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Microbial Characteristics of Chronic Respiratory Disease

Monday, December 17, 2018

1:00 PM-3:00 PM

BIOMED PhD Thesis Defense

Microbial Characteristics of Chronic Respiratory Disease 

Joshua Earl, PhD Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University

Garth Ehrlich, PhD
Department of Microbiology and Immunology, Otolaryngology
Drexel University College of Medicine

Andres Kriete, PhD
Associate Dean for Academic Affairs
Teaching Professor
School of Biomedical Engineering, Science and Health Systems
Drexel University

Respiratory illness is the third leading medical expense category in the United States. Chronic respiratory conditions were the third leading cause of death in the United States in 2011; there is therefore an urgent need for accurate clinical diagnostics, and deeper understanding of organisms associated with these diseases.

This study examines in detail new DNA sequence technology that can be used to identify to the species level essentially all bacterial organisms present in clinical samples. A new bioinformatic pipeline designed specifically to leverage this new long read DNA sequence is introduced: MCSMRT. This new analytical method is validated with both simple, and complex mock communities illustrating this pipeline’s sensitivity and specificity capabilities compared to previous efforts using short read technology.

The methods are applied to 12 patient’s sino-nasal surgery samples, showing the clinical relevance of this diagnostic. In addition, to further illustrate the power of genomic DNA sequence methods, Moraxella catarrhalis, the third leading cause of the chronic respiratory illness otitis media (OM) is characterized at a detailed genomic level. This new analysis examines the supragenome in unprecedented detail, including analysis of community composition, phylogenetic relatedness, virulence factor distribution, horizontal gene transfer, and antibiotic capabilities of 31 clinical isolates. 

Contact Information

Ken Barbee

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Drexel University College of Medicine, New College Building (NCB), Room 3219


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