Complete Genome Sequence of Mycobacterium chimaera Strain AH16

GENOME ANNOUNCEMENT

Mycobacterium chimaera is a nontuberculous mycobacterial species within the Mycobacterium avium complex (MAC). The use of single genes such as the 16s rRNA or rpoB for species identification often misidentifies M. chimaera as the closely related MAC species M. intracellulare (1, 2). M. chimaera is an opportunistic environmental pathogen implicated in cardiovascular and pulmonary infections (1, 3). In health-care settings, the occurrence and spread of M. chimaera infections have increased in prevalence in recent years, including recent outbreaks that have been attributed to contaminated medical equipment (4–6). Despite the public health relevance of M. chimaera, only three draft genomes are publicly available, none of which is a complete genome (7). To improve our understanding of this emerging pathogen, we sequenced and report here the first complete genome of M. chimaera.

M. chimaera strain AH16, isolated from an 87-year-old male with suspected mycobacterial lung disease in O'ahu, Hawai'i, was identified using partial rpoB sequencing. The genome of M. chimaera AH16 was sequenced using Pacific Biosciences (PacBio) RSII single-molecule real-time (SMRT) technology. PacBio sequencing produced 243,370 reads (mean: 6,808 bp; min: 50 bp; max: 45,065 bp; ~262× genome coverage). The de novo genome assembly was performed using the Hierarchical Genome Assembly Process (8). The assembly was compared to other MAC genomes using Mauve version 2.3.1 (9). Genomic features were identified and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (10).

The genome of M. chimaera AH16 consists of 4 scaffolds equaling 6,328,534 bp (5,851,561-bp chromosome; 437,456-bp plasmid; 25,007-bp plasmid; 14,510-bp plasmid) and a G+C content of 67.56%. A total of 4,926 coding sequences (CDSs) were predicted, including 3,161 CDSs (64.17%) with functional annotations and 1,765 CDSs (35.83%) annotated as hypothetical proteins. Our genome assembly contains 74 tRNAs, one ncRNA, and one rRNA cistron consisting of the 16S, 23S, and 5S rRNA genes.

Whole-genome alignments of M. chimaera AH16 and six MAC genomes revealed 511,189 variable single nucleotide polymorphisms (SNPs), including: 459,672 SNPs compared to M. avium subsp. hominis suis TH135; 64,709 SNPs compared to M. intracellulare ATCC 13950; 50,875 SNPs compared to Mycobacterium sp. MOTT 36Y; 49,805 SNPs compared to M. yongonense 05-0390^T; and 49,524 SNPs compared to Mycobacterium sp. H4Y. Comparing the M. chimaera AH16 genome against the M. avium subsp. hominis suis TH135, M. intracellulare ATCC 13950, M. yongonense 05-0390^T, Mycobacterium sp. MOTT 36Y, and Mycobacterium sp. H4Y genomes, the average nucleotide identities (ANIs) were 85.55%, 96.87%, 97.14%, 97.16%, and 97.22%, respectively. The limited SNP variation (0.78 to 7.26% of the M. chimaera AH16 genome) and ANI values observed between M. chimaera AH16 and MAC species suggests that the non–M. avium MAC species have limited genomic variation. Furthermore, intraspecies genome comparisons of M. chimaera AH16 to M. chimaera MCIMRL6, MCIMRL4, and MCIMRL2 (accession nos. LJHN00000000, LJHM00000000, and LJHL00000000) have 99.14%, 99.11%, and 99.18% ANIs, respectively, which are within the 95 to 96% cutoff for species boundaries (11).