Abstracts
Résumé
Les puces à ADN sont des multicapteurs permettant de caractériser et quantifier un acide nucléique dans un échantillon. Elles apportent une solution innovante au problème ancien de la détection, de l’identification et du typage de bactéries dans un échantillon. Elles permettent la caractérisation génomique rapide de bactéries pathogènes et facilitent les études épidémiologiques, par exemple pour le contrôle des maladies nosocomiales ou la surveillance du bioterrorisme. Ces puces sont développées dans les laboratoires de recherche pour l’étude de la diversité et de l’évolution du monde bactérien, pour rechercher des gènes de résistance aux antibiotiques et pour la caractérisation de communautés bactériennes constituées de centaines d’espèces. L’industrialisation du processus de fabrication et d’utilisation, rendant la technologie robuste tout en en diminuant son coût, devrait permettre son utilisation dans les laboratoires hospitaliers et d’analyses spécialisées, puis sa généralisation aux laboratoires de ville.
Summary
DNA-arrays are mainly known for their application in transcriptome analysis leading for instance to the discovery of new marker genes for diagnostics and prognostics in oncology. However, DNA arrays are also used for massively parallel analysis of DNA molecules allowing their quantification, the detection of single nucleotide polymorphisms and re-sequencing. This multi detection system is now applied to the « old » problems of detecting and identifying bacteria in a biological sample and for the fine molecular characterization of a bacterial isolate. This new tool should serve for the diagnostic of an infection and for epidemiological studies such as those performed for the control of nosocomial infections or for the surveillance of bioterrorism attacks. DNA arrays carrying probes for 16S RNA specific of hundreds of bacterial species allow the identification of bacteria within a community by a single hybridization of amplified 16S rDNAs with universal primers and re-sequencing DNA arrays are used for multi locus sequence typing in a single step. Finally, the genome of an isolate could be characterized by DNA-arrays focused on a specific question like presence of toxin or antibiotic resistance genes. Up to now, DNA arrays are used in research laboratories for the rapid characterization at the genomic level of a strain collection, for evolutionary and population genetics studies and for the characterization of bacterial communities. Industrializing the process of DNA-array construction and hybridization is now needed in order to transfer this technology to hospitals and diagnostic laboratories.
Appendices
Références
- 1. Koch R. Die Aetiologie der Milzbrand-Krankheit, begründet auf die Entwicklungsgeschichte des Bacillus anthracis.Beiträge zur Biologie der Pflanzen 1876 ; 1 : 277-308.
- 2. Struelens M. Molecular typing : a key tool for the surveillance and control of nosocomial infection. Curr Opin Infect Dis 2002 ; 15 : 383-5.
- 3. Raoult D, Fournier PE, Drancourt M. What does the future hold for clinical microbiology ? Nat Rev Microbiol 2004 ; 2 : 151-9.
- 4. Fleischmann RD, Adams MD, White O, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995 ; 269 : 496-512.
- 5. Lan R, Reeves PR. Intraspecies variation in bacterial genomes : the need for a species genome concept. Trends Microbiol 2000 ; 8 : 396-401.
- 6. Stackebrandt E, Goebel BM. Taxonomic note : a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994 ; 44 : 846-9.
- 7. Van Belkum A. High-throughput epidemiologic typing in clinical microbiology. Clin Microbiol Infect 2003 ; 9 : 86-100.
- 8. Schena M, Shalon D, Heller R, et al. Parallel human genome analysis : microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 1996 ; 93 : 10614-9.
- 9. Southern EM. DNA chips : analysing sequence by hybridization to oligonucleotides on a large scale. Trends Genet 1996 ; 12 : 110-5.
- 10. Van Leeuwen WB, Jay C, Snijders S, et al. Multilocus sequence typing of Staphylococcus aureus with DNA array technology. J Clin Microbiol 2003 ; 41 : 3323-6.
- 11. Troesch A, Nguyen H, Miyada CG, et al.Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J Clin Microbiol 1999 ; 37 : 49-55.
- 12. Doumith M, Cazalet C, Simoes N, et al. New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics. Infect Immun 2004 ; 72 : 1072-83.
- 13. Trad S, Allignet J, Frangeul L, et al. DNA macroarray for identification and typing of Staphylococcus aureus isolates. J Clin Microbiol 2004 ; 42 : 2054-64.
- 14. Bryant PA, Venter D, Robins-Browne R, Curtis N. Chips with everything : DNA microarrays in infectious diseases. Lancet Infect Dis 2004 ; 4 : 100-11.