Here, we report whole-genome sequences (WGS) of eight clinical isolates of Burkholderia pseudomallei obtained from melioidosis patients with sepsis in eastern Sri Lanka.
ABSTRACT
Here, we report whole-genome sequences (WGS) of eight clinical isolates of Burkholderia pseudomallei obtained from melioidosis patients with sepsis in eastern Sri Lanka.
ANNOUNCEMENT
Whole-genome sequencing of Burkholderia pseudomallei, the causative agent of melioidosis, provides a better understanding about the phylogeography, transmission, evolution, virulence, epidemiology, and antibiotic resistance (1) of this organism. It is now clearly established that melioidosis is endemic in Sri Lanka with a wide geographic distribution (2). Whole-genome sequences (WGS) of B. pseudomallei are available for Southeast Asian (3) and northern Australian (4) strains. However, only a few WGS data sets have been published for the Indian subcontinent (5).
Here, we report eight complete genome sequences of clinical isolates of B. pseudomallei (BPs110, BPs111, BPs112, BPs114, BPs115, BPs116, BPs122, and BPs133) from melioidosis patients with acute sepsis in eastern Sri Lanka.
Strains were isolated from blood samples collected from melioidosis patients under sterile conditions, and blood agar base (Oxoid, UK) supplemented with 5% blood was used for the isolation of the organism. Subculturing was done several times on the same medium. One well-isolated single colony was restreaked on the fresh medium, a few well-isolated single colonies were pooled, and genomic DNA was extracted using a mini-QIAamp DNA isolation kit as recommended by the manufacturer (Qiagen, Germany). Multiple real-time PCR assays (Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region [YLF/BTFC]) were performed (6, 7). Further, real-time lpxo PCR was used for confirmation of presumptive B. pseudomallei (6). High-quality genomic DNA of each isolate was subjected to whole-genome sequencing from a paired end with 300 nucleotide reads (Nextera DNA library prep kit) using the MiSeq 2000 platform at Agiomix FZ LLC in the United Arab Emirates.
Raw sequence data were processed with Trimmomatic 0.36 (8) and FASTX-Toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/) to remove Illumina adaptor sequences and low-quality bases and reads. The quality of the raw sequence data was assessed using FastQC 0.11.4 (9) and MultiQC 1.0 (10). The Burrows-Wheeler Aligner (BWA) 0.7.12-r1039 (11) and Qualimap 2.2.1 (12) were used for raw read alignments and quality control of the alignment sequencing data. SPAdes 3.10.1 (13), ABACAS 1.3.1 (14), NCBI local BLAST 2.6.0, and online RAST (15) were used for genome assembly, annotation, and validation. All tools were used with default parameters, and cleaned sequences were used for downstream analysis. The assemblies were reorganized relative to the closed B. pseudomallei K96243 genome (GenBank accession numbers NC_006350 and NC_006351). All genomes reported here have been annotated using a best-placed reference protein set, GeneMarkS-2+, and the NCBI annotation provider (NCBI Prokaryotic Genome Annotation Pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/). The genomes of the B. pseudomallei isolates reported here contain two chromosomes, and the features annotated are reported in Table 1.
TABLE 1.
Characteristics and accession numbers of genomes of Burkholderia pseudomallei isolates sequenced in this study
| Strain designation | Multilocus sequence typea | Genome size (bp) (GC content [%]) | No. of ncRNAsb | No. of CDSsc | YLF/BTFC PCRd | No. of pseudogenes | No. of RNA genes | No. of tRNA genes | No. of contigs | N50 (bp) | No. of raw reads | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BPs110 | 1152 | 6,962,327 (68.39) | 4 | 6,670 | BTFC | 514 | 77 | 61 | 132 | 115,980 | 2,192,501 | CP036451, CP036452 |
| BPs111 | 1364 | 6,721,089 (68.17) | 4 | 6,670 | YLF | 513 | 76 | 60 | 147 | 113,263 | 2,007,588 | CP036453, CP036454 |
| BPs112 | 1442 | 6,258,284 (68.36) | 4 | 6,608 | YLF | 537 | 78 | 62 | 163 | 83,750 | 1,993,557 | CP037975, CP037976 |
| BPs114 | 594 | 6,022,338 (68.39) | 4 | 6,638 | BTFC | 508 | 77 | 77 | 158 | 101,821 | 2,617,163 | CP037973, CP037974 |
| BPs115 | 1413 | 6,756,482 (68.24) | 4 | 6,663 | YLF | 504 | 77 | 61 | 160 | 103,836 | 2,427,392 | CP037757, CP037758 |
| BPs116 | 1179 | 6,693,503 (68.32) | 4 | 6,593 | BTFC | 512 | 76 | 61 | 141 | 106,427 | 2,009,396 | CP037759, CP037760 |
| BPs122 | 594 | 6,242,888 (68.36) | 4 | 6,709 | BTFC | 504 | 77 | 61 | 129 | 122,561 | 4,042,684 | CP038194, CP038195 |
| BPs133 | 594 | 6,106,529 (68.39) | 4 | 6,647 | BTFC | 509 | 77 | 61 | 138 | 122,504 | 3,362,629 | CP037971, CP037972 |
Based on the scheme at http://pubmlst.org/bpseudomallei.
ncRNAs, noncoding RNAs.
CDSs, protein-coding sequences.
YLF, Yersinia-like fimbrial region; BTFC, Burkholderia thailandensis-like flagellum chemotaxis region.
Data availability.
All of the whole-genome sequencing projects have been deposited in GenBank, and the accession numbers are given in Table 1. The raw data are also publicly accessible under the accession numbers SRR8658974, SRR8618097, SRR8741027, SRR8759108, SRR8661621, SRR8660934, SRR8867837, and SRR8867836.
ACKNOWLEDGMENTS
We thank Jayanthi Masakorala, Department of Microbiology, Faculty of Medicine, University of Colombo, for her valuable service during the isolation and maintenance of pure cultures of the clinical isolates. Agiomix FFZ LLC, United Arab Emirates, provided the consultation for all raw sequencing data analysis.
This research was financially supported by the U.S. Army Medical Research Acquisition Activity (USAMRAA), grant number W81XWH-16-C-0223.
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Associated Data
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Data Availability Statement
All of the whole-genome sequencing projects have been deposited in GenBank, and the accession numbers are given in Table 1. The raw data are also publicly accessible under the accession numbers SRR8658974, SRR8618097, SRR8741027, SRR8759108, SRR8661621, SRR8660934, SRR8867837, and SRR8867836.