Draft Genome Sequence of Mycobacterium peregrinum Strain CSUR P2098.

Mycobacterium peregrinum is a nonpigmented rapid growing nontuberculosis species belonging to the Mycobacterium fortuitum group. The draft genome of M. peregrinum type I CSUR P2098 comprises 7,109,836 bp exhibiting a 66.23% G+C content, 6,894 protein-coding genes, and 100 predicted RNA genes. Its genome analysis suggests this species differs from Mycobacterium senegalense.

GENOME ANNOUNCEMENT

Initially reported in 1962, Mycobacterium peregrinum (1) was officially described 30 years later as a rapidly growing nontuberculous mycobacterium in the Mycobacterium fortuitum complex (2, 3). It was further divided into pipemidic acid-susceptible M. peregrinum type I and pipemidic acid-resistant M. peregrinum type II (4), regarded as a human strain of Mycobacterium senegalense (5). M. peregrinum has been isolated from various water-related sources (6–8). M. peregrinum accounts for only 1% to 2% of infections due to rapid growing mycobacteria (9–13).

We performed whole-genome sequencing of M. peregrinum CSUR P2098 strain, a type I, in order to firmly ensure its taxonomic relationships within the M. fortuitum complex.

Genomic DNA was isolated from M. peregrinum CSUR P2098 cultured in MGIT Middlebrook liquid culture (Becton, Dickinson, Le Pont-de-Claix, France) at 37°C in a 5% CO2 atmosphere. M. peregrinum genomic DNA was sequenced by Illumina MiSeq runs (Illumina Inc., San Diego) using a 5-kb mate-paired library. Reads were trimmed using Trimmomatic (14), and assembled using Spades v3.5 (15, 16). Contigs were combined together by SSPACE v2 (17) and Opera v2 (18) helped by GapFiller v1.10 (19). This resulted in a draft genome consisting in six scaffolds and seven contigs for a total of 7,109,836 bp and a G+C content of 66.23%. Noncoding genes and miscellaneous features were predicted using RNAmmer (20), ARAGORN (21), Rfam (22), PFAM (23), and Infernal (24). Coding DNA sequences (CDSs) were predicted using Prodigal (25) and functional annotation was achieved using BLASTp against the GenBank database (26) and the Clusters of Orthologous Groups (COGs) database (27, 28). The genome was shown to encode at least 100 predicted RNA including six rRNA, 64 tRNA, one tmRNA, and 29 miscellaneous RNA. A total of 6,894 identified genes yielded a coding capacity of 7,054,578 bp (coding percentage, 99.22%). Among these genes, 5,101 (74%) were found as putative proteins and 1,282 (18.6%) were assigned as hypothetical proteins. Moreover, 4,020 (58.3%) genes matched a least one sequence in the COGs database with BLASTp default parameters. Further, M. peregrinum CSUR P2098 genome was incorporated into in silico DNA-DNA hybridation (DDH) (29) with the M. fortuitum complex species and other reference genomes selected on the basis of their 16S rRNA gene sequence proximity with M. peregrinum and DDH values were estimated using the GGDC v2.0 online tool (30). This analysis yielded 33.8% ± 2.47 similarity with Mycobacterium septicum DSM 44393 (31), 33.6% ± 2.47 Mycobacterium fortuitum ATCC 6841 (32), 33.5% ± 2.47 with Mycobacterium sp. VKM Ac-1817D (33), 32.3% ± 2.46 with Mycobacterium senegalense CK2 and Mycobacterium neworleansense ATCC 49404 (34), 31.8% ± 2.46 with Mycobacterium conceptionense D16 (unpublished data) (35), 31.6% ± 2.46 with Mycobacterium farcinogenes DSM43637 (36), and 20.7% ± 2.32 to Mycobacterium gilvum Spyr1 (37).

These data confirm M. peregrinum as a unique species within the M. fortuitum complex. In particular, these data suggest that M. peregrinum differs from M. senegalense.

Nucleotide sequence accession numbers.

The M. peregrinum genome sequence has been deposited at EMBL under the accession numbers CYSH01000001 to CYSH01000007.