Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177

Standards in Genomic Sciences

Volumn 8, Issue 3, 2013, Pages 539-547

  Coolen, Jordy P M ^a   Sjödin, Andreas ^b   Maraha, Boulos ^c   Hajer, Gerard F ^d   Forsman, Mats ^b   Verspui, Ellen ^e   Frenay, Hendrina M E ^c   Notermans, Daan W ^f   de Vries, Maaike C ^f   Reubsaet, Frans A G ^f   Paauw, Armand ^a   Roeselers, Guus ^a  

^a TNO   (Netherlands)

^b SWEDISH DEFENCE RESEARCH AGENCY   (Sweden)

^c ALBERT SCHWEITZER HOSPITAL   (Netherlands)

^d Beatrix Hospital   (Netherlands)

^e Munic Hlth Serv Zuid Holland Zuid   (Netherlands)

^f NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

Author keywords

Biodefence; Netherlands; Phylogeography; Tularaemia; Zoonotic infection

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; DNA ISOLATION; DNA SEQUENCE; FRANCISELLA HISPANIENSIS; FRANCISELLA NOVICIDA; FRANCISELLA PHILOMIRAGIA; FRANCISELLA TULARENSIS; GENE SEQUENCE; GENOME ANALYSIS; HOLARCTICA; NONHUMAN; OPEN READING FRAME; SEQUENCE ANALYSIS; TULAREMIA;

BACTERIA (MICROORGANISMS); FRANCISELLA TULARENSIS; FRANCISELLA TULARENSIS SUBSP. HOLARCTICA; GAMMAPROTEOBACTERIA;

EID: 84881586640     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.4217923     Document Type: Article

References (41)

1. Sjostedt A. Family XVII. Francisellaceae, genus I. Francisella. In: Brenner D, Krieg N, Staley J, Garrity G, Boone D, Vos P, et al., editors. Bergey's Manual of Systematic Bacteriology. New York: Springer US; 2005. p. 200-210.
2. Rotz LD, Khan AS, Lillibridge SR, Ostroff SM, Hughes JM. Public health assessment of potential biological terrorism agents. Emerg Infect Dis 2002; 8:225-230. [doi:10.3201/eid0802.010164] [pmid:11897082]
3. Forsman M, Sandström G, Sjöstedt A. Analysis of 16S ribosomal DNA sequences of Francisella strains and utilization for determination of the phylogeny of the genus and for identification of strains by PCR. Int J Syst Bacteriol 1994; 44:38-46. [doi:10.1099/00207713-44-1-38] [pmid:8123561]
4. Brevik OJ, Ottem KF, Kamaishi T, Watanabe K, Nylund A. Francisella halioticida sp. nov., a pathogen of farmed giant abalone (Haliotis gigantea) in Japan. J Appl Microbiol 2011; 111:1044-1056. [doi:10.1111/j.1365-2672.2011.05133.x] [pmid:21883728]
5. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domainsArchaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. [doi:10.1073/pnas.87.12.4576] [pmid:2112744]
6. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
7. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Microbiol 2005; 55:2235-2238. [doi:10.1099/ijs.0.64108-0]
8. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
9. Garrity GM, Bell JA, Lilburn T. Order V. Thiotrichales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 131.
10. Sjöstedt AB. Family III. Francisellaceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 199-200.
11. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980;30:225-420. [doi:10.1099/00207713-30-1-225]
12. Dorofe'ev KA. Classification of the causative agent of tularemia. Symposium Research Works Institute Epidemiology and Microbiology Chita 1947; 1:170-180.
13. Owen CR. Genus Francisella Dorofe'ev 1947, 176. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 283-285.
14. Huber B, Escudero R, Busse H-J, Seibold E, Scholz HC, Anda P, Kämpfer P, Splettstoesser WD. Description of Francisella hispaniensis sp. nov., isolated from human blood, reclassification of Francisella novicida(Larson et al. 1955) Olsufiev et al. 1959 as Francisella tularensis subsp. novicida comb. nov., and emended description of the genus Francisella. Int J Syst Evol Microbiol 2010; 60:1887-1896. [doi:10.1099/ijs.0.015941-0] [pmid:19783615]
15. Olsufjev NG, Meshcheryakova IS. Subspecific taxonomy of Francisella tularensis McCoy and Chapin 1912. Int J Syst Bacteriol 1983; 33:872-874. [doi:10.1099/00207713-33-4-872]
16. Olsufjev NG, Emelyanova OS, Dunaeva TN. Comparative study of strains of B. tularense in the Old and New World and their taxonomy. J Hyg Epidemiol Microbiol Immunol 1959; 3:138-149. [pmid:14428832]
17. Sjödin A, Svensson K, Ohrman C, Ahlinder J, Lindgren P, Duodu S, Johansson A, Colquhoun DJ, Larsson P, Forsman M. Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish. BMC Genomics 2012; 13:268. [doi:10.1186/1471-2164-13-268] [pmid:22727144]
18. Wenger JD, Hollis DG, Weaver RE, Baker CN, Brown GR, Brenner DJ, Broome CV. Infection caused byFrancisella philomiragia (formerly Yersinia philomiragia). A newly recognized human pathogen. Ann Intern Med 1989; 110:888-892. [doi:10.7326/0003-4819-110-11-888] [pmid:2541646]
19. Larson CL, Wicht W, Jellison WL. A new organism resembling P. tularensis isolated from water. Public Health Rep 1955; 70:253-258. [doi:10.2307/4589039] [pmid:14357545]
20. Mörner T, Addison E. Tularemia. In: Williams ES, Barker IK, editors. Infectious diseases of wild animals. 3rd ed. Ames: Iowa Stae University; 2001. p. 303-312.
21. Keim P, Johansson A, Wagner DM. Molecular epidemiology, evolution, and ecology of Francisella. Ann N Y Acad Sci 2007; 1105:30-66. [doi:10.1196/annals.1409.011] [pmid:17435120]
22. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38(Database issue):D346-D354. [doi:10.1093/nar/gkp848] [pmid:19914934]
23. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. [doi:10.1186/1471-2105-11-119] [pmid:20211023]
24. Boisvert S, Laviolette F, Corbeil J. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of computational biology: a journal of computational molecular cell biology. 2010 Nov;17(11):1519-1533.
25. Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics 2007; 8:18. [doi:10.1186/1471-2105-8-18] [pmid:17239253]
26. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100-3108. [doi:10.1093/nar/gkm160] [pmid:17452365]
27. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2004; 33(Database issue):D121-D124. [doi:10.1093/nar/gki081] [pmid:15608160]
28. Vogler AJ, Birdsell D, Price LB, Bowers JR, Beckstrom-Sternberg SM, Auerbach RK, Beckstrom-Sternberg JS, Johansson A, Clare A, Buchhagen JL, et al. Phylogeography of Francisella tularensis: global expansion of a highly fit clone. J Bacteriol 2009; 191:2474-2484. [doi:10.1128/JB.01786-08] [pmid:19251856]
29. Svensson K, Granberg M, Karlsson L, Neubauerova V, Forsman M, Johansson A. A real-time PCR array for hierarchical identification of Francisella isolates. PLoS ONE 2009; 4:e8360. [doi:10.1371/journal.pone.0008360] [pmid:20027310]
30. Barabote RD, Xie G, Brettin TS, Hinrichs SH, Fey PD, Jay JJ, Engle JL, Godbole SD, Noronha JM, Scheuermann RH. Complete genome sequence of Francisella tularensis subspecies holarctica FTNF002-00. PLoS ONE 2009; 4:e7041. [doi:10.1371/journal.pone.0007041] [pmid:19756146]
31. Dempsey MP, Dobson M, Zhang C, Zhang M, Lion C, Gutiérrez-Martín CB. Genomic deletion marking an emerging subclone of Francisella tularensis subsp. holarctica in France and the Iberian Peninsula. Appl Environ Microbiol 2007; 73:7465-7470. [doi:10.1128/AEM.00646-07] [pmid:17890329]
32. Pilo P, Johansson A, Frey J. Identification of Francisella tularensis cluster in central and western Europe. Emerg Infect Dis 2009; 15:2049-2051. [doi:10.3201/eid1512.080805] [pmid:19961699]
33. Gyuranecz M, Birdsell DN, Splettstoesser W, Seibold E, Beckstrom-Sternberg SM, Makrai L, Fodor L, Fabbi M, Vicari N, Johansson A, et al. Phylogeography of Francisella tularensis subsp. holarctica, Europe. Emerg Infect Dis 2012; 18:290-293. [doi:10.3201/eid1802.111305] [pmid:22305204]
34. Vogler AJ, Birdsell DN, Lee J, Vaissaire J, Doujet CL, Lapalus M, Wagner DM, Keim P. Phylogeography ofFrancisella tularensis ssp. holarctica in France. Lett Appl Microbiol 2011; 52:177-180. [doi:10.1111/j.1472-765X.2010.02977.x] [pmid:21214606]
35. Gehringer H, Schacht E, Maylaender N, Zeman E, Kaysser P, Oehme R, et al. Presence of an emerging subclone of Francisella tularensis holarctica in Ixodes ricinus ticks from south-western Germany. Ticks and tick-borne diseases. 2013 Feb;4(1-2):93-100.
36. Svensson K, Sjödin A, Byström M, Granberg M, Brittnacher MJ, Rohmer L, Jacobs MA, Sims-Day EH, Levy R, Zhou Y, et al. Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia. J Bacteriol 2012; 194:6965-6966. [doi:10.1128/JB.01040-12] [pmid:23209222]
37. Petrosino JF, Xiang Q, Karpathy SE, Jiang H, Yerrapragada S, Liu Y, Gioia J, Hemphill L, Gonzalez A, Raghavan TM, et al. Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J Bacteriol 2006; 188:6977-6985. [doi:10.1128/JB.00506-06] [pmid:16980500]
38. La Scola B, Elkarkouri K, Li W, Wahab T, Fournous G, Rolain JM, Biswas S, Drancourt M, Robert C, Audic S, et al. Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensisparadigm. Genome Res 2008; 18:742-750. [doi:10.1101/gr.071266.107] [pmid:18407970]
39. Chanturia G, Birdsell DN, Kekelidze M, Zhgenti E, Babuadze G, Tsertsvadze N, Tsanava S, Imnadze P, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS. Phylogeography of Francisella tularensis subspecies holarctica from the country of Georgia. BMC Microbiol 2011; 11:139. [doi:10.1186/1471-2180-11-139] [pmid:21682874]
40. Karlsson E, Svensson K, Lindgren P, Byström M, Sjödin A, Forsman M, Johansson A. The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia. Environ Microbiol 2013; 15:634-645. [doi:10.1111/1462-2920.12052] [pmid:23253075]
41. Antwerpen MH, Schacht E, Kaysser P, Splettstoesser WD. Complete Genome Sequence of a Francisella tularensis subsp. holarctica Strain from Germany Causing Lethal Infection in Common Marmosets. Genome announcements. 2013 Jan;1(1).