). Like many other nontuberculous mycobacteria (NTM), M. fortuitum is found worldwide in natural and processed water sources, including chlorine-treated water, as well as in sewage, dirt, and hospital environments (4, 8). Major types of disease caused by M. fortuitum include, in decreasing order of frequency, infections of postsurgical wounds, soft tissue, skin, and lung (3, 5, 11). Occasionally reported miscellaneous infections include keratitis, endocarditis, lymphadenitis, meningitis, hepatitis, peritonitis, catheter-related sepsis, and disseminated infections (3, 6, 11). The M. fortuitum group is attracting attention due to its increasing number of cases, its virulence, and its emerging resistance to antibiotics. However, in the genome database, there is no whole genome of this species present until now. To facilitate a more reliable genetic identification in the M. fortuitum complex, we have characterized the complete genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.

To sequence the genome of M. fortuitum subsp. fortuitum type strain DSM46621, we used a shotgun sequencing method and Illumina HiSeq 2000 technology using a paired-end library, with a read length of 100 bp and an insert size of 500 bp. A total of 2.95 million Illumina sequencing reads were generated. These short sequence reads were first quality trimmed before de novo assembled using Velvet (12). The draft genome was further improved with iCORN (7) and IMAGE (10), as described in PAGIT (9), before it was scaffolded with SSPACE (2). The final assembly has 82 supercontigs and an N₅₀ of 159,889 bp. The genome annotation was performed using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP).

The M. fortuitum subsp. fortuitum type strain DSM46621 genome sequence is 6,349,738 bp in length, with 6,241 predicted coding sequences. The overall GC content of the chromosome was 66%. There are 54 tRNA genes and four sets of rRNA operons as predicted by the PGAAP pipeline. It was possible to assign a biological function to 67.7% (4,225) of the coding sequences on the M. fortuitum subsp. fortuitum chromosome.

The RAST server annotation pipeline (1) revealed that M. fortuitum subsp. fortuitum has the highest similarity with Mycobacterium smegmatis strain MC2 155, among all mycobacteria with complete genome sequences determined. The M. fortuitum subsp. fortuitum genome was found to be smaller (6.38 Mb) than the genome of M. smegmatis MC2 155 (6.99 Mb) and to contain fewer genes (6,076 versus 6,816). Comparative genomic analysis with M. smegmatis MC2 155 revealed that M. fortuitum subsp. fortuitum contains more virulence-associated mammalian cell entry (MCE) operons. In addition, several methyltransferases, glycosyltransferases, and dehydrogenases, which probably participate in the cell wall synthesis and modification, were present in the M. fortuitum genome. We expect that this genome sequence will serve as a valuable reference for understanding the disparity in virulence and epidemiologic traits in the M. fortuitum complex.