Résumé
Le diagnostic des infections bactériennes repose sur l’isolement du pathogène, qui ne peut pas être réalisé dans le temps du soin. Egalement, la culture est mal adaptée au diagnostic des infections polymicrobiennes. Une alternative est la détection de séquences ADN spécifiques dans l’échantillon clinique par les puces à ADN. La première utilisation des puces à ADN en tant qu’outil diagnostic date de 1995. Cette revue porte sur la mise au point de différentes puces à ADN pour la détection des bactéries pathogènes au cours des infections respiratoires, digestives et systémiques. Ces études ont permis de montrer que les puces à ADN sont un outil fiable, rapide et reproductible pour le diagnostic des maladies infectieuses d’origine bactérienne. Le coût et la technicité demeurent deux freins au déploiement en routine de cette technologie pour le diagnostic des infections bactériennes.
Abstract
The diagnosis of bacterial infections relies on isolation of the pathogen, which cannot be achieved in the time of care. Also, culture is poorly suited to the diagnosis of polymicrobial infections. An alternative is the detection of specific DNA sequences in clinical specimen by DNA microarrays. The first use of microarrays as a diagnostic tool dates from 1995. This review focuses on the development of different DNA chips for diagnosing bacterial infections such as respiratory, digestive or systemic diseases. These studies demonstrated that DNA microarrays are a reliable, rapid and reproducible for the diagnosis of infectious diseases caused by bacteria. High cost and technicity are two limits for the actual use of DNA microarray for the routine diagnosis of bacterial infections.
Article PDF
Avoid common mistakes on your manuscript.
Références
Candela M, Consolandi C, Severgnini M et al. (2010) High taxonomic level fingerprint of the human intestinal microbiota by Ligase Detection Reaction — Universal Array approach. BMC Microbiology 10: 116
Zoetendal EG, Akkermans AD, de Vos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64: 3854–3859
Suau A, Bonnet R, Sutren M et al. (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65: 4799–4807
Heid CA, Stevens J, Livak K et al. (1996) Real time quantitative PCR. Genome Res 6: 986–994
Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470
Wilson KH, Blitchington RB, Greene RC (1990) Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 28: 1942–1946
Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17: 37–45
Chomezynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanante-phenol-chloroform extraction. Anal Biochem 162: 156–159
Zoetendal EG, Heilig HGHJ, Klaassens ES et al. (2006) Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nature Protocols 1: 870–873
Zoetendal EG, Booijink CCGM, Klaassens ES et al. (2006) Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nature Protocols 1: 954–959
Stabler RA, Marsden GL, Witney AA et al. (2005) Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Nesseiria species. Microbiology 151: 2907–2922
You Y, Fu C, Zeng X et al. (2008) A novel DNA microarray for rapid diagnosis of enteropathogenic bacteria in stool specimens of patients with diarrhea. J Microbiol Methods 75: 566–571
Suo B, He Y, Paoli G et al. (2010) Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Mol Cell Probes 24: 77–86
Jaluria P, Konstantopoulos K, Betenbaugh M, Shiloach J (2007) A perspective on microarrays: current applications, pitfalls, and potential uses. Microb Cell Fact 6: 4
Leroy Q, Raoult D (2010) Review of microarray studies for host-intracellular pathogen interactions. J Microbiol Methods 81: 81–95
Huyghe A, Francois P, Schrenzel J (2009) Characterization of microbial pathogens by DNA microarray. Infection, Genetics and Evolution 9: 987–995
Min YS, Choi JH, Lee SY, Yoo NC (2009) Applications of DNA microarray in disease diagnostics. J Microbiol Biotechnol 19: 635–646
Elliot AJ, Cross KW, Fleming DM (2008) Acute respiratory infections and winter 390 pressures on hospital admissions in England and Wales 1990–2005. J. Public Health (Oxf) 30: 91–98
Roth SB, Jalava J, Ruuskanen O et al. (2004) Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections. J Clin Microbiol 42: 4268–4274
Cannon GA, Carr MJ, Yandle Z et al. (2010) A low density oligonucleotide microarray for the detection of viral and atypical bacterial respiratory pathogens. J Virol Methods 163: 17–24
Zhu L, Jiang G, Wang S et al. (2010) Biochip system for rapid and accurate identification of Mycobacterial species from isolates and sputum. J Clin Microbiol 48: 3654–3660
Jin DZ, Wen SY, Chen SH et al. (2006) Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays. Mol Cell Probes 20: 337–347
Drancourt M (2011) Chapter 35: Acute Diarrhea In: Cohen J, Opal SM, Powderly WG, Infectious Diseases. Elsevier
Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M (2009) High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One 4: e7063
Mead PS, Slutsker L, Dietz V et al. (1999) Food-related illness and death in the United States. Emerg Infect Dis 5: 607–625
Hong BX, Jiang LF, Hu YS et al. (2004) Application of oligonucleotide array technology for the rapid detection of pathogenic bacteria of foodborne infections. J Microbiol Methods 58: 403–411
Kim DH, Lee BK, Kim YD et al. (2010) Detection of representative enteropathogenic bacteria, Vibrio spp., pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, using a virulence factor gene-based oligonucleotide microarray. J Microbiol 48: 682–688
Wang Q, Wang S, Beutin L et al. (2010) Development of a DNA microarray for detection and serotyping of Enterotoxigenic Escherichia coli. J Clin Microbiol 48: 1066–2074
Black RE (1993) Epidemiology of diarrhoeal disease: implications for control by vaccines. Vaccine 11: 100–106
Järvinen AK, Laakso S, Piiparinen P et al. (2009) Rapid identification of bacterial pathogens using a PCR- and microarray-based assay. BMC Microbiology 9: 161
Kim CM, Song ES, Jang HJ et al. (2010) Development and evaluation of oligonucleotide chip based on the 16S–23S rRNA gene spacer region for detection of pathogenic microorganisms associated with sepsis. J Clin Microbiol 48: 1578–1583
Musser JM (1995) Antimicrobial agent resistance in mycobacteria: molecular genetic insights. Clin Microbiol Rev 8: 496–514
E Ramaswamy S, Musser JM (1998) Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis. Tuber Lung Dis 79: 3–29
Rattan A, Kalia A, Ahmad N (1998) Multidrug-resistant Mycobacterium tuberculosis: molecular perspectives. Emerg Infect Dis 4: 195–209
Mdluli K, Sherman DR, Hickey MJ et al. (1996) Biochemical and genetic data suggest that inhA is not the primary target for activated isoniazid in Mycobacterium tuberculosis. J Infect Dis 174: 1085–1090
Park H, Ju Song E, Sil Song E et al. (2006) Comparison of a conventional antimicrobial susceptibility assay to an oligonucleotide chip system for detection of drug resistance in Mycobacterium tuberculosis isolates. J Clin Microbiol 44: 1619–1624
Escalante P, Ramaswamy S, Sanabria H et al. (1998) Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru. Tuber Lung Dis. 79: 111–118
Monecke S, Ehricht R (2005) Rapid genotyping of méthicilline-resistant Staphylococcus aureus (MRSA) isolates using miniaturized oligonucleotide arrays. Clin Microbiol Infect 11: 825–833
Zhu LX, Zhang ZW, Wang C et al. (2007) Use of a DNA microarray for simultaneous detection of antibiotic resistance genes among Staphylococcal clinical isolates. J Clin Microbiol 45: 3514–3521
Barken KB, Haagensen JAJ, Tolker-Nielsen T (2007) Advances in nucleic acid-based diagnostics of bacterial infections. Clinica Chimica Acta 384: 1–11
Chambers HF (1997) Methicillin resistance in staphylococci: molecular and biochemical basis and clinical implications. Clin Microbiol Rev 10: 781–791
Ninove L, Nougairede A, Gazin C et al. (2010) POC tests: from antigen detection to molecular methods. Future trends. J Clin Virol 4: 304–305
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Donatin, E., Drancourt, M. Diagnostic des infections bactériennes par les puces à ADN. Bio trib. mag. 39, 4–13 (2011). https://doi.org/10.1007/s11834-011-0051-y
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11834-011-0051-y