Evaluation and selection of tandem repeat loci for Streptococcus pneumoniae MLVA strain typing

BMC Microbiology

Volumn 5, Issue , 2005, Pages

  Koeck, Jean Louis ^a   Njanpop Lafourcade, Berthe Marie ^b   Cade, Sonia ^a   Varon, Emmanuelle ^c   Sangare, Lassana ^d   Valjevac, Samina ^e,f   Vergnaud, Gilles ^e,f   Pourcel, Christine ^e  

^a HÔPITAL D'INSTRUCTION DES ARMÉES ROBERT PICQUÉ   (France)

^b Association Pour l'Aide À la Médecine Préventive   (France)

^c HÔPITAL EUROPÉEN GEORGES POMPIDOU   (France)

^d CENTRE HOSPITALIER UNIVERSITAIRE YALGADO OUÉDRAOGO   (Burkina Faso)

^e UNIVERSITÉ PARIS SACLAY   (France)

^f CENTRE D ETUDES DU BOUCHET   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CLONAL VARIATION; CONTROLLED STUDY; DNA POLYMORPHISM; GENE ISOLATION; GENE LOCUS; GENE TRANSFER; GENETIC ISOLATION BY DISTANCE; GENOME ANALYSIS; GENOTYPE; GEOGRAPHICAL VARIATION (SPECIES); HORIZONTAL GENE TRANSFER; NONHUMAN; POLYMERASE CHAIN REACTION; RIBOTYPING; SEROTYPE; STREPTOCOCCUS PNEUMONIAE; TANDEM REPEAT;

BACTERIAL TYPING TECHNIQUES; GENOME, BACTERIAL; GENOTYPE; HUMANS; PNEUMOCOCCAL INFECTIONS; POLYMORPHISM, GENETIC; PULMONARY ALVEOLI; REPETITIVE SEQUENCES, NUCLEIC ACID; SPUTUM; STREPTOCOCCUS PNEUMONIAE;

BACTERIA (MICROORGANISMS); STREPTOCOCCUS PNEUMONIAE;

EID: 29144492142     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-5-66     Document Type: Article

References (32)

1. Mar ID, Denis F, Cadoz M: [Epidemiologic features of pneumococcal meningitis in Africa. Clinical and serotypical aspects (author's transl)]. Pathol Biol (Paris) 1979, 27:543-548.
2. Parent du Chatelet I, Traore Y, Gessner BD, Antignac A, Naccro B, Njanpop-Lafourcade BM, Ouedraogo MS, Tiendrebeogo SR, Varon E, Taha MK: Bacterial meningitis in Burkina Faso: surveillance using field-based polymerase chain reaction testing. Clin Infect Dis 2005, 40:17-25.
3. Brueggemann AB, Spratt BG: Geographic distribution and clonal diversity of Streptococcus pneumoniae serotype 1 isolates. J Clin Microbiol 2003, 41:4966-4970.
4. Hall LM, Whiley RA, Duke B, George RC, Efstratiou A: Genetic relatedness within and between serotypes of Streptococcus pneumoniae from the United Kingdom: analysis of multilocus enzyme electrophoresis, pulsed-field gel electrophoresis, and antimicrobial resistance patterns. J Clin Microbiol 1996, 34:853-859.
5. Enright MC, Spratt BG: A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 1998, 144(Pt 11):3049-3060.
6. van Belkum A, Sluijuter M, de Groot R, Verbrugh H, Hermans PW: Novel BOX repeat PCR assay for high-resolution typing of Streptococcus pneumoniae strains. J Clin Microbiol 1996, 34:1176-1179.
7. Hermans PW, Sluijter M, Hoogenboezem T, Heersma H, van Belkum A, de Groot R: Comparative study of five different DNA fingerprint techniques for molecular typing of Streptococcus pneumoniae strains. J Clin Microbiol 1995, 33:1606-1612.
8. Dunne WMJ, Kehl KS, Holland-Staley CA, Brueggeman AB, Pfaller MA, Doern GV: Comparison of results generated by serotyping, pulse-field restriction analysis, ribotyping, and repetitive-sequence PCR used to characterize penicillin-resistant pneumococci from the United States. J Clin Microbiol 2001, 39:1791-1795.
9. Mollerach M, Garcia E: The galU gene of Streptococcus pneumoniae that codes for a UDP-glucose pyrophosphorylase is highly polymorphic and suitable for molecular typing and phylogenetic studies. Gene 2000, 260:77-86.
10. Lawrence ER, Arias CA, Duke B, Beste D, Broughton K, Efstratiou A, George RC, Hall LMC: Evaluation of serotype prediction by cpsA-cpsB gene polymorphism in Streptococcus pneumoniae. J Clin Microbiol 2000, 38:1319-1323.
11. Lindstedt BA: Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005, 26:2567-2582.
12. Vergnaud G, Pourcel C: Multiple Locus VNTR (Variable Number of Tandem Repeat) Analysis. In Molecular Identification, Systematics, and Population Structure of Prokaryotes Edited by: Stackebrandt E. Berlin Heidelberg: Springer-Verlag; 2006:83-104.
13. Le Flèche P, Hauck Y, Onteniente L, Prieur A, Denoeud F, Ramisse V, Sylvestre P, Benson G, Ramisse F, Vergnaud G: A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis. BMC Microbiol 2001, 1:2.
14. Le Flèche P, Fabre M, Denoeud F, Koeck JL, Vergnaud G: High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing. BMC Microbiol 2002, 2:37.
15. Pourcel C, Andre-Mazeaud F, Neubauer H, Ramisse F, Vergnaud G: Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol 2004, 4:22.
16. Denoeud F, Vergnaud G: Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains: a Web-based resource. BMC Bioinformatics 2004, 5:4.
17. The Microorganisms Tandem Repeats Database [http://minisatellites.u-psud. fr]
18. Martin B, Humbert O, Camara M, Guenzi E, Walker J, Mitchell T, Andrew P, Prudhomme M, Alloing G, Hakenbeck R, et al.: A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res 1992, 20:3479-3483.
19. Sanchez-Beato AR, Lopez R, Garcia JL: Molecular characterization of PcpA: a novel choline-binding protein of Streptococcus pneumoniae. FEMS Microbiol Lett 1998, 164:207-214.
20. Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580.
21. The MLVA web service [http://bacterial-genotyping.igmors.upsud.fr]
22. Coffey TJ, Enright MC, Daniels M, Morona JK, Morona R, Hryniewicz W, Paton JC, Spratt BG: Recombinational exchanges at the capsular polysaccharide biosynthetic locus lead to frequent serotype changes among natural isolates of Streptococcus pneumoniae. Mol Microbiol 1998, 27:73-83.
23. McEllistrem MC, Noller AC, Visweswaran S, Adams JM, Harrison LH: Serotype 14 variants of the France 9V(-3) clone from Baltimore, Maryland, can be differentiated by the cpsB gene. J Clin Microbiol 2004, 42:250-256.
24. Leimkugel J, Adams Forgor A, Gagneux S, Pfluger V, Flierl C, Awine E, Naegeli M, Dangy JP, Smith T, Hodgson A, Pluschke G: An Outbreak of Serotype 1 Streptococcus pneumoniae Meningitis in Northern Ghana with Features That Are Characteristic of Neisseria meningitidis Meningitis Epidemics. J Infect Dis 2005, 192:192-199.
25. PubMLST - Multilocus sequence typing (MLST) databases and software [http://pubmlst.org]
26. Société Française de Microbiologie [http://www.sfm.asso.fr]
27. Vergnaud G, Denoeud F: Minisatellites: mutability and genome architecture. Genome Res 2000, 10:899-907.
28. Hoskins J, Alborn WE Jr, Arnold J, Blaszczak LC, Burgett S, DeHoff BS, Estrem ST, Fritz L, Fu DJ, Fuller W, et al.: Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 2001, 183:5709-5717.
29. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, et al.: Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 2001, 293:498-506.
30. The Sanger Institute [http://www.sanger.ac.uk/Projects/S_pneumoniae/]
31. The Institute for Genomic Research [http://www.tigr.org/]
32. Hunter PR, Gaston MA: Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 1988, 26:2465-2466.