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. 2015 Oct 1;3(5):e01075-15. doi: 10.1128/genomeA.01075-15

Draft Genome Sequences of Burkholderia pseudomallei and Staphylococcus aureus, Isolated from a Patient with Chronic Rhinosinusitis

Hanna E Sidjabat a,✉, Kyra Cottrell a, Anders Cervin a,b,c
PMCID: PMC4591299  PMID: 26430027

Abstract

Here, we report the draft genome sequences of Burkholderia pseudomallei and Staphylococcus aureus causing chronic rhinosinusitis. Whole-genome sequencing determined the B. pseudomallei as sequence type (ST) 1381 and the S. aureus as ST8. B. pseudomallei possessed the blaOXA-59 gene. This study illustrates the potential emergence of B. pseudomallei in cases of chronic rhinosinusitis.

GENOME ANNOUNCEMENT

Burkholderia pseudomallei is a Gram-negative soil- and water-associated pathogen causing melioidosis (1). In our region, B. pseudomallei is more commonly found in tropical parts of Australia (2). Burkholderia spp. were occasionally isolated from cystic fibrosis patients (3, 4). Recently, isolation of the Burkholderia cepacia complex was reported among patients with nonpolypoid chronic rhinosinusitis (5). Here, we report the draft genome sequences of B. pseudomallei and Staphylococcus aureus, isolated from a patient with chronic rhinosinusitis.

A 59-year-old woman with a history of arthritis suffered from chronic rhinosinusitis with purulent discharge and retro-orbital pain over the past 3 years. The patient was regularly in contact with soil due to her gardening activities. The patient underwent sinus surgery for 3 consecutive years, from 2012 to 2014. Heavy and nearly pure growth of Burkholderia spp. (HS-CRS-17A) type of colonies grew from the nasal swab obtained in March 2015. Light growth of S. aureus (HS-CRS-17B) was identified from the same specimen.

Both Burkholderia spp. and S. aureus were subjected to whole-genome sequencing. The DNA was extracted using Ultraclean DNA extraction kit (Mobio, USA). Nextera XT DNA sample preparation kit (Illumina, USA) was used to prepare the library and the HiSeq 2000 platform for whole-genome sequencing using a previously described method (6). The CLC genomic workbench version 8.0 (CLC Bio, Aarhus, Denmark) was used for de novo assembly using minimum 600-bp thresholds, resulting in 269 and 60 contigs in Burkholderia spp. and S. aureus, respectively. The draft genomes of the two isolates consisted of 7,240,926 bp and 2,734,587 nucleotides, respectively. The draft genomes were annotated using Rapid Annotations using Subsystems Technology (RAST) (7). RAST annotation identified that Burkholderia mallei ATCC 23344 (score 530) and Burkholderia pseudomallei 1026a (score 504) were the two closest neighbors of our B. pseudomallei. S. aureus NN50 (score 519) and S. aureus T0131 were the two closest neighbors of our S. aureus.

The in silico species identification using rspU of HS-CRS-17A was 100% identical to B. pseudomallei. In silico MLST analysis (http://bpseudomallei.mlst.net) determined a novel ST, B. pseudomallei ST1381. The alleles were as follows: ace (8), gltb (1), gmhd (3), lepa (2), lipa (1), nark (2), and ndh (1). An oxacillinase gene, blaOXA-59, was identified in B. pseudomallei. In silico analysis of S. aureus MLST (http://saureus.mlst.net) identified S. aureus HS-CRS-17B as sequence type (ST) 8. The alleles were as follows, arcc (3), aroe (3), glpf (1), gmk (1), pta (4), tpi (4), and yqil (3). Of note, S. aureus ST8 has been reported previously among the indigenous population in Australia (8). The Panton-Valentine leucocidin (PVL) gene, which often causes serious soft tissue infection, was not detected in S. aureus HS-CRS-17B.

There have been approximately 200 published Burkholderia pseudomallei genomes (http://www.ncbi.nlm.nih.gov/genome/?term=burkholderia+pseudomallei), including genomes of B. pseudomallei from Australia (9–12). Most of the draft genomes were isolates from environmental and cystic fibrosis patients (9–12). Our study illustrates the emergence of Burkholderia spp. among chronic rhinosinusitis patients in Australia. The prevalence of Burkholderia spp. among patients with chronic rhinosinusitis and the need for accurate species identification warrant further investigation in our region.

Nucleotide sequence accession numbers.

This project is registered as BioProject PRJNA291304. The BioSample numbers of B. pseudomallei HS-CRS-17A ST1381 and S. aureus HS-CRS-17B ST8 are SAMN03938520 and SAMN03938521, respectively. The GenBank accession numbers are LHQO00000000 and LGVN00000000 for B. pseudomallei HS-CRS-17A ST1381 and S. aureus HS-CRS-17B ST8, respectively.

ACKNOWLEDGMENTS

The work was approved by RBWH Human Research Ethics Committee EC00172 (HREC/14/QRBW/274) (title: The Sinus Microbiome: A Comparison between the Healthy Sinus and Chronic Rhinosinusitis). This study is partially funded by the RBWH Foundation (title: The Role of Bacterial, Fungal and Viral Sinus Microbiome in Chronic Rhinosinusitis Patients). A.C. is a recipient of funding from the Garnett Passe and Rodney Williams Memorial Foundation.

Footnotes

Citation Sidjabat HE, Cottrell K, Cervin A. 2015. Draft genome sequences of Burkholderia pseudomallei and Staphylococcus aureus, isolated from a patient with chronic rhinosinusitis. Genome Announc 3(5):e01075-15. doi:10.1128/genomeA.01075-15.

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