Short description
(English)
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Bioterrorism and biocrimes are among the major threats in today's world security. Appropriate decisions should be taken rapidly, and major concerns lie in the rapid detection of these bioagents. We propose here the development of efficient and rapid microarray-based detection methods for assessing the presence of known pathogens, but also for identifying and characterizing new/unexpected ones. Our contribution will consist in the separate but self-complementary projects benefiting from the combined knowledge and expertise of the Geneva and Bern research groups. We will develop an affordable micro-array for the rapid identification of known BSL3 bacterial pathogens together with the detection of a panel of virulence genes found in Gram-positive pathogens. In parallel, we will implement a 'non-cognate hybridization system' (NCHS), i.e. arrays designed to provide enough discrimination for bacterial identification, even for organisms that are not even considered at the time of array design. This open strategy will identify the genetic background of the analyzed sample and provide the possibility to compare its signature against a reference database. Such arrays will also offer generic genotyping capabilities, i.e. without a priori knowledge of the analyzed genome contents. The Swiss participation to this Action will play a key role by contributing to the development of i) a rapid and disposable diagnostic micro-array, and ii) a more elaborated open-design NCHS array.
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Partners and International Organizations
(English)
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AT, BE, BG, CH, CZ, DE, DK, ES, FR, GR, LU, NL, PT, RO, RS, SE, SK, TR, UK
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Abstract
(English)
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Assessing bacterial flora composition appears of increasing importance to fields as diverse as physiology, development, medicine, epidemiology, environment, and the food industry. We report here on the development and validation of an original microarray strategy that allows analysis of the phylogenic composition of complex bacterial mixtures. The microarray contains 9,500 feature elements targeting 16S rRNA gene-specific regions. Probe design was performed by selecting oligonucleotide sequences specific to each node of the seven levels of the bacterial phylogenetic tree (domain, phylum, class, order, family, genus, and species). This approach, based on sequence information, allows analysis of the bacterial contents of complex bacterial mixtures to detect both known and unknown microorganisms. The presence of unknown organisms can be suspected and mapped on the phylogenetic tree, indicating where to refine analysis. Initial proof-of-concept experiments were performed on oral bacterial communities. Our results show that this hierarchical approach can reveal minor changes (<1%) in gingival flora content when samples collected in individuals from similar geographical origins are compared [A. Huyghe, Appl. Environ. Microbiol, 2008, 74(6):1876-1885]. We are currently comparing this array-based metagenomics analysis with high-throughput sequencing approaches, which could reveal more flexible yet at the expense of more sophisticated data analysis [D. Hernandez Genome Research, 2008, 18:802-809]. Finally, we have recently published one book chapter on 'Non-Cognate Approaches for Pathogen Detection on Microarrays' as well as a review chapter entitled 'Introduction to Microarray-Based Detection Methods', both of which published in a COST-subsidized booklet that was contributed to by all participants of WP1 and that I had the priviledge to edit and coordinate. Two reviews describing some of the developped methods were published very recently [A. Huyghe, Infection, Genetics and Evolution, 2009. 9(5):987-995] and [M. Beaume, Intern. J. Med. Microbiol, 2010, 300:88-97].
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