Development of Biomarkers for Clinical Assessment of Occult Infection and Forecasting Emerging Disease Outbreaks

Members of the United States Armed Forces are faced with a wide variety of existing, genetically engineered and emerging biological threats. There is a critical need for a fieldable system for rapid microbial assessment of environmental and clinical samples. A system is needed to identify signatures in a complex background with extremely low false positives. Genetic biomarkers target molecular elements that are key to determining course of action, such as virulence mechanisms and antibiotic resistance. GenArraytion proposes to develop a signature sequence microarray for various Staphylococcus aureus strains, including those that are antibiotic resistant. Our hybridization based microsequencing approach provides rapid, accurate and sensitive identification and characterization for early detection of outbreaks. The massively parallel genetic analysis can identify novel, previously uncharacterized organisms and can be automated for field and hospital use. GenArraytion’s Sniper Sequencing identifies hundreds to thousands of unique and functional biomarkers per genome, including markers that are specific at the genus, species and strain levels. Functional elements of pathogens, such as virulence factors, infectious pathway elements and antibiotic resistance, are combined with organism-specific signatures to provide a detailed fingerprint that can discriminate between closely related microbial strains, characterize previously unknown strains, and provide indications of genetic manipulation.