title: Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification.
abstract: Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription.
authors.affiliation: University Hospitals of Geneva, Genomic Research Laboratory, Service of Infectious Diseases, Switzerland. patrice.francois@genomic.ch
authors.forename: Patrice
authors.initials: P
authors.lastname: Francois
authors.forename: Yvan
authors.initials: Y
authors.lastname: Charbonnier
authors.forename: Jean
authors.initials: J
authors.lastname: Jacquet
authors.forename: Dominic
authors.initials: D
authors.lastname: Utinger
authors.forename: Manuela
authors.initials: M
authors.lastname: Bento
authors.forename: Daniel
authors.initials: D
authors.lastname: Lew
authors.forename: Gerhard M
authors.initials: GM
authors.lastname: Kresbach
authors.forename: Markus
authors.initials: M
authors.lastname: Ehrat
authors.forename: Werner
authors.initials: W
authors.lastname: Schlegel
authors.forename: Jacques
authors.initials: J
authors.lastname: Schrenzel
mesh_terms: D016470:Bacteremia / Q000382:microbiology*; D015373:Bacterial Typing Techniques; D006090:Gram-Negative Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006094:Gram-Positive Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D016571:Neural Networks, Computer; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D015345:Oligonucleotide Probes; D012329:RNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D013997:Time Factors
chemical_list: D015345:Oligonucleotide Probes; D012329:RNA, Bacterial