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Announcement
11 May 2017

Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia

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 (13). 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
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
a
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.

REFERENCES

1.
Kracalik I, Malania L, Tsertsvadze N, Manvelyan J, Bakanidze L, Imnadze P, Tsanava S, and Blackburn JK. 2014. Human cutaneous anthrax, Georgia 2010–2012. Emerg Infect Dis20:261–264.
2.
Kracalik IT, Malania L, Tsertsvadze N, Manvelyan J, Bakanidze L, Imnadze P, Tsanava S, and Blackburn JK. 2013. Evidence of local persistence of human anthrax in the country of Georgia associated with environmental and anthropogenic factors. PLoS Negl Trop Dis7:e2388.
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Radnedge L, Agron PG, Hill KK, Jackson PJ, Ticknor LO, Keim P, and Andersen GL. 2003. Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol69:2755–2764.
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Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, and Hugh-Jones ME. 2000. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J Bacteriol182:2928–2936.
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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, and Keim P. 2007. Global genetic population structure of Bacillus anthracis. PLoS One2:e461.
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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, and 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 One9:e102651.
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Li PE, Lo CC, Anderson JJ, Davenport KW, Bishop-Lilly KA, Xu Y, Ahmed S, Feng S, Mokashi VP, and Chain PSG. 2017. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res45:67–80.
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Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity GM, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, and White O. 2008. Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. Omics12:137–141.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 5Number 1911 May 2017
eLocator: 10.1128/genomea.00256-17

History

Received: 2 March 2017
Accepted: 16 March 2017
Published online: 11 May 2017

Contributors

Authors

Ekaterine Khmaladze
National Center for Disease Control & Public Health (NCDC), Tbilisi, Georgia
Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
Giorgi Dzavashvili
National Center for Disease Control & Public Health (NCDC), Tbilisi, Georgia
Georgian American University, Tbilisi, Georgia
Gvantsa Chanturia
National Center for Disease Control & Public Health (NCDC), Tbilisi, Georgia
U.S. Army Medical Research Unit–Georgia, Tbilisi, Georgia
Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
Patrick S. G. Chain
Los Alamos National Laboratory, Los Alamos, New Mexico, USA
Los Alamos National Laboratory, Los Alamos, New Mexico, USA
Paata Imnadze
National Center for Disease Control & Public Health (NCDC), Tbilisi, Georgia

Notes

Address correspondence to Ekaterine Khmaladze, [email protected].

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