title: A functional gene array for detection of bacterial virulence elements.
abstract: Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known or novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples.
authors.affiliation: Chemistry, Materials, Earth and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America. jaing2/at/llnl.gov
authors.forename: Crystal
authors.initials: C
authors.lastname: Jaing
authors.forename: Shea
authors.initials: S
authors.lastname: Gardner
authors.forename: Kevin
authors.initials: K
authors.lastname: McLoughlin
authors.forename: Nisha
authors.initials: N
authors.lastname: Mulakken
authors.forename: Michelle
authors.initials: M
authors.lastname: Alegria-Hartman
authors.forename: Phillip
authors.initials: P
authors.lastname: Banda
authors.forename: Peter
authors.initials: P
authors.lastname: Williams
authors.forename: Pauline
authors.initials: P
authors.lastname: Gu
authors.forename: Mark
authors.initials: M
authors.lastname: Wagner
authors.forename: Chitra
authors.initials: C
authors.lastname: Manohar
authors.forename: Tom
authors.initials: T
authors.lastname: Slezak
mesh_terms: D001419:Bacteria / Q000472:pathogenicity*; D020137:Base Pair Mismatch; D001483:Base Sequence; D017931:DNA Primers; D015342:DNA Probes; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012680:Sensitivity and Specificity; D013816:Thermodynamics; D014774:Virulence / Q000235:genetics*
chemical_list: D017931:DNA Primers; D015342:DNA Probes; D004269:DNA, Bacterial