A tandem repeats database for bacterial genomes: Application to the genotyping of Yersinia pestis and Bacillus anthracis

BMC Microbiology

Volumn 1, Issue , 2001, Pages 1-14

  Le Flèche, Philippe ^a,b   Hauck, Yolande ^b   Onteniente, Lucie ^b   Prieur, Agnès ^a,b   Denoeud, France ^b   Ramisse, Vincent ^a   Sylvestre, Patricia ^a   Benson, Gary ^c   Ramisse, Françoise ^a   Vergnaud, Gilles ^a,b  

^a CENTRE D ETUDES DU BOUCHET   (France)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGAR GEL ELECTROPHORESIS; ARTICLE; BACILLUS ANTHRACIS; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; DATA BASE; DNA POLYMORPHISM; GENE LOCUS; GENOTYPE; NONHUMAN; VARIABLE NUMBER OF TANDEM REPEAT; YERSINIA PESTIS; CLASSIFICATION; FACTUAL DATABASE; GENETIC POLYMORPHISM; GENETICS; POLYMERASE CHAIN REACTION; STATISTICS; TANDEM REPEAT;

BACILLUS ANTHRACIS; BACTERIA (MICROORGANISMS); YERSINIA; YERSINIA PESTIS;

BACTERIAL DNA;

BACILLUS ANTHRACIS; DATABASES, FACTUAL; DNA, BACTERIAL; GENOME, BACTERIAL; GENOTYPE; MINISATELLITE REPEATS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; STATISTICS; TANDEM REPEAT SEQUENCES; YERSINIA PESTIS;

EID: 19044366369     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-1-2     Document Type: Article

References (24)

1. van Belkum A, Scherer S, van Leeuwen W, Willemse D, van Alphen L, Verbrugh H: Variable number of tandem repeats in clinical strains of Haemophilus influenzae. Infect Immun 1997, 65:5017-27
2. Keim P, Price LB, Klevytska AM, Smith KL, Schupp JM, Okinaka R, Jackson PJ, Hugh-Jones ME: Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis. J Bacteriol 2000, 182:2928-2936
3. Frothingham R, Meeker-O'Connell WA: Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 1998, 144:1189-96
4. Supply P, Mazars E, Lesjean S, Vincent V, Gicquel B, Locht C: Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol Microbiol 2000, 36:762-71
5. Adair DM, Worsham PL, Hill KK, Klevytska AM, Jackson PJ, Friedlander AM, Keim P: Diversity in a variable-number tandem repeat from Yersinia pestis. J Clin Microbiol 2000, 38:1516-9
6. van Ham SM, van Alphen L, Mooi FR, van Putten JP: Phase variation of H. influenzae fimbriae: transcriptional control of two divergent genes through a variable combined promoter region. Cell 1993, 73:1187-96
7. Weiser JN, Love JM, Moxon ER: The molecular mechanism of phase variation of H. influenzae lipopolysaccharide. Cell 1989, 59:657-65
8. Bayliss CD, Field D, Moxon ER: The simple sequence contingency loci of Haemophilus influenzae and Neisseria meningitidis. J Clin Invest 2001, 107:657-66
9. Henderson IR, Owen P, Nataro JP: Molecular switches - the ON and OFF of bacterial phase variation. Mol Microbiol 1999, 33:919-32
10. Wang G, Ge Z, Rasko DA, Taylor DE: Lewis antigens in Helicobacter pylori: biosynthesis and phase variation. Mol Microbiol 2000, 36:1187-96
11. Wilton JL, Scarman AL, Walker MJ, Djordjevic SP: Reiterated repeat region variability in the ciliary adhesin gene of Mycoplasma hyopneumoniae. Microbiology 1998, 144:1931-43
12. Vergnaud G, Denoeud F: Minisatellites: Mutability and Genome Architecture. Genome Res 2000, 10:899-907
13. Kokoska RJ, Stefanovic L, Tran HT, Resnick MA, Gordenin DA, Petes TD: Destabilization of yeast micro- and minisatellite DNA sequences by mutations affecting a nuclease involved in Okazaki fragment processing (rad27) and DNA polymerase delta (pol3-t). Mol Cell Biol 1998, 18:2779-88
14. Debrauwère H, Buard J, Tessier J, Aubert D, Vergnaud G, Nicolas A: Meiotic instability of human minisatellite CEB1 in yeast requires DNA double-strand breaks. Nat Genet 1999, 23:367-71
15. De Bolle X, Bayliss CD, Field D, van de Ven T, Saunders NJ, Hood DW, Moxon ER: The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases. Mol Microbiol 2000, 35:211-22
16. van Belkum A, Scherer S, van Alphen L, Verbrugh H: Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 1998, 62:275-93
17. Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, Carniel E: Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis [published erratum appears in Proc Natl Acad Sci U S A 2000 Jul 5;97(14):8192]. Proc Natl Acad Sci U S A 1999, 96:14043-8
18. Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, Carniel E: Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis [published erratum appears in Proc Natl Acad Sci U S A 2000 Jul 5;97(14):8192]. Proc Natl Acad Sci U S A 1999, 96:14043-8
19. Helgason E, Okstad OA, Caugant DA, Johansen HA, Fouet A, Mock M, Hegna I, Kolsto: Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis - one species on the basis of genetic evidence. Appl Environ Microbiol 2000, 66:2627-30
20. Keim P, Kalif A, Schupp J, Hill K, Travis SE, Richmond K, Adair DM, Hugh-Jones M, Kuske CR, Jackson P: Molecular evolution and diversity in Bacillus anthracis as detected by amplified fragment length polymorphism markers. J Bacteriol 1997, 179:818-24
21. Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-80
22. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Barrell BG, et al: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393:537-44
23. Engelke DR, Krikos A, Bruck ME, Ginsburg D: Purification of Thermus aquaticus DNA polymerase expressed in Escherichia coli. Anal. Biochem. 1990, 191:396-400
24. Felsenstein J: PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166