SBIR-STTR Award

Sepsis is a whole-body Inflammatory Response to infection that affects approximately 1 million people each year in the United States and kills up to 50 percent of severely affected patients. Rapid and appropriate antimicrobial administration is critical for the management of Sepsis. Each hour of treatment delay is associated with an 8% decrease of survival in septic shock patients. Blood culture is the gold standard diagnostic method, however, it takes more than one day to provide results. Therefore, patients receive broad-spectrum antibiotics or may not receive treatment in the initial hours. Molecular detection is an attractive solution, however, currently available tests are based on PCR amplification of bacterial genomic DNA followed by complex detection strategies. These techniques suffer from DNA contamination, lack sufficient sensitivity and are expensive. Here, we propose the development of a novel platform for rapid and inexpensive identification of microorganisms in Whole Blood without blood culture. The new platform will be based on Single Molecule Scanning (SM-Scanning), a novel molecular detection method in which probe hybridization to a target nucleic acid is detected without PCR amplification (Patent Pending). SM-Scanning uses a straight forward and inexpensive detection strategy. Preliminary results demonstrate that SM-Scanning can detect 5 Escherichia coli cells. In this proposal, we will demonstrate the properties of SM-Scanning by developing an assay capable of detecting microorganisms in blood samples in less than 1.5 hours with extremely high sensitivity. Aim 1 focuses on developing a rapid test capable of detecting the presence of bacteria in 5 ml Whole Blood samples with high sensitivity. Aim 2 focuses on developing and determining the performance of a multiplex assay capable of detecting bacteria and fungi in a single assay.

Public Health Relevance Statement:


Public Health Relevance:
There is a major unmet need in microbiology laboratories for faster and more sensitive microorganism detection methods so that appropriate treatment can be initiated in a timely manner. Here, we propose the development of a rapid molecular test capable of detecting microorganism within 1.5 hours with high sensitivity and without blood culture.

Bloodstream infection detection directly on whole blood Summary Sepsis is a life-threatening condition triggered by the presence of fungi or bacteria in the bloodstream that affects 1.3 million people each year in the United States.1 Rapid antimicrobial administration is critical for sepsis treatment.2-4 However, the current gold standard for bloodstream infection diagnosis is blood culture (BC), which takes one to five days.5 In order to provide physicians with the needed diagnostic information to properly treat patients, we propose the development of an automated platform for rapid, broad and cost-effective identification of microorganisms in whole-blood without BC. In this proposal, we will focus on the development of the instrument and the first assay which will detect fungi directly on whole-blood. The new platform will be based on Single Molecule Scanning (SMS), a novel sample preparation and molecular detection method developed at Scanogen. The fungi assay (SMS-Fungi) will detect and identify the five most common Candida species that cause bloodstream infections as well as the Cryptococcus genus. The assay will also utilize probes that target broadly conserved sequences to detect the presence of any fungi in the whole- blood specimen. The goal is to develop a 1-hour, accurate, broad, multiplexed, fully-automated and cost-effective assay, that will aid physicians to start proper antifungal therapy without delay. In phase I, we developed an assay protocol capable of detecting fungi directly in whole-blood. We tested both specific and broad-range probes with four species of fungi commonly found in bloodstream infections. We found that the assay is highly specific and has the high sensitivity required for the diagnosis of clinical cases with a limit of detection (LOD) as low as 1 CFU/ml. In this project, we will complete the development of the assay protocol by including new probes and optimizing the overall assay (Aim 1), develop a beta-prototype system consisting of an automated instrument and disposable cartridge (Aim 2) and evaluate the new system in pilot analytical and clinical validation studies (Aim 3). We will leverage the experience attained in the development of a rapid assay for point of care detection of Tuberculosis currently under development at Scanogen, and work with a multidisciplinary team that includes experts in assay development and instrument development including the former Vice President of Engineering at Becton Dickinson, experts in fungal infection diagnosis and treatment from Johns Hopkins University and engineers from Key Technologies. Our goal is to develop and validate an automated molecular platform for rapid analysis of microorganisms in whole-blood and develop its first assay for fungi detection. If successful, the new assay will dramatically improve the management of patients with fungemia by reducing diagnostic delay and enabling timely initiation of proper antifungal treatment.

Public Health Relevance Statement:
Project Narrative We propose the development of a novel platform for rapid detection and identification pathogens directly in whole blood for the diagnosis of bloodstream infections. The proposal is focused on the development of an automated and cost effective assay for the detection of fungi in blood in one hour.

Project Terms:
Affect; Anti-Bacterial Agents; Antifungal Agents; Antifungal Therapy; antimicrobial; assay development; Bacteria; base; Biological Assay; Blood; Blood Circulation; Blood specimen; Candida; candidemia; Clinical; clinical Diagnosis; Clinical Research; Conserved Sequence; cost effective; Cryptococcus; Detection; Development; Device or Instrument Development; Diagnosis; Diagnostic; Diagnostic Procedure; Engineering; experience; Fungemia; fungus; Goals; Gold; Hospitals; Hour; improved; instrument; Laboratories; Life; manufacturability; Methods; Microbiology; microorganism; Molecular; mortality; multidisciplinary; Mycoses; novel; Nucleic Acid Hybridization; pathogen; Patients; Performance; Phase; Physicians; Pilot Projects; point of care; Predisposition; Preparation; Price; protocol development; Protocols documentation; prototype; rapid detection; Resources; Ribosomal RNA; Sampling; Scanning; Sepsis; single molecule; System; Techniques; Technology; Testing; Time; Tuberculosis; United States; United States Food and Drug Administration; Universities; usability; Validation; validation studies; Whole Blood; Work