Abstract
The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention Category B listed), and nonpathogenic Gram-negative bacilli. Here we present full genome sequences for a panel of 59 Burkholderia strains, selected to aid in detection assay development.
GENOME ANNOUNCEMENT
Burkholderia mallei and Burkholderia pseudomallei are among the bacterial species considered to be potential bioweapons, along with Bacillus anthracis, Brucella melitensis, Brucella abortus, and Yersinia pestis (1, 2). B. pseudomallei causes melioidosis, often a respiratory infection mimicking tuberculosis, while B. mallei generally infects horses, causing glanders. The listing of these bacteria as potential biothreats is due to their easy availability (B. pseudomallei is often recovered from soils in regions where it is endemic), their ability to cause severe and often fatal disease, multiple routes of infection, native antibiotic resistance, lack of available vaccines, wide host range, and ability to persist in the environment for weeks to years (3–9). B. mallei was reportedly used as a biological weapon on several occasions (10–14); however, while B. pseudomallei was investigated for its use as a bioweapon, there are no reports that it has been employed in this fashion (5, 11). Other Burkholderia species are opportunistic pathogens (e.g., the Burkholderia cepacia complex [Bcc] that adversely affects cystic fibrosis patents [including 7 species sequenced here]), plant pathogens (such as Burkholderia gladioli) and/or common soil microorganisms. Here we present full genome sequences of 59 strains useful for detection assay development, including both species that should be detected (inclusivity) and those that should not be (exclusivity).
Draft genome assemblies included two or more data sets (specific data types and coverages are listed in the NCBI records): Illumina (short- and/or long-insert paired data), Roche 454 (long-insert paired data), and PacBio long reads. Short- and long-insert paired data were assembled together in both Newbler and Velvet, and computationally shredded into 1.5-kbp overlapping shreds. If the PacBio coverage was 100× or greater, the data were assembled using PacBio’s Hierarchical Genome Assembly Process (HGAP) (15). All data were additionally assembled together in Allpaths whenever possible (16). Consensus sequences from both HGAP and Allpaths were computationally shredded into 10-kbp overlapping pieces. All shreds were integrated using Phrap. Possible misassemblies were corrected and repeat regions verified using in-house scripts and manual editing in Consed (17–19). All of the genomes were assembled into finished-quality complete genomes (20). Each genome assembly was annotated using an Ergatis-based (21) workflow with minor manual curation.
Genome assemblies range from 5.4 to 9.7 Mb (Table 1, mean 6.96 ± 0.014 Mb), with two or three chromosomes and up to three plasmids. As expected for the genus, the G+C content was high, averaging 67.7%.
TABLE 1 .
Listing of Burkholderia isolate genomes released to NCBI
| Species and isolate | Accession no. (no. of contigs)a | Panelb | Genome (bp) | No. of plasmids | No. of CDSsc | G+C content (%) |
|---|---|---|---|---|---|---|
| B. ambifaria | ||||||
| AMMD | CP009797–CP009800 | E | 7,528,578 | 1 | 6,602 | 67 |
| B. cepacia | ||||||
| LMG 16656 | JTDP00000000 (5) | E | 7,923,342 | 1 | 7,278 | 68 |
| B. dolosa | ||||||
| AU0158 | CP009793–CP009795 | E | 6,409,095 | 2 | 5,657 | 67 |
| B. fungorum | ||||||
| ATCC BAA-463 | CP010024–CP010027 | E | 9,058,983 | 1 | 8,206 | 62 |
| B. gladioli | ||||||
| ATCC 10248 | CP009319–CP009322 | E | 8,899,459 | 3 | 7,561 | 68 |
| B. glumae | ||||||
| ATCC 33617 | CP009432–CP009435 | E | 6,820,727 | 2 | 5,864 | 68 |
| B. mallei | ||||||
| 6 | CP008710–CP008711 | I | 5,647,769 | 0 | 4,872 | 68 |
| 11 | CP009587–CP009588 | I | 5,913,134 | 0 | 5,083 | 68 |
| NCTC 10247 | CP007801–CP007802 | I | 5,827,656 | 0 | 5,001 | 68 |
| 2000031063 | CP008731–CP008732 | I | 5,874,930 | 0 | 5,067 | 68 |
| 2002721276 | CP010065–CP010066 | I | 5,780,439 | 0 | 4,954 | 69 |
| 2002734299 | CP009337–CP009338 | I | 5,740,115 | 0 | 4,966 | 68 |
| 2002734306 | CP009707–CP009708 | I | 5,409,162 | 0 | 4,703 | 68 |
| China5 | JPNX00000000 (2) | I | 5,869,855 | 0 | 5,043 | 68 |
| FMH 23344 | CP008704–CP008705 | I | 5,625,292 | 0 | 4,883 | 68 |
| India86-567-2 | CP009642–CP009643 | I | 5,686,446 | 0 | 4,911 | 68 |
| KC_1092 | CP009942–CP009943 | I | 5,661,851 | 0 | 4,868 | 68 |
| B. multivorans | ||||||
| BAA-247 | CP009830–CP009832 | E | 6,322,746 | 0 | 5,607 | 67 |
| B. oklahomensis | ||||||
| C6786 | CP009555–CP009556 | E | 7,135,022 | 0 | 6,083 | 67 |
| EO147 | CP008726–CP008727 | E | 7,313,673 | 0 | 6,312 | 67 |
| B. pseudomallei | ||||||
| 9 | CP008753–CP008755 | I | 7,228,737 | 1 | 5,978 | 68 |
| 576 | CP008777–CP008778 | I | 7,266,604 | 0 | 5,944 | 68 |
| 1026b | CP004379–CP004380 | I | 7,450,511 | 0 | 6,113 | 68 |
| 1106a | CP008758–CP008759 | I | 7,086,433 | 0 | 5,758 | 68 |
| 7894 | CP009535–CP009536 | I | 7,381,912 | 0 | 6,036 | 68 |
| PB08298010 | CP009550–CP009551 | I | 7,375,551 | 0 | 6,023 | 68 |
| K96243 | CP009537–CP009538 | I | 7,247,614 | 0 | 5,933 | 68 |
| MSHR 146 | CP004042–CP004043 | I | 7,313,103 | 0 | 5,963 | 68 |
| MSHR 1655 | CP008779–CP008780 | I | 7,027,950 | 0 | 5,798 | 68 |
| MSHR 2543 | CP009477–CP009478 | I | 7,446,569 | 0 | 6,183 | 68 |
| MSHR 305 | CP006469–CP006470 | I | 7,428,072 | 0 | 6,105 | 68 |
| MSHR 346 | CP008763–CP008764 | I | 7,354,416 | 0 | 6,015 | 68 |
| MSHR 406e | CP009297–CP009298 | I | 7,271,506 | 0 | 5,927 | 68 |
| MSHR 491 | CP009484–CP009485 | I | 7,356,376 | 0 | 6,080 | 68 |
| MSHR 511 | CP004023–CP004024 | I | 7,316,085 | 0 | 5,964 | 68 |
| MSHR 520 | CP004368–CP004369 | I | 7,447,511 | 0 | 6,113 | 68 |
| MSHR 668 | CP009545–CP009546 | I | 7,042,714 | 0 | 5,793 | 68 |
| MSHR 840 | CP009473–CP009474 | I | 7,129,813 | 0 | 5,860 | 68 |
| NAU 20B-16 | CP004003–CP004004 | I | 7,313,851 | 0 | 5,969 | 68 |
| NAU 35A-3 | CP004377–CP004378 | I | 7,204,083 | 0 | 5,844 | 68 |
| NCTC 13178 | CP004001–CP004002 | I | 7,408,007 | 0 | 6,133 | 68 |
| NCTC 13179 | CP003976–CP003977 | I | 7,337,157 | 0 | 6,085 | 68 |
| Pasteur 52237 | CP009898–CP009899 | I | 7,325,318 | 0 | 6,015 | 68 |
| PHLS 112 | CP009585–CP009586 | I | 7,202,363 | 0 | 5,868 | 68 |
| B. thailandensis | ||||||
| 2002721643 | CP009601–CP009602 | E | 6,722,801 | 0 | 5,649 | 68 |
| 2002721687 | CP009547–CP009549 | E | 7,285,824 | 1 | 6,327 | 67 |
| 2002721723 | CP004097–CP004098 | E | 6,577,133 | 0 | 5,533 | 68 |
| 2003015869 | CP008914–CP008915 | E | 6,728,980 | 0 | 5,679 | 68 |
| 34 | CP010016–CP010018 | E | 7,120,198 | 1 | 6,129 | 67 |
| E254 | CP004381–CP004382 | E | 6,676,730 | 0 | 5,591 | 68 |
| E264 | CP008785–CP008786 | E | 6,722,099 | 0 | 5,655 | 68 |
| E444 | CP004117–CP004118 | E | 6,651,696 | 0 | 5,571 | 68 |
| H0587 | CP004089–CP004090 | E | 6,768,375 | 0 | 5,629 | 68 |
| Malaysia 20 | CP004383–CP004384 | E | 6,684,359 | 0 | 5,620 | 68 |
| MSMB 121 | CP004095–CP004096 | E | 6,731,379 | 0 | 5,758 | 68 |
| Phuket 4W-1 | AQQJ00000000 (3) | E | 6,674,944 | 0 | 5,635 | 68 |
| B. ubonensis | ||||||
| MSMB 22 | CP009486–CP009488 | E | 7,189,071 | 0 | 6,257 | 67 |
| B. vietnamiensis | ||||||
| LMG 10929 | CP009629–CP009632 | E | 6,930,496 | 1 | 6,120 | 67 |
| B. xenovorans | ||||||
| LB400 | CP008760–CP008762 | E | 9,702,951 | 0 | 8,684 | 63 |
Contig count is listed only for genomes at Improved High Quality Draft (IHQD) quality; all others are finished (20).
E, exclusivity strain; I, inclusivity strain.
CDS, coding sequence.
Nucleotide sequence accession numbers.
Accession numbers for all 59 genomes are listed in Table 1.
ACKNOWLEDGMENTS
Funding for this effort was provided by the Defense Threat Reduction Agency’s Joint Science and Technology Office (DTRA J9-CB/JSTO) and Department of Homeland Security Science and Technology Directorate, award HSHQDC-08-X-00790. This article is approved by LANL for unlimited release (LA-UR-14-29605).
The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Navy, Department of Defense, or the United States Government.
Bacterial strains were obtained from the Department of Defense’s Unified Culture Collection (http://www.usamriid.army.mil/ucc/) or BEI Resources (http://beiresources.org/).
Footnotes
Citation Johnson SL, Bishop-Lilly KA, Ladner JT, Daligault HE, Davenport KW, Jaissle J, Frey KG, Koroleva GI, Bruce DC, Coyne SR, Broomall SM, Li P-E, Teshima H, Gibbons HS, Palacios GF, Rosenzweig CN, Redden CL, Xu Y, Minogue TD, Chain PS. 2015. Complete genome sequences for 59 Burkholderia isolates, both pathogenic and near neighbor. Genome Announc 3(2):e00159-15. doi:10.1128/genomeA.00159-15.
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