Insights from Comparative Genomics for the Treatment of Pneumococcal Infections

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7. Project Summary This proposal consists of 1 year of mentored research for the development of a career in microbial pathogenesis as it relates to otitis media (OM), followed by 3 years of independent research in the same discipline. The principal investigator completed a doctorate in Immunology and Microbial Pathogenesis at Northwestern University under the mentorship of Dr. Kasturi Haldar. As part of her dissertation work she identified bioinformatically a novel eukaryotic secretome associated with malarial infection that has vastly expanded the pool of potential anti-malarial drug targets. She continued her training as a post-doctoral fellow with Dr. Garth Ehrlich, where she switched her emphasis to prokaryotic pathogens focusing on bacterially- induced otitis media and the development of a suite of bioinformatic tools for comparative genomics to identify genotype-phenotype correlations. Her work has exposed the very extensive genomic diversity among clinical S. pneumoniae strains, and has shown that horizontal gene transfer (HGT) is the major mechanism of diversity generation during chronic polyclonal S. pneumoniae infections. The plan of action outlined in the incumbent proposal will continue to expand her scientific skills through a unique integration of educational opportunities; cutting-edge facilities and resources; and scientific and mentoring expertise available at the Center for Genomic Sciences (CGS). The mentored section will be carried out under the guidance of Dr. Garth Ehrlich. Dr. Ehrlich is the Executive Director of the CGS, and is responsible for the major paradigm shift that states that culture-negative, antibiotic-resistant chronic bacterial infections result from a metabolic change from a planktonic to a biofilm form. He is also the author of the Distributed Genome Hypothesis, a genetic parallel to the biofilm concept and is the pioneer of many of the tools of comparative bacterial genomics. He has trained numerous graduate students, postdoctoral fellows, and junior faculty. Scientific and career advice will also be provided by the CGS Biofilm Director, Dr. J. William Costerton who is a fellow of the Royal Society and of the American Society for Microbiology. Moreover, Dr. Costerton is the originator of the modern biofilm paradigm (1978), and a pioneer researcher in many aspects of microbial biofilms, ecology, and polymicrobial communities. Dr. Costerton has received numerous master teacher awards from student groups around the world and is recognized as an expert in developing and advancing the careers of junior scientists with whom he works. Computational coursework, a bioinformatic workshop, and scientific meetings, as well as the development of multiple recent collaborations, some of which have been incorporated into this project's design, will further enhance the PI's training experience. Collaborations with outside scientists include: 1) Dr. Darren Martin at Cape Town University, an expert in the detection of recombination and it's role in evolution; 2) Dr. David Sherman at the University of Michigan, a specialist in biochemical synthesis; 3) Drs. Herve Tettelin at the University of Maryland and Claudio Donati at Novartis who have developed many mathematical tools for comparative genomics and led the effort to create a universal pneumococcal annotation system; 4) Drs. Alexander Tomasz at the Rockefeller and Dr. Herminia de Lencastre at the Universidade Nova de Lisboa who are authorities on the pathogenesis and epidemiology of pneumococcus and who have collected an outstanding library of strains; and 5) Dr. Wenyuan Shi at University of California in Los Angeles who has developed specifically targeted anti-microbial peptides (STAMPs). The candidate is devoted to a career in bacterial pathogenesis designed to improve the diagnosis and treatment of bacterially-induced OM. The focus of this proposal is on a clinically important subset of Streptococcus pneumoniae strains (the SP-1) that are pandemic and drug resistant. The aims are to: 1) develop an S. pneumoniae supragenome gene chip to provide a high-throughput and cost-effective means to perform comparative genomic hybridizations (CGH) on large numbers of clinical isolates, and ultimately to function as a molecular diagnostic to guide treatment of OM; 2) investigate the molecular mechanism of a novel SP-1-specific restriction-modification system, and determine the treatment potential of using inhibitors to block the methyltransferase; and 3) investigate the mechanism of action of an novel SP-1 lantibiotic-quorum sensing locus, and the potential to use a peptide encoded within this locus to target anti-microbials to S. pneumoniae and treat infections. The CGS provides an ideal setting for this work by combining expertise in bacterial biofilms, comparative genomics, and otitis media animal models, with a state-of-the-art facilities for DNA sequencing, comparative genomic hybridization, computational biology, and confocal laser scanning microscopy. In summary, this project, combined with the outstanding personnel and facilities resources available at the CGS, will maximize the potential for the principal investigator to establish a scientific niche, initiate multiple collaborations, apply for NIH R01 funding within the next three years, and commence an independent career in the microbiology of OM and related chronic bacterial infections.