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Title: A functional gene array for detection of bacterial virulence elements

We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. 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. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistancemore » gene families in a greatly expanded set of organisms.« less
Authors:
Publication Date:
OSTI Identifier:
1018837
Report Number(s):
UCRL-JRNL-236055
TRN: US201114%%366
DOE Contract Number:
W-7405-ENG-48
Resource Type:
Journal Article
Resource Relation:
Journal Name: PLoS ONE, vol. 3, no. 5, May 14, 2008, e2163; Journal Volume: 3; Journal Issue: 5
Research Org:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AEROSOLS; ANTIBIOTICS; DESIGN; DETECTION; DNA; ESCHERICHIA COLI; FUNCTIONALS; GENES; LAWRENCE LIVERMORE NATIONAL LABORATORY; MICROORGANISMS; PATHOGENS; PROBES; STAPHYLOCOCCUS; STRAINS; TARGETS; TOLERANCE; VIRULENCE