Universal Nucleic Acid Amplification Test (NAAT) platforms rely on the discovery that conserved and variable sequences contained in all human pathogens can be exploited for development of robust rapid diagnostic methods. We will grow two already advanced broad based diagnostic platforms which will both support Program Projects in the Center, and establish utility for dual use, i.e. biodefense/emerging infections and commonly encountered clinical infections, increasing likelihood of commercialization. Complementary but distinct strengths of each platform will be harnessed - speed for the 16S rRNA PCR (16S), and ability to genotype and identify a wide range of pathogens for IBIS T-5000 (T-5000). The program will have 6 specific aims:
Specific Aim 1 : Optimizing sample preparation methods (whole blood and peritoneal fluid) for extraction of nucleic acids and determine analytic and clinical accuracy of 16S and T-5000 in mock-ups, animal samples and banked human samples.
Specific Aim 2 : Evaluating diagnostic accuracy of 16S and T- 5000 methods for organisms of interest to MARCE-2 collaborators, including those which invade the Gl mucosa (Program II) or respiratory tract (Program III) and cause sepsis or peritonitis;and demonstrating capacity to differentiate strains and serovars, using both established and novel post-amplification methods.
Specific Aim 3 : Developing customized panels of bioinformatic software for, and determine clinical utility of, T-5000 for rapid detection, identification, and genotyping of pathogens (common, biothreat [BT] and emerging) which invade and cause disease of the respiratory tract. The capacity of the T-5000 will be determined to identify mixed cultures and the ability to provide genotying at a basic level.
Specific Aim 4 : Applying the 16S and/or T-5000 to MARCE Programs project for which vaccines are being developed and tested in animal models. Since several projects in MARCE-2 will include discovery, development and testing of broad-spectrum enteric vaccines, determination of the presence of pathogen (especially those at low levels) in animal challenged following vaccine delivery may be necessary. For later years, screening vaccines that are grown in tissue culture for adventitious agents will be done by T-5000.
Specific Aim 5 : Developing Good Manufacturing Practice (GMP) validated protocols to produce a T-5000 diagnostic kit for commercialization that could be used in hospitals, State laboratories, Centers for Disease Control and Prevention (CDC) and World Health Organization (WHO) reference laboratories, and;to work towards filing new patents and pursuing license commercial opportunities for 16S related assays. Manufacturing and Quality personnel will prepare development of kit testing reagents which will include participation in building and testing prototype runs of reagents.

Public Health Relevance

The objective of this program is to accelerate development, clinical evaluation and deployment of genomic and proteomic based diagnostics for effective public health response to a bioterrorist or emerging infectious disease even

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZAI1-DDS-M)
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University of Maryland Baltimore
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