ABSTRACT
Bacillus anthracis causes the acute fatal disease anthrax, is a proven biological weapon, and is endemic in Georgia, where human and animal cases are reported annually. Here, we present whole-genome sequences of 10 historical B. anthracis strains from Georgia.
GENOME ANNOUNCEMENT
Bacillus anthracis causes cutaneous anthrax in humans and animals in Georgia and displays subspecies-specific differences in virulence, geographic distribution, and genetic diversity (1–3). Different molecular genotyping tools such as multiple-locus variable-number tandem repeat analysis (MLVA) and canonical single nucleotide polymorphisms (canonical SNPs) are used for genetic characterization of this organism (4, 5). In Georgia as well as other locations, SNPs are routinely used to subtype B. anthracis isolates and place them into a global phylogeographic context. We found two geographically distinct and relatively distant populations of B. anthracis that belong to different genetic groups defined by canonical SNPs (6). Five sequenced Georgian B. anthracis isolates belonged to the A.Br.013/015 clade and five to the A.Br.008/009 (Transeurasia) clade.
DNA fragment libraries were generated from genomic DNA according to the Illumina next-generation sequencing sample preparation method. B. anthracis DNAs were shredded by nebulization. The final size with an average of ca. 450 bp of the prepared libraries was determined by an Agilent 2100 bioanalyzer. Sequencing was performed using an Illumina 300 cycle sequencing kit on the MiSeq platform at NCDC Lugar Center in Tbilisi, Georgia. Obtained raw data of 150-bp length reads were analyzed using EDGE Bioinformatics (7). We assembled each draft genome using IDBA (7) in EDGE after quality trimming (standard parameters). Assemblies were aligned to the closest SNP subclade reference genomes, Ames ancestor and Sterne, for B. anthracis.
The draft genomes were annotated by utilizing the NCBI prokaryotic genomes automatic annotation pipeline (8) (PGAAP revision 3.3; http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html).
Accession number(s).
The whole-genome sequences for B. anthracis are available through GenBank under BioProject PRJNA336484 with the accession numbers listed in Table 1.
TABLE 1 .
Strain identifying information and basic statistics on assemblies and annotations
| Strain ID | Yr of collection | Source of isolation | GenBank accession no. | No. of de novo contigs | Coverage depth (fold) | Contig N50 (bp) | No. of CDSsa |
|---|---|---|---|---|---|---|---|
| Ba-1802/12-Geo | 2012 | Patient ulcer | MVKJ00000000 | 78 | 119.35 | 365,205 | 5,722 |
| Ba-1897/12-Geo | 2012 | Beef | MVKH00000000 | 88 | 132.10 | 413,677 | 5,723 |
| Ba-8776/92-Geo | 1992 | Patient ulcer | MVKI00000000 | 81 | 141.80 | 331,561 | 5,719 |
| Ba-9065/08-Geo | 2008 | Patient ulcer | MVKG00000000 | 70 | 209.11 | 331,561 | 5,724 |
| Ba-9108/08-Geo | 2008 | Patient ulcer | MVKF00000000 | 95 | 157.55 | 432,600 | 5,727 |
| Ba-7673/89-Geo | 1989 | Soil | MVKE00000000 | 86 | 211.16 | 868,539 | 5,618 |
| Ba-8782/92-Geo | 1992 | Sheep skin | MVKD00000000 | 84 | 98.30 | 287,604 | 5,618 |
| Ba-8784/92-Geo | 1992 | Beef | MVKC00000000 | 72 | 195.48 | 266,373 | 5,618 |
| Ba-8785/92-Geo | 1992 | Patient ulcer | MVKB00000000 | 70 | 154.38 | 313,727 | 5,616 |
| Ba-8884/94-Geo | 1994 | Patient ulcer | MVIR00000000 | 69 | 168.97 | 320,727 | 5,616 |
CDSs, coding sequences.
ACKNOWLEDGMENTS
This study was funded by the Cooperative Research and Development Foundation (CRDF Global/GRDF, Minigrant award GMG 09/13), Walter Reed Army Institute of Research (WRAIR, under DTRA CBD grant CBCALL12-DIAGB1-2-0194), and Defense Threat Reduction Agency (DTRA).
The findings and opinions expressed herein belong to the authors and do not necessarily reflect the official views of the WRAIR, the U.S. Army, the Department of Defense, or Los Alamos National Laboratory.
Footnotes
Citation Khmaladze E, Dzavashvili G, Chanturia G, Nikolich MP, Chain PSG, Johnson SL, Imnadze P. 2017. Ten genome sequences of human and livestock isolates of Bacillus anthracis from the country of Georgia. Genome Announc 5:e00256-17. https://doi.org/10.1128/genomeA.00256-17.
REFERENCES
- 1.Kracalik I, Malania L, Tsertsvadze N, Manvelyan J, Bakanidze L, Imnadze P, Tsanava S, Blackburn JK. 2014. Human cutaneous anthrax, Georgia 2010–2012. Emerg Infect Dis 20:261–264. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Kracalik IT, Malania L, Tsertsvadze N, Manvelyan J, Bakanidze L, Imnadze P, Tsanava S, Blackburn JK. 2013. Evidence of local persistence of human anthrax in the country of Georgia associated with environmental and anthropogenic factors. PLoS Negl Trop Dis 7:e2388. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Radnedge L, Agron PG, Hill KK, Jackson PJ, Ticknor LO, Keim P, Andersen GL. 2003. Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol 69:2755–2764. doi: 10.1128/AEM.69.5.2755-2764.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol 182:2928–2936. doi: 10.1128/JB.182.10.2928-2936.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U’Ren JM, Kachur SM, Leadem-Dougherty RR, Rhoton SD, Zinser G, Farlow J, Coker PR, Smith KL, Wang B, Kenefic LJ, Fraser-Liggett CM, Wagner DM, Keim P. 2007. Global genetic population structure of Bacillus anthracis. PLoS One 2:e461. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G, Zhgenti E, Zakalashvili M, Malania L, Babuadze G, Tsertsvadze N, Abazashvili N, Kekelidze M, Tsanava S, Imnadze P, Ganz HH, Getz WM, Pearson O, Gajer P, Eppinger M, Ravel J, Wagner DM, Okinaka RT, Schupp JM, Keim P, Pearson T. 2014. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes. PLoS One 9:e102651. doi: 10.1371/journal.pone.0102651. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Li PE, Lo CC, Anderson JJ, Davenport KW, Bishop-Lilly KA, Xu Y, Ahmed S, Feng S, Mokashi VP, Chain PSG. 2017. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res 45:67–80. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity GM, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. Omics 12:137–141. doi: 10.1089/omi.2008.0017. [DOI] [PMC free article] [PubMed] [Google Scholar]