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Genome Sequences

Draft Genome Sequences of Five Historical Bacillus anthracis Strains

Daniel D. Sommer, Shashikala Ratnayake, Diana Radune, Kisha Parker, Sana Enke, Tracy M. Ferguson, Marie Lovett, Adam Mallonee, Zach Rae, M. J. Rosovitz, Lynn F. Diviak, Mary Beth Friss, Joy P. Klubnik, Kathy H. Fronda, Gregory P. Horn, Thomas E. Blank, Robert K. Pope, Philip C. Hanna, Nicholas H. Bergman, Adam L. Bazinet
David A. Baltrus, Editor
Daniel D. Sommer
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Shashikala Ratnayake
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Diana Radune
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Kisha Parker
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Sana Enke
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Tracy M. Ferguson
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Marie Lovett
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Adam Mallonee
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Zach Rae
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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M. J. Rosovitz
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Lynn F. Diviak
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Mary Beth Friss
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Joy P. Klubnik
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Kathy H. Fronda
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Gregory P. Horn
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Thomas E. Blank
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Robert K. Pope
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Philip C. Hanna
bUniversity of Michigan Medical School, Ann Arbor, Michigan, USA
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Nicholas H. Bergman
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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Adam L. Bazinet
aNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Maryland, USA
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  • ORCID record for Adam L. Bazinet
David A. Baltrus
University of Arizona
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DOI: 10.1128/MRA.01130-19
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ABSTRACT

Bacillus anthracis is the causative agent of anthrax, a disease of livestock, wildlife, and humans. Here, we present the draft genome sequences of five historical B. anthracis strains that were preserved as lyophilates in glass vials for decades.

ANNOUNCEMENT

Eight glass vials of Bacillus anthracis produced at ATCC from 1962 to 1988 were opened, and the lyophilized contents were resuspended in tryptic soy broth (TSB) and cultured in TSB and on 5% sheep blood agar (SBA) at 35°C. The glass vials were originally sealed such that they would have had to be broken to be tampered with or otherwise contaminated, thus adding a degree of confidence as to the origin of the material being sequenced. Viable bacteria were not recovered from three of the vials (ATCC 10 lot number 1982-Aug-20, ATCC 938 lot number 1963-May-02, and ATCC 11949 lot number 1962-July-19). The remaining five vials (Table 1) yielded nonhemolytic Gram-positive rods that were sensitive to both penicillin and gamma phage. Frozen stocks were prepared from the cultured material. Starting from these stocks, bacteria were subcultured overnight at 35°C to form a lawn on SBA. DNA was extracted from the subcultured material using the Promega Wizard genomic DNA purification kit and filtered through a 0.1-μm spin filter. Ten percent of the DNA volume was inoculated into 10 ml of TSB and incubated at 35°C for at least 48 hours, and then 100 μl of the broth was plated to SBA and incubated at 35°C for at least 48 additional hours to confirm sterility. B. anthracis strains were handled according to Federal Select Agent Program regulations.

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TABLE 1

Strain information and assembly statistics

Illumina Nextera XT libraries were prepared from the extracted DNA samples using the standard Illumina protocol. The final libraries were pooled and sequenced on the Illumina HiSeq 2500 instrument, generating paired-end reads of 250 bp. For the bioinformatic analyses that followed, default parameters were used with all software programs unless otherwise noted. Reads were preprocessed before assembly using bmap_preprocess (https://github.com/bioforensics/asm_tools/) with the parameters –qual 20 and –length 75. The bmap_preprocess workflow filtered the reads using fastp version 0.19.3 (1) to ensure the minimum length (75 bp) and quality value (20) for at least 60% of the bases, estimated the genome size by building a k-mer profile using Jellyfish (2), and randomly downsampled the reads to an estimated 150× genome coverage. Genome assembly was performed using SPAdes version 3.12.0 (3), and genome quality assessment was performed using QUAST version 4.6.3 (4). All reads were mapped back to the assembly using Bowtie 2 (5) to determine the average genome coverage values (Table 1). The assembled genomes had an estimated size of 5.3 to 5.5 Mb with ≈35% GC content. The presence or absence of pXO plasmids was determined by aligning assembled contigs to reference pXO sequences (Ames Ancestor) using MUMmer (NUCmer) version 3.1 (6). In our analysis, four strains were found to lack the pXO1 plasmid (NC_007322); all strains contained the pXO2 plasmid (NC_007323) (Table 1). Core genome alignment and phylogenetic analysis of the five ATCC strains together with all publicly available B. anthracis genomes was performed using Parsnp version 1.0 (7) and RAxML version 8.2.12 (8) with the GTR+Gamma+I substitution model (-m GTRGAMMAI). The phylogenetic results were compared to previously published B. anthracis phylogenies (9) to determine the phylogenetic clade label for each strain (Table 1).

The provenance of the five strains was previously described (10, 11). ATCC 240 and ATCC 937 were part of the ATCC collection prior to 1931 (12), and ATCC 4728 and ATCC 6603 were part of the collection by 1952 (11). ATCC 4728 was previously sequenced as Smith 1013 and A0157 (NCBI nucleotide accession numbers JNOD00000000, CP010342, and CP010343; 13). Further analysis of the sequence of ATCC 11966, a laboratory-derived nonproteolytic mutant of the Vollum strain (14), may identify mutations affecting the expression or activity of proteases.

Data availability.This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the BioSample accession numbers SAMN12620928, SAMN12620929, SAMN12620930, SAMN12620931, and SAMN12620932. The raw Illumina paired-end sequencing reads have been deposited in the Sequence Read Archive under the accession numbers SRR10019497, SRR10019498, SRR10019499, SRR10019500, and SRR10019501.

ACKNOWLEDGMENTS

We thank Sean Lovett and Martina Eaton for reviewing drafts of the manuscript.

This work was funded under contract number HSHQDC-15-C-00064 awarded by the Department of Homeland Security (DHS) Science and Technology Directorate (S&T) to the National Biodefense Analysis and Countermeasures Center (NBACC), a Department of Homeland Security (DHS) federal laboratory sponsored by the DHS Science and Technology Directorate and operated by the Battelle National Biodefense Institute. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the DHS or S&T. In no event shall DHS, NBACC, S&T, or Battelle National Biodefense Institute have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. DHS does not endorse any products or commercial services mentioned in this publication.

FOOTNOTES

    • Received 10 September 2019.
    • Accepted 26 November 2019.
    • Published 2 January 2020.
  • Copyright © 2020 Sommer et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Chen S,
    2. Zhou Y,
    3. Chen Y,
    4. Gu J
    . 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi:10.1093/bioinformatics/bty560.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Marçais G,
    2. Kingsford C
    . 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770. doi:10.1093/bioinformatics/btr011.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Mikheenko A,
    2. Valin G,
    3. Prjibelski A,
    4. Saveliev V,
    5. Gurevich A
    . 2016. Icarus: visualizer for de novo assembly evaluation. Bioinformatics 32:3321–3323. doi:10.1093/bioinformatics/btw379.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Langmead B,
    2. Salzberg SL
    . 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923.
    OpenUrlCrossRefPubMedWeb of Science
  6. 6.↵
    1. Kurtz S,
    2. Phillippy A,
    3. Delcher AL,
    4. Smoot M,
    5. Shumway M,
    6. Antonescu C,
    7. Salzberg SL
    . 2004. Versatile and open software for comparing large genomes. Genome Biol 5:R12. doi:10.1186/gb-2004-5-2-r12.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Treangen TJ,
    2. Ondov BD,
    3. Koren S,
    4. Phillippy AM
    . 2014. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15:524. doi:10.1186/s13059-014-0524-x.
    OpenUrlCrossRefPubMed
  8. 8.↵
    1. Stamatakis A
    . 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. doi:10.1093/bioinformatics/btu033.
    OpenUrlCrossRefPubMedWeb of Science
  9. 9.↵
    1. Sahl JW,
    2. Pearson T,
    3. Okinaka R,
    4. Schupp JM,
    5. Gillece JD,
    6. Heaton H,
    7. Birdsell D,
    8. Hepp C,
    9. Fofanov V,
    10. Noseda R,
    11. Fasanella A,
    12. Hoffmaster A,
    13. Wagner DM,
    14. Keim P
    . 2016. A Bacillus anthracis genome sequence from the Sverdlovsk 1979 autopsy specimens. mBio 7:e01501-16. doi:10.1128/mBio.01501-16.
    OpenUrlAbstract/FREE Full Text
  10. 10.↵
    American Type Culture Collection. 1992. Bacillus anthracis Cohn, p 36–37. In Gherna R, Pienta P, Cote R (ed), Catalogue of bacteria and bacteriophages, 18th ed. American Type Culture Collection, Rockville, MD.
  11. 11.↵
    1. Smith NR,
    2. Gordon RE,
    3. Clark FE
    . 1952. Aerobic sporeforming bacteria. Monograph no. 16. United States Department of Agriculture, Washington, DC.
  12. 12.↵
    1. Cowles PB
    . 1931. A bacteriophage for B. anthracis. J Bacteriol 21:161–166.
    OpenUrlFREE Full Text
  13. 13.↵
    1. Daligault HE,
    2. Davenport KW,
    3. Minogue TD,
    4. Bishop-Lilly KA,
    5. Broomall SM,
    6. Bruce DC,
    7. Chain PS,
    8. Coyne SR,
    9. Frey KG,
    10. Gibbons HS,
    11. Jaissle J,
    12. Koroleva GI,
    13. Ladner JT,
    14. Lo CC,
    15. Munk C,
    16. Palacios GF,
    17. Redden CL,
    18. Rosenzweig CN,
    19. Scholz MB,
    20. Johnson SL
    . 2014. Twenty whole-genome Bacillus sp. assemblies. Genome Announc 9:e00958-14. doi:10.1128/genomeA.00958-14.
    OpenUrlCrossRef
  14. 14.↵
    1. Wright GG,
    2. Hedberg MA,
    3. Feinberg RJ
    . 1951. Studies on immunity in anthrax. II. In vitro elaboration of protective antigen by non-proteolytic mutants of Bacillus anthracis. J Exp Med 93:523–527. doi:10.1084/jem.93.6.523.
    OpenUrlAbstract/FREE Full Text
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Draft Genome Sequences of Five Historical Bacillus anthracis Strains
Daniel D. Sommer, Shashikala Ratnayake, Diana Radune, Kisha Parker, Sana Enke, Tracy M. Ferguson, Marie Lovett, Adam Mallonee, Zach Rae, M. J. Rosovitz, Lynn F. Diviak, Mary Beth Friss, Joy P. Klubnik, Kathy H. Fronda, Gregory P. Horn, Thomas E. Blank, Robert K. Pope, Philip C. Hanna, Nicholas H. Bergman, Adam L. Bazinet
Microbiology Resource Announcements Jan 2020, 9 (1) e01130-19; DOI: 10.1128/MRA.01130-19

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Draft Genome Sequences of Five Historical Bacillus anthracis Strains
Daniel D. Sommer, Shashikala Ratnayake, Diana Radune, Kisha Parker, Sana Enke, Tracy M. Ferguson, Marie Lovett, Adam Mallonee, Zach Rae, M. J. Rosovitz, Lynn F. Diviak, Mary Beth Friss, Joy P. Klubnik, Kathy H. Fronda, Gregory P. Horn, Thomas E. Blank, Robert K. Pope, Philip C. Hanna, Nicholas H. Bergman, Adam L. Bazinet
Microbiology Resource Announcements Jan 2020, 9 (1) e01130-19; DOI: 10.1128/MRA.01130-19
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