Whole-Genome Sequence of Mycobacterium kyorinense.

We report here the first draft genome sequence of Mycobacterium kyorinense, which was described in 2009 and exhibits significant pathogenicity to humans.

GENOME ANNOUNCEMENT

Mycobacterium kyorinense is a slow-growing mycobacterium that was first described in 2009 (1). M. kyorinense is closely related to M. celatum, M. branderi, and M. fragae, and exhibits significant pathogenicity for humans, causing pneumonia, lymphadenitis, and arthritis (2–4). Antimicrobial susceptibility tests demonstrated that M. kyorinense is generally resistant to rifampin, isoniazid, and ethambutol (4). Further investigation is needed to clarify the genomics, biology, epidemiology, and pathogenicity of this species.

We sequenced the genomic DNA of the M. kyorinense type strain KUM060204T on an Ion PGM system (Life Technologies) and assembled the reads using CLC Genomics Workbench 7.0. A total of 4,133,490 reads were generated, with an average read length of 203 bp, yielding a total sequence of 837,657,777 bp.

The assembled sequences of KUM060204T comprised 453 contigs, with a combined length of 5,302,980 bp, with a G+C ratio of 66.9%. The average cover depth was 50×, the N50 contig size was 53,523, the average contig was 11,706 bp long, and the longest contig was 137,319 bp.

Genome annotation was performed using the RAST prokaryotic genome annotation server (http://www.nmpdr.org/FIG/wiki/view.cgi/Main/RAST). RAST predicted 5,405 putative open reading frames, including 5,351 coding sequences and 54 RNAs (46 tRNAs and 8 rRNAs). RAST functional analysis of the predicted protein-coding genes showed 78 genes involved in cell walls and capsules, 64 in membrane transport, 206 in protein metabolism, 93 in DNA metabolism, 141 in virulence and defense, 135 in respiration, 331 in fatty acids, lipids, and isoprenoids, 395 in cofactors, vitamins, prosthetic groups, and pigments, and 356 in amino acids and derivatives.

To explore the molecular mechanism underlying the resistance of M. kyorinense to anti-tuberculosis drugs, we selected several genes known to be responsible for resistance to rifampin (rpoB), ethambutol (embB), and isoniazid (inhA, katG, and ahpC). The sequences of these genes in M. kyorinense were compared with those in M. tuberculosis H37Rv to clarify whether they contain specific mutations associated with resistance to anti-tuberculosis drugs in M. tuberculosis. Analysis of the rpoB gene confirmed our previous finding that KUM060204T harbors a Ser531Asp amino acid substitution, the most frequent mutation in rifampin-resistant M. tuberculosis (4, 5). In contrast, we did not detect a substitution at Met306 of embB, the major mutation in ethambutol-resistant M. tuberculosis (6). Nor did we find a Ser315Thr substitution of katG, a mutation in the regulatory region (nucleotides [nt] −48, −51, −54, −81, and −88) of ahpC, a Ser94Ala substitution in the inhA gene or a mutation in the regulatory region (nt −15 and −17) of inhA, which are common mutations in isoniazid-resistant M. tuberculosis (6). These results suggested that the mechanism underlying drug resistance in M. kyorinense is significantly different from that in M. tuberculosis.

In conclusion, we report the genome sequence of KUM060204T which to the best of our knowledge is the first genome sequence of the species M. kyorinense.

Nucleotide sequence accession numbers.

The whole genome sequence of KUM060204T has been deposited in DDBJ/EMBL/GenBank under the accession numbers BBKA01000001 to BBKA01000453.