There is an urgent need to develop rapid sample-to-answer clinic and field deployable diagnostics for NIAID Category A, B and C biothreat pathogens to protect both military and civilian populations. The goal of this application is to advance and validate a lead candidate diagnostic - a novel microfluidics nucleic acid detection and sequencing diagnostic platform recently developed by NetBio-to identify Category B pathogen Chlamydia psittaci (Cps) that causes life-threatening respiratory diseases and has historically been a focus of bioweapons development as well as being a vastly understudied pathogen. We will also detect emerging Cps pathogens and non-biothreat pathogens that are the leading cause of atypical pneumonia and often confused with biothreat agents in clinical presentation: Chlamydia trachomatis (Ct), Chlamydia pneumoniae (Cpn), Mycoplasma pneumoniae (Mp) and Legionella pneumophila (Lp). Indeed, the Biodefense RFA-AI-11-014 we are responsive to states, "Medical diagnostics that use platforms to rapidly distinguish whether an individual is infected with a biological threat agent or a common infection with similar, generalized symptoms are of high priority." There are currently few or no commercial diagnostics for these pathogens in the US. The NetBio platform consists of a ruggedized, analytic instrument that accepts a biochipset (BCS)-shown in Preliminary Studies to purify genomic DNA from clinical samples, amplify, electrophoretically separate and laser detect and type Ct. The entire system from DNA purification to detection takes ~1 hour.
The Aims are to: 1) genome sequence representative Cps biothreat and non- biothreat atypical respiratory pathogens for robust primer selection;2) modify the BCS to purify genomic DNA from human clinical nasopharyngeal (NP) swab and sputum samples;3) employ the primer selection pipeline developed by Dr. Read to identify primers based on comparative genomics of available genomes and those sequenced in Aim 1 for differentiating biothreat and non-biothreat atypical respiratory pathogens, and develop a multiplexed assay for DNA amplification to distinguish each pathogen;and 4) evaluate the sensitivity, specificity and positive and negative predictive value of the NetBio assay using first spiked samples and then clinical NP swabs and sputum samples compared to the available commercial nucleic acid amplification tests for Ct, Cpn, Mp and Lp (none exist for Cps), and compared to highly sensitive in-house RT-PCR assays prior to clinical trials for FDA approval. A future goal will be to expand the assay to other biothreat respiratory pathogens. We envision that the NetBio sample-to-answer assay will be used in ERs, MD offices, clinics, military facilities, hospitals and the field to advance our understanding of the epidemiology of atypical respiratory diseases and best treatment strategies, which will inform biothreat preparedness. A broadly used diagnostic will detect patients with common but also biothreat infection, enabling early identification of an attack and rapid treatment of infecte military and civilian populations.

Public Health Relevance

Chlamydia psittaci is a Category B Biodefense agent that is difficult to distinguish from the clinical presentation of Chlamydia pneumoniae, Chlamydia trachomatis, Mycoplasma pneumoniae and Legionella pneumophila;all are respiratory pathogens and represent the major causes of atypical pneumonia in the world today. There are no reliable commercial diagnostics available for any of these human pathogens. We plan to develop an easy to use, cheap, one-hour diagnostic that will detect and differentiate each pathogen for use in ERs, clinics, hospitals, military facilities and the field to advance our understanding of the epidemiology of atypical respiratory diseases and the best therapeutic strategies, which will inform biothreat preparedness. A broadly-used diagnostic will identify patients with common but also with biothreat infections, enabling the identification of an attack i the early stages and assisting health care personnel in rapidly treating infected military and civilian populations to save lives.

National Institute of Health (NIH)
Research Project (R01)
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Special Emphasis Panel (ZAI1)
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Taylor, Christopher E,
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Children's Hospital & Res Ctr at Oakland
United States
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Joseph, Sandeep J; Li, Ben; Ghonasgi, Tanvi et al. (2014) Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples. PLoS One 9:e99290
Batteiger, Byron E; Wan, Raymond; Williams, James A et al. (2014) Novel Chlamydia trachomatis strains in heterosexual sex partners, Indianapolis, Indiana, USA. Emerg Infect Dis 20:1841-7
Wang, Anyou; Al-Kuhlani, Mufadhal; Johnston, S Claiborne et al. (2013) Transcription factor complex AP-1 mediates inflammation initiated by Chlamydia pneumoniae infection. Cell Microbiol 15:779-94
Read, Timothy D; Joseph, Sandeep J; Didelot, Xavier et al. (2013) Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range. MBio 4: