Culture-free identification of pathogens common in endocarditis directly from patient specimens

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PROJECT SUMMARY Infective Endocarditis (IE) is a life-threatening disease that affects roughly 45,000 Americans annually. IE is characterized by microbial vegetations on the endocardial surface which induce serious heart damage and persistent bloodstream infections (BSIs) leading to sepsis. Left untreated IE is fatal. Among the criteria to establish IE and treat patients most effectively, blood cultures are indispensable to identify the etiologic agent. Cultures, however, display two major weaknesses which delay the administration of the proper antimicrobials: (1) High turnaround time of days or even weeks and (2) high prevalence of false-negative results due to either pre-treatment with antibiotics or the presence of difficult to culture pathogens. As time is of essence for optimal outcomes with minimal complications, treatment is often initiated prior to diagnosis with a cocktail of broad spectrum (i.e. not targeted) antimicrobials, leaving the majority of patients treated inappropriately and those without the disease treated unnecessarily. It is therefore critical to advance innovative diagnostic approaches, which do not rely on culturing, in order to rapidly transition to personalized antimicrobial interventions. To address this unmet need, HelixBind will develop the first culture-free diagnostic assay capable of identifying pathogens which induce IE in under 2.5 hours. HelixBind’s approach leverages multiple novel innovations from sample-to-answer. Further, as detection does not require cultures, our approach is particularly suited to the detection of fastidious pathogens, which today’s diagnostic standard frequently fail to detect. Our proposed Infective Endocarditis Pathogen Identification assay, termed IE/PID, is expected to have a profound clinical impact by enabling the physician to apply a personalized and evidence-driven intervention within a few hours, rather than days; ultimately improving both outcomes and antimicrobial stewardship. Previously, HelixBind demonstrated a Core Pathogen Identification (C/PID) platform, aimed at the ‘general’ patient population at-risk for sepsis caused by bloodstream infections (BSIs). C/PID detects 21 of the most prevalent BSI-causing pathogens in a single test directly from blood, requires less than 2.5 hours from sample-to-answer, and displayed single CFU/ml LODs across the entire panel. C/PID was validated in a blinded pilot study utilizing clinical specimens and demonstrated >95% sensitivity and >89% specificity. IE/PID will utilize similar processes as C/PID and will detect the most prevalent pathogens associated with IE including fastidious and uncultureable pathogens. Our Specific Aims with quantifiable deliverables are designed to demonstrate feasibility within the time and capital constraints of a Phase I. To succeed, we have assembled a team of experts in assay development and artificial nucleic acids, supported by leading clinical microbiologists for guidance. Having achieved our Specific Aims, we will, in Phase II, develop deployable instrumentation/consumables, expand the test panel to include pathogens generally deemed as ‘unculturable’, such as Coxiella burnetii and Bartonella spp., and verify and validate an automated diagnostic platform with clinical specimens in a blinded study.