ABSTRACT
We report here the draft genome sequence of Burkholderia pseudomallei H0901. This strain was isolated in 2003 from the first melioidosis patient in South Korea.
GENOME ANNOUNCEMENT
Burkholderia pseudomallei is a Gram-negative bacterium that can cause melioidosis, a severe infectious disease (1). The pathogen is found mainly in southeastern Asia, northern Australia, and on various Pacific and Indian Ocean islands, where melioidosis is endemic (2, 3). Diagnosis of melioidosis is confirmed through isolation of the bacterium from a sample taken from the blood, sputum, skin lesions, abscesses, or urine of patients (4). The melioidosis patient may display various conditions, ranging from subclinical to overwhelming protean manifestations resembling chronic and acute bacterial infections (5). As treatment of B. pseudomallei infections can be lengthy, accurate and rapid diagnosis of melioidosis is necessary for efficacious antimicrobial therapy (4, 6).
In 2003, we encountered the first case of melioidosis in South Korea. The patient was a 47-year-old male with septicemia and septic pneumonia who had a history of traveling to Malaysia and suffered from diabetes mellitus (5). The bacterial isolate from the blood of the patient was identified as B. pseudomallei based on DNA sequencing of the 16S rRNA gene and on biochemical tests (7).
For the draft genome sequence of B. pseudomallei H0901, genomic DNA was isolated from B. pseudomallei H0901 grown in Ashdown’s medium with gentamicin for 24 h at 37°C (8). The paired-end sequencing library was prepared using a genomic DNA prep kit (Qiagen, USA). A MiSeq instrument (Illumina, San Diego, CA) was used as the sequencing platform. A total of 7,956,141 reads were obtained by whole-genome sequencing, and fold coverage was 235. Finally, 142 contigs were assembled from all reads in CLC Genomic Workbench (CLCbio, version 10.0) using thresholds with a minimum of 500 bp (9). The number of N50 contigs was 88,367. The draft genome of the H0901 strain consisted of 7,001,996 bp of nucleotides (G+C content, 68.2%). The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted 6,836 protein-coding genes, 2 rRNAs, 54 tRNAs, and 407 pseudogenes.
From 2003 to 2014, 11 cases of melioidosis were reported in South Korea (10). Each patient had a history of traveling to southeastern Asian countries, and melioidosis is still considered an imported infectious disease in South Korea. However, due to the increase of traffic to countries where melioidosis is endemic and the increase of environmental temperature by global warming, it is possible that the occurrence of melioidosis is increasing in South Korea. In this study, we report the draft genome sequence of B. pseudomallei H0901, isolated from the first melioidosis patient in South Korea. B. pseudomallei H0901 will be used as a reference strain for the confirmatory identification of B. pseudomallei in the Korea Centers for Disease Control and Prevention.
Accession number(s).
This whole-genome shotgun project was deposited in DDBJ/EMBL/GenBank under the accession number NEGN00000000. The version described in this paper is the second version, NEGN02000000.
ACKNOWLEDGMENT
This work was supported by the Korea Centers for Disease Control and Prevention (grant CDC 4800-4840-302).
Footnotes
Citation Shin Y-W, Choi M-M, Chun J-H, Yu J-Y, Kim D-W, Rhie G-E. 2018. Draft genome sequence of the first South Korean clinical isolate of Burkholderia pseudomallei, H0901. Genome Announc 6:e00336-18. https://doi.org/10.1128/genomeA.00336-18.
REFERENCES
- 1.Wiersinga WJ, Currie BJ, Peacock SJ. 2012. Melioidosis. N Engl J Med 367:1035–1044. doi: 10.1056/NEJMra1204699. [DOI] [PubMed] [Google Scholar]
- 2.Cheng AC, Currie BJ. 2005. Melioidosis: epidemiology, pathophysiology, and management. Clin Microbiol Rev 18:383–416. doi: 10.1128/CMR.18.2.383-416.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Currie BJ, Dance DA, Cheng AC. 2008. The global distribution of Burkholderia pseudomallei and melioidosis: an update. Trans R Soc Trop Med Hyg 102:S1–S4. doi: 10.1016/S0035-9203(08)70002-6. [DOI] [PubMed] [Google Scholar]
- 4.Limmathurotsakul D, Peacock SJ. 2011. Melioidosis: a clinical overview. Br Med Bull 99:125–139. doi: 10.1093/bmb/ldr007. [DOI] [PubMed] [Google Scholar]
- 5.Seok HJ, Kim JI, Lee JH, Choo EJ, Kwak YG, Jang S, Kim NJ, Kim YS, Woo JH, Ryu J. 2004. A case of septicemia and septic pneumonia due to Burkholderia pseudomallei. Infect Chemother 36:114–117. [Google Scholar]
- 6.Dance D. 2014. Treatment and prophylaxis of melioidosis. Int J Antimicrob Agents 43:310–318. doi: 10.1016/j.ijantimicag.2014.01.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Shin YW, Cho MH, Chun JH, Kim CM, Oh HB, Rhie GE, Yoo CK. 2011. The laboratory diagnosis of melioidosis in a Korean patient. J Bacteriol Virol 41:19–25. doi: 10.4167/jbv.2011.41.1.19. [DOI] [Google Scholar]
- 8.Peacock SJ, Chieng G, Cheng AC, Dance DA, Amornchai P, Wongsuvan G, Teerawattanasook N, Chierakul W, Day NP, Wuthiekanun V. 2005. Comparison of Ashdown's medium, Burkholderia cepacia medium, and Burkholderia pseudomallei selective agar for clinical isolation of Burkholderia pseudomallei. J Clin Microbiol 43:5359–5361. doi: 10.1128/JCM.43.10.5359-5361.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272. doi: 10.1101/gr.097261.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Kim SW, Kwon GY, Kim BY, Kwon DH, Shin JS, Bae GR. 2015. Imported melioidosis in South Korea: a case series with a literature review. Osong Public Health Res Perspect 6:363–368. doi: 10.1016/j.phrp.2015.10.014. [DOI] [PMC free article] [PubMed] [Google Scholar]