Draft Genome Sequence of Mycobacterium chelonae Type Strain ATCC 35752

Mycobacterium chelonae is an opportunistic environmental pathogen (1) found in diverse habitats, including water, sewage, and soil (2). M. chelonae can cause corneal, cutaneous, and pulmonary infections in humans and other hosts. In many health care settings, the occurrence and spread of atypical mycobacterial infections, including those caused by M. abscessus and M. chelonae, have increased in prevalence in recent years. M. chelonae outbreaks have been attributed to factors ranging from resistance to glutaraldehyde, a commonly used hospital disinfectant (3–6) to contaminated medical equipment (7) and contaminated reagents (8).

We have sequenced and report here the first draft genome of a representative of the M. chelonae species. The type strain ATCC 35752 was originally isolated from the lungs of sea turtles (Chelona corticata), and shares phylogenetic similarity to human pathogens of this species. The genome of the M. chelonae type strain ATCC 35752 was assembled using 400-bp sequence reads generated from the Life Technologies Ion Torrent PGM (Thermo, Fisher Sciences, Carlsbad, CA) and 250 × 250 bp paired-end reads from the Illumina MiSeq (Illumina, Inc., San Diego, CA), at 220× coverage. Sequence reads were quality filtered using the Fastx_Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and assembled into scaffolded contigs using the Newbler v2.9 (454 Life Sciences, Branford, CT) software package. The contigs were ordered in relation to the M. abscessus subsp. abscessus ATCC 19977 genome as a reference (9), employing the progressive Mauve 2.3.1 whole-genome alignment algorithm (10). Genomic features were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (11).

The M. chelonae ATCC 35752 draft genome is a pseudomolecule composed of 24 contigs, with linking sequences of 100 N's in between each contig, resulting in a total assembly size of 4,898,027 bp and a G+C content of 63.96%. The average contig length is 204,084 bp with an N₅₀ of 462,745 bp. A total of 4,489 coding sequences (CDSs) were predicted, including 3,274 CDSs (72.93%) with functional annotations and 1,215 CDSs (27.07%) annotated as hypothetical proteins. Our genome assembly contains 48 tRNAs, 1 noncoding RNA (ncRNA), and 1 rRNA cistron consisting of the 5S, 16S, and 23S rRNA genes. A comparative analysis between M. chelonae ATCC 35752 and M. abscessus ATCC 19977 revealed 3,803 orthologous CDSs that are shared between the two strains.

Whole-genome sequence alignments of M. chelonae ATCC 35752 and five representative M. abscessus genomes revealed an average of 620,054 single nucleotide polymorphisms (SNPs), including 628,647 SNPs compared to M. abscessus ATCC 19977, 629,586 SNPs compared to M. bolletii BD^T, 631,431 SNPs compared to M. bolletii M24, 621,641 SNPs compared to M. massiliense GO-06, and 588,967 SNPs compared to M. massiliense CCUG 48898 (= JCM15300). These SNP differences (12.02 to 12.85% of the M. chelonae ATCC 35752 genome) underscore the genomic divergence between M. chelonae and its sister taxa (M. abscessus complex).

N.A.H. and B.J.G. acknowledge support from an NIH Biomedical Informatics training grant 2T15LM009451-06. M.S. acknowledges support from the Colorado Bioscience Discovery Evaluation Grant Program, the William and Ella Owens Medical Research Foundation, the Potts Foundation, and the Boettcher Foundation Webb-Waring Award. M.S., R.M.D, and L.E.E. acknowledge support from the NTM Center of Excellence at National Jewish Health, supported in part by the Amon G. Carter Foundation. This work was supported in part by the National Institutes of Health/National Institute of Allergy and Infectious Diseases grant AI089718 (to M.J.).