ABSTRACT
Mycobacterium sp. strain shizuoka-1 is a rapidly growing scotochromogenic mycobacterium and was isolated from well water for a bathing facility in Shizuoka Prefecture in Japan. Here, we report the draft sequence of its genome, comprising a 6.5-Mb chromosome. This mycobacterium has 83.1% identity with Mycobacterium rhodesiae, a human pathogen.
GENOME ANNOUNCEMENT
Hot springs and bathing facilities are the most frequent places where Legionella pneumonia occurs in Japan (1). To control this fatal infection, we are collaborating with prefectural and municipal public health institutes and periodically evaluating bath water to check for contamination by Legionella species (1, 2). Our recent data suggest that there is a risk of legionellosis in a variety of aquatic environments, even in residential houses, not only in public baths (3). As a by-product of these examinations, we frequently isolate other varieties of mycobacteria, suggesting that they commonly live in the environmental water. This time, we isolated a novel rapidly growing scotochromogenic mycobacterium from well water for a hot bathing facility in Shizuoka prefecture, Japan. Here, we report the draft genome sequence of this mycobacterium, named Mycobacterium sp. strain shizuoka-1.
The strain was grown with Middlebrook 7H9 medium. DNA was extracted using the NucleoSpin plant II kit (Macherey-Nagel, Düren, Germany). The genome sequence was determined using Illumina 300 × 2 paired-end reads (4,367,175 reads) obtained with a MiSeq sequencer (Illumina, San Diego, CA, USA) (4). The reads were assembled with Platanus version 1.1 into 162 contigs (5). Automated annotation was carried out with the DDBJ Fast Annotation and Submission Tool (DFAST) (https://dfast.nig.ac.jp/).
The genome of Mycobacterium sp. shizuoka-1 is 6,533,596 bp in length, with 67.6% G+C content. The average nucleotide identity to Mycobacterium rhodesiae (strain DSM 44223) was 83.1%, with M. rhodesiae being reported as a cause of continuous ambulatory peritoneal dialysis (CAPD)-associated peritonitis (6, 7). The chromosome contains 6,207 predicted protein-coding sequences (CDS), 2 rRNAs, and 49 tRNAs. The genome sequence of Mycobacterium sp. shizuoka-1 represents essential data for future investigation of various environmentally contaminating mycobacteria (8).
Accession number(s).
This whole-genome sequence has been deposited at DDBJ/ENA/GenBank under the accession numbers BEWG01000001 to BEWG01000162.
ACKNOWLEDGMENTS
This work was supported by a grant from the Japan Agency for Medical Research and Development/Japan International Cooperation Agency (to Y. Hoshino) and by grants-in-aid for Scientific Research (C) from the Japan Society for the Promotion of Science (JSPS) (to Y. Hoshino), and partial support was provided by a Health and Labor Sciences Research grant (H28-Kenki-Ippan-006) from the Ministry of Health, Labor and Welfare, Japan. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Footnotes
Citation Yoshida M, Izumiyama S, Fukano H, Sugiyama K, Suzuki M, Shibayama K, Hoshino Y. 2017. Draft genome sequence of Mycobacterium sp. strain shizuoka-1, a novel mycobacterium isolated from groundwater of a bathing facility in Shizuoka, Japan. Genome Announc 5:e01309-17. https://doi.org/10.1128/genomeA.01309-17.
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