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Diagnostic Testing Platform to Assess Antibiotic Activity on Microbial Communities of Cystic Fibrosis Patients


Phase I SBIR proposals will be accepted. Fast-Track proposals will not be accepted. Phase I clinical trials will be accepted. Number of anticipated awards: 1-2 Budget (total costs): Phase I: up to $150,000 for up to 6 months PROPOSALS THAT EXCEED THE BUDGET OR PROJECT DURATION LISTED ABOVE MAY NOT BE FUNDED. Background Each year approximately 1,000 new cases of cystic fibrosis (CF) are diagnosed, with over 30,000 living with CF in the United States. Over half of the CF patient population is now over the age of 18; these patients are living longer and, consequently, are exposed to more and more antibiotics over time, often as part of the daily care regimen. Critically important for their care, these chronic and repeated antibiotic treatments can have unintended consequences, such as the development and spread of antibiotic resistance and multidrug-resistant organisms, including Pseudomonas aeruginosa. More than other patients, those with CF have suffered longest under the threat of untreatable pan-resistant infections Antimicrobial susceptibility testing (AST) relies on standardized microbiological techniques assessing growth of pure cultures using either solid or liquid media and various concentrations of antibiotics. The inhibition of growth is predictive of treatment success and is reported by the clinical laboratory to guide therapy. Although this has been the standard for decades, such testing often fails to estimate treatment outcome when an infection is caused by multiple strains or species of bacteria or yeast (i.e., mixed infection), especially if the infection involves a community of microorganisms growing on a surface (i.e., biofilm). Lung infections in cystic fibrosis patients is one example of such infections; traditional antibiotic susceptibility testing fails to account for the impact of an antibiotic on the overall microbial community. Microbial communities can involve cooperative (or antagonistic) communication between members, recruitment of secondary pathogens, and biofilm matrix effects – all of which can impact inherent drug resistance that is not reflected in traditional susceptibility testing methods and results. Project Goals The goal of this project is to support the development of a standardized diagnostic platform for use in a clinical laboratory to determine the microbial community susceptibility/antibiogram of an infection using primary cystic fibrosis (CF) clinical specimens (i.e., sputum). This test should produce data useful for informing clinical treatment decisions. The proposal should incorporate appropriate methods for specimen management and processing, medium composition, including potential host factors that affect microbial growth or antibiotic activity in vivo, standard methodologies to arrive at a quantitative measurement of minimum inhibitory concentration, and back end detection/verification of target pathogen activity. Such work may involve laboratory-developed test methodologies/models or significantly adapted commercial platforms for use in parallel and in comparative assessments with standard clinical isolate-level AST analysis. All should have the potential to be validated for use in the clinical setting for treatment decisions. Phase I Activities and Expected Deliverables It is anticipated that such diagnostic test development will require dedicated and highly refined approaches specific to primary specimen and pathogen combination. The technical merit or feasibility of the proposed methodology should be assessed through initial bench-top (in vitro) studies of sputum, with the focus on a single pathogen and associated/community and matrix attributes. For these efforts, an existing set or bank of clinical sputum specimens from CF patients, collected longitudinally before, during, and after antibiotic treatment, and with complete data available (antibiotic treatment, single pathogen antimicrobial susceptibility testing results, clinical indicators and outcomes) is needed. These studies should be designed to provide a proof-of-concept. Expected deliverables would include: 1. Establish a laboratory-developed in vitro test methodology/model, or significantly adapt an existing commercial platform, that can test clinical sputum specimens for microbial community-susceptibilities or yield a microbial community-antibiogram. 2. Apply the method/model from deliverable #1 to sputum from an existing set or bank of clinical specimens (described above), to track sequential sputum community composition (or changes in sputum community) following treatment with one or more antibiotics (same antibiotics as the patient received). Microbial community composition would be defined using next generation sequencing. 3. Proof of concept: Compare these in vitro community changes to microbial community changes observed in clinical sputum specimens from the same patient during/following antibiotic treatment. Demonstrate whether the in vitro microbial communities are or are not significantly different from the sequential clinical sputum specimens from the same patient. Microbial community composition would be defined using next generation sequencing. Impact This project has the potential to impact antibiotic stewardship and therapeutic practice using available primary sputum specimens to produce a rapid, more clinically relevant estimation of potential drug efficacy, including reduction in potential resistance development. Generation of such a system or model may also identify and highlight the relative disparities that exist with reference-based testing and help redefine clinical practice. The broad use of such a system also may have profound impact on directing future drug-specific design by incorporating such considerations (and associated underlying mechanisms thereof) during the drug development phase. Commercialization Potential The commercialization potential of such technology is high, with a potential for wide-scale use, including patenting of processes, universal enrichment/growth media, matrix inhibitors and/or community parameterization. If the design involves laboratory-developed test protocols, kitting of reagents, developed controls, and/or mock communities, these may also provide additional avenues for commercialization. Development of such tools may be employed as front-end, value-added adaptation for commercial platforms. The results of this project have the potential to impact other settings involving intellectual property rights extended to preserving microbial community strata formulations for modeling biological interactions.
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