Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2012 Feb 25;39(1):4–13. [Article in French] doi: 10.1007/s11834-011-0051-y

Diagnostic des infections bactériennes par les puces à ADN

Diagnosis of bacterial infections by DNA microarray

E Donatin 1,✉, M Drancourt 1,2
PMCID: PMC7149027

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.

Keywords: Bacterial infections, diagnosis, DNA microarray

Contributor Information

E. Donatin, Email: emilie.donatin@gmail.com

M. Drancourt, Email: Michel.Drancourt@univmed.fr

Références

  • 1.Candela M., Consolandi C., Severgnini M., et al. High taxonomic level fingerprint of the human intestinal microbiota by Ligase Detection Reaction — Universal Array approach. BMC Microbiology. 2010;10:116. doi: 10.1186/1471-2180-10-116. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Zoetendal E.G., Akkermans A.D., de Vos W.M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol. 1998;64:3854–3859. doi: 10.1128/aem.64.10.3854-3859.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Suau A., Bonnet R., Sutren M., et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol. 1999;65:4799–4807. doi: 10.1128/aem.65.11.4799-4807.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Heid C.A., Stevens J., Livak K., et al. Real time quantitative PCR. Genome Res. 1996;6:986–994. doi: 10.1101/gr.6.10.986. [DOI] [PubMed] [Google Scholar]
  • 5.Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  • 6.Wilson K.H., Blitchington R.B., Greene R.C. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol. 1990;28:1942–1946. doi: 10.1128/jcm.28.9.1942-1946.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Adékambi T., Drancourt M., Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol. 2009;17:37–45. doi: 10.1016/j.tim.2008.09.008. [DOI] [PubMed] [Google Scholar]
  • 8.Chomezynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanante-phenol-chloroform extraction. Anal Biochem. 1987;162:156–159. doi: 10.1006/abio.1987.9999. [DOI] [PubMed] [Google Scholar]
  • 9.Zoetendal E.G., Heilig H.G.H.J., Klaassens E.S., et al. Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nature Protocols. 2006;1:870–873. doi: 10.1038/nprot.2006.142. [DOI] [PubMed] [Google Scholar]
  • 10.Zoetendal E.G., Booijink C.C.G.M., Klaassens E.S., et al. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nature Protocols. 2006;1:954–959. doi: 10.1038/nprot.2006.143. [DOI] [PubMed] [Google Scholar]
  • 11.Stabler R.A., Marsden G.L., Witney A.A., et al. Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Nesseiria species. Microbiology. 2005;151:2907–2922. doi: 10.1099/mic.0.28099-0. [DOI] [PubMed] [Google Scholar]
  • 12.You Y., Fu C., Zeng X., et al. A novel DNA microarray for rapid diagnosis of enteropathogenic bacteria in stool specimens of patients with diarrhea. J Microbiol Methods. 2008;75:566–571. doi: 10.1016/j.mimet.2008.09.007. [DOI] [PubMed] [Google Scholar]
  • 13.Suo B., He Y., Paoli G., et al. Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Mol Cell Probes. 2010;24:77–86. doi: 10.1016/j.mcp.2009.10.005. [DOI] [PubMed] [Google Scholar]
  • 14.Jaluria P., Konstantopoulos K., Betenbaugh M., Shiloach J. A perspective on microarrays: current applications, pitfalls, and potential uses. Microb Cell Fact. 2007;6:4. doi: 10.1186/1475-2859-6-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Leroy Q., Raoult D. Review of microarray studies for host-intracellular pathogen interactions. J Microbiol Methods. 2010;81:81–95. doi: 10.1016/j.mimet.2010.02.008. [DOI] [PubMed] [Google Scholar]
  • 16.Huyghe A., Francois P., Schrenzel J. Characterization of microbial pathogens by DNA microarray. Infection, Genetics and Evolution. 2009;9:987–995. doi: 10.1016/j.meegid.2008.10.016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Min Y.S., Choi J.H., Lee S.Y., Yoo N.C. Applications of DNA microarray in disease diagnostics. J Microbiol Biotechnol. 2009;19:635–646. [PubMed] [Google Scholar]
  • 18.Elliot A.J., Cross K.W., Fleming D.M. Acute respiratory infections and winter 390 pressures on hospital admissions in England and Wales 1990–2005. J. Public Health (Oxf) 2008;30:91–98. doi: 10.1093/pubmed/fdn003. [DOI] [PubMed] [Google Scholar]
  • 19.Roth S.B., Jalava J., Ruuskanen O., et al. Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections. J Clin Microbiol. 2004;42:4268–4274. doi: 10.1128/JCM.42.9.4268-4274.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Cannon G.A., Carr M.J., Yandle Z., et al. A low density oligonucleotide microarray for the detection of viral and atypical bacterial respiratory pathogens. J Virol Methods. 2010;163:17–24. doi: 10.1016/j.jviromet.2009.07.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Zhu L., Jiang G., Wang S., et al. Biochip system for rapid and accurate identification of Mycobacterial species from isolates and sputum. J Clin Microbiol. 2010;48:3654–3660. doi: 10.1128/JCM.00158-10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Jin D.Z., Wen S.Y., Chen S.H., et al. Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays. Mol Cell Probes. 2006;20:337–347. doi: 10.1016/j.mcp.2006.03.005. [DOI] [PubMed] [Google Scholar]
  • 23.Drancourt M (2011) Chapter 35: Acute Diarrhea In: Cohen J, Opal SM, Powderly WG, Infectious Diseases. Elsevier
  • 24.Dridi B., Henry M., El Khéchine A., Raoult D., Drancourt M. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One. 2009;4:e7063. doi: 10.1371/journal.pone.0007063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Mead P.S., Slutsker L., Dietz V., et al. Food-related illness and death in the United States. Emerg Infect Dis. 1999;5:607–625. doi: 10.3201/eid0505.990502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Hong B.X., Jiang L.F., Hu Y.S., et al. Application of oligonucleotide array technology for the rapid detection of pathogenic bacteria of foodborne infections. J Microbiol Methods. 2004;58:403–411. doi: 10.1016/j.mimet.2004.05.005. [DOI] [PubMed] [Google Scholar]
  • 27.Kim D.H., Lee B.K., Kim Y.D., et al. 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. 2010;48:682–688. doi: 10.1007/s12275-010-0119-5. [DOI] [PubMed] [Google Scholar]
  • 28.Wang Q., Wang S., Beutin L., et al. Development of a DNA microarray for detection and serotyping of Enterotoxigenic Escherichia coli. J Clin Microbiol. 2010;48:1066–2074. doi: 10.1128/JCM.02014-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Black R.E. Epidemiology of diarrhoeal disease: implications for control by vaccines. Vaccine. 1993;11:100–106. doi: 10.1016/0264-410X(93)90002-F. [DOI] [PubMed] [Google Scholar]
  • 30.Järvinen A.K., Laakso S., Piiparinen P., et al. Rapid identification of bacterial pathogens using a PCR- and microarray-based assay. BMC Microbiology. 2009;9:161. doi: 10.1186/1471-2180-9-161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Kim C.M., Song E.S., Jang H.J., et al. 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. 2010;48:1578–1583. doi: 10.1128/JCM.01130-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Musser J.M. Antimicrobial agent resistance in mycobacteria: molecular genetic insights. Clin Microbiol Rev. 1995;8:496–514. doi: 10.1128/cmr.8.4.496. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Ramaswamy S., Musser J.M. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis. Tuber Lung Dis. 1998;79:3–29. doi: 10.1054/tuld.1998.0002. [DOI] [PubMed] [Google Scholar]
  • 34.Rattan A., Kalia A., Ahmad N. Multidrug-resistant Mycobacterium tuberculosis: molecular perspectives. Emerg Infect Dis. 1998;4:195–209. doi: 10.3201/eid0402.980207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Mdluli K., Sherman D.R., Hickey M.J., et al. Biochemical and genetic data suggest that inhA is not the primary target for activated isoniazid in Mycobacterium tuberculosis. J Infect Dis. 1996;174:1085–1090. doi: 10.1093/infdis/174.5.1085. [DOI] [PubMed] [Google Scholar]
  • 36.Park H., Ju Song E., Sil Song E., et al. Comparison of a conventional antimicrobial susceptibility assay to an oligonucleotide chip system for detection of drug resistance in Mycobacterium tuberculosis isolates. J Clin Microbiol. 2006;44:1619–1624. doi: 10.1128/JCM.44.5.1619-1624.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Escalante P., Ramaswamy S., Sanabria H., et al. Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru. Tuber Lung Dis. 1998;79:111–118. doi: 10.1054/tuld.1998.0013. [DOI] [PubMed] [Google Scholar]
  • 38.Monecke S., Ehricht R. Rapid genotyping of méthicilline-resistant Staphylococcus aureus (MRSA) isolates using miniaturized oligonucleotide arrays. Clin Microbiol Infect. 2005;11:825–833. doi: 10.1111/j.1469-0691.2005.01243.x. [DOI] [PubMed] [Google Scholar]
  • 39.Zhu L.X., Zhang Z.W., Wang C., et al. Use of a DNA microarray for simultaneous detection of antibiotic resistance genes among Staphylococcal clinical isolates. J Clin Microbiol. 2007;45:3514–3521. doi: 10.1128/JCM.02340-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Barken K.B., Haagensen J.A.J., Tolker-Nielsen T. Advances in nucleic acid-based diagnostics of bacterial infections. Clinica Chimica Acta. 2007;384:1–11. doi: 10.1016/j.cca.2007.07.004. [DOI] [PubMed] [Google Scholar]
  • 41.Chambers H.F. Methicillin resistance in staphylococci: molecular and biochemical basis and clinical implications. Clin Microbiol Rev. 1997;10:781–791. doi: 10.1128/cmr.10.4.781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 42.Ninove L., Nougairede A., Gazin C., et al. POC tests: from antigen detection to molecular methods. Future trends. J Clin Virol. 2010;4:304–305. doi: 10.1016/j.jcv.2010.08.012. [DOI] [PubMed] [Google Scholar]

Articles from Bio tribune magazine are provided here courtesy of Nature Publishing Group

RESOURCES