Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay

BMC Microbiology

Volumn 9, Issue , 2009, Pages

  Pandya, Gagan A ^a   Holmes, Michael H ^a   Petersen, Jeannine M ^b   Pradhan, Sonal ^a   Karamycheva, Svetlana A ^a   Wolcott, Mark J ^c   Molins, Claudia ^b   Jones, Marcus ^a   Schriefer, Martin E ^b   Fleischmann, Robert D ^a   Peterson, Scott N ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b NATIONAL CENTER FOR EMERGING AND ZOONOTIC INFECTIOUS DISEASES   (United States)

^c UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CONTROLLED STUDY; FRANCISELLA; FRANCISELLA NOVICIDA; FRANCISELLA TULARENSIS; GENE SEQUENCE; GENOME; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDITY; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BIOLOGY; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETICS; METHODOLOGY; POLYMERASE CHAIN REACTION;

FRANCISELLA; FRANCISELLA TULARENSIS; FRANCISELLA TULARENSIS SUBSP. TULARENSIS;

BACTERIAL DNA;

BACTERIAL TYPING TECHNIQUES; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; FRANCISELLA TULARENSIS; GENOME, BACTERIAL; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 70449380983     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-9-213     Document Type: Article

References (28)

1. Genome diversity among regional populations of Francisella tularensis subspecies tularensis and Francisella tularensis subspecies holarctica isolated from the US. MM Samrakandi C Zhang M Zhang J Nietfeldt J Kim PC Iwen ME Olson PD Fey GE Duhamel SH Hinrichs, et al. FEMS Microbiol Lett 2004 237 1 9 17 10.1111/j.1574-6968.2004.tb09672.x 15268932
2. Molecular epidemiology, evolution, and ecology of Francisella. P Keim A Johansson DM Wagner, Ann N Y Acad Sci 2007 1105 30 66 10.1196/annals.1409.011 17435120
3. Tularemia: emergence/re-emergence. JM Petersen ME Schriefer, Vet Res 2005 36 3 455 467 10.1051/vetres:2005006 15845234
4. Phylogeography of Francisella tularensis: global expansion of a highly fit clone. AJ Vogler D Birdsell LB Price JR Bowers SM Beckstrom-Sternberg RK Auerbach JS Beckstrom-Sternberg A Johansson A Clare JL Buchhagen, et al. J Bacteriol 2009 191 8 2474 2484 10.1128/JB.01786-08 19251856
5. Family XVII. Francisellaceae, genus I. Francisella. A Sjostedt, Bergey's Manual of Systematic Bacteriology New York: Springer, DJ Brenner NRK, Staley JT, Garrity GM, 2005 200 210
6. Vaccination strategies for Francisella tularensis. KE Isherwood RW Titball DH Davies PL Felgner WJ Morrow, Adv Drug Deliv Rev 2005 57 9 1403 1414 10.1016/j.addr.2005.01.030 15919131
7. WHO guidelines on tularemia. World Health Organization, Geneva, Switzerland: World Health Organization 2007 http://www.cdc.gov/tularemia/ resources/whotularemiamanual.pdf
8. The development of tools for diagnosis of tularemia and typing of Francisella tularensis. A Johansson M Forsman A Sjostedt, APMIS 2004 112 898 907 10.1111/j.1600-0463.2004.apm11211-1212.x 15638842
9. Molecular Epidemiology of Francisella tularensis in the United States. KJ Kugeler PS Mead AM Janusz JE Staples KA Kubota LG Chalcraft JM Petersen, Clin Infect Dis 2009 48 7 863 870 10.1086/597261 19245342
10. Canonical insertion-deletion markers for rapid DNA typing of Francisella tularensis. P Larsson K Svensson L Karlsson D Guala M Granberg M Forsman A Johanssont, Emerg Infect Dis 2007 13 11 1725 1732 18217558
11. Potential source of Francisella tularensis live vaccine strain attenuation determined by genome comparison. L Rohmer M Brittnacher K Svensson D Buckley E Haugen Y Zhou J Chang R Levy H Hayden M Forsman, et al. Infect Immun 2006 74 12 6895 6906 10.1128/IAI.01006-06 17000723
12. Chips and SNPs, bugs and thugs: a molecular sleuthing perspective. TA Cebula SA Jackson EW Brown B Goswami JE LeClerc, J Food Prot 2005 68 6 1271 1284 15954721
13. A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform. GA Pandya MH Holmes S Sunkara A Sparks Y Bai K Verratti K Saeed P Venepally B Jarrahi RD Fleischmann, et al. Nucleic Acids Res 2007 35 21 148 10.1093/nar/gkm918 18006572
14. Epidemiologic and molecular analysis of human tularemia, United States, 1964-2004. JE Staples KA Kubota LG Chalcraft PS Mead JM Petersen, Emerg Infect Dis 2006 12 7 1113 1118 16836829
15. MRBAYES: Bayesian inference of phylogenetic trees. JP Huelsenbeck F Ronquist, Bioinformatics 2001 17 8 754 755 10.1093/bioinformatics/17.8.754 11524383
16. Bayesian inference of phylogeny and its impact on evolutionary biology. JP Huelsenbeck F Ronquist R Nielsen JP Bollback, Science 2001 294 5550 2310 2314 10.1126/science.1065889 11743192
17. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839
18. PHYLIP - Phylogeny Inference Package (Version 3.2). J Felsenstein, Cladistics 1989 5 164 166
19. Primer3 on the WWW for general users and for biologist programmers. S Rozen H Skaletsky, Methods Mol Biol 2000 132 365 386 10547847
20. Genetic diversity of Francisella tularensis subspecies holarctica strains isolated in Japan. O Fujita A Uda A Hotta A Okutani S Inoue K Tanabayashi A Yamada, Microbiol Immunol 2008 52 5 270 276 10.1111/j.1348-0421.2008.00036.x 18557897
21. Worldwide genetic relationships among Francisella tularensis isolates determined by multiple-locus variable-number tandem repeat analysis. A Johansson J Farlow P Larsson M Dukerich E Chambers M Bystrom J Fox M Chu M Forsman A Sjostedt, et al. J Bacteriol 2004 186 17 5808 5818 10.1128/JB.186.17.5808-5818. 2004 15317786
22. Francisella tularensis in the United States. J Farlow DM Wagner M Dukerich M Stanley M Chu K Kubota J Petersen P Keim, Emerg Infect Dis 2005 11 12 1835 1841 16485467
23. Evolution of subspecies of Francisella tularensis. K Svensson P Larsson D Johansson M Bystrom M Forsman A Johansson, J Bacteriol 2005 187 11 3903 3908 10.1128/JB.187.11.3903-3908.2005 15901721
24. Francisella tularensis: unravelling the secrets of an intracellular pathogen. PC Oyston, J Med Microbiol 2008 57 Pt 8 921 930 10.1099/jmm.0.2008/ 000653-0 18628490
25. Discrimination of human pathogenic subspecies of Francisella tularensis by using restriction fragment length polymorphism. R Thomas A Johansson B Neeson K Isherwood A Sjostedt J Ellis RW Titball, J Clin Microbiol 2003 41 1 50 57 10.1128/JCM.41.1.50-57.2003 12517824
26. Evaluation of PCR-based methods for discrimination of Francisella species and subspecies and development of a specific PCR that distinguishes the two major subspecies of Francisella tularensis. A Johansson A Ibrahim I Goransson U Eriksson D Gurycova JE Clarridge 3rd A Sjostedt, J Clin Microbiol 2000 38 11 4180 4185 11060087
27. Comparison of different PCR approaches for typing of Francisella tularensis strains. VA de la Puente-Redondo NG del Blanco CB Gutierrez-Martin FJ Garcia-Pena EF Rodriguez Ferri, J Clin Microbiol 2000 38 3 1016 1022 10698989
28. An optimized, multiplexed multi-locus variable-number tandem repeat analysis system for genotyping Francisella tularensis. AJ Vogler D Birdsell DM Wagner P Keim, Lett Appl Microbiol 2009 48 1 140 144 10.1111/j.1472-765X.2008. 02484.x 19018964