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Multiplexed, Non-Amplified, Nucleic Acid-Based Identification of Multidrug Resistant Pathogens Using an Integrated Optofluidic Platform

Award Number: R01AI116989
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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¿ DESCRIPTION (provided by applicant): Antibiotic resistance has emerged as a major public health threat. Patients infected with drug- resistant pathogens suffer significantly higher rates o morbidity and mortality, most often due to delays in the administration of effective antimicrobial therapies. In particular for bloodstream infections, the need to rapidly identify both pathogen and resistance profile is crucial, as treatment with antibiotics to which the organism is sensitive is essential and time-critical. Indeed, sepsis is involved in up to half of all hospital deaths. Drug susceptibility information for a pathogen is typically not received by clinicians until at least 24 hours post-sampling, because of reliance on culture-based diagnostic methods. Recently, bloodstream infections caused by carbapenem-resistant Enterobacteriaceae (CRE) have become increasingly problematic. A rapid diagnostic assay for the detection and resistance determination of these pathogens is urgently needed. Although PCR-based assays are rapid, specific, and amenable to multiplexing, they have largely failed to perform in blood samples. Our industrial partner, Great Basin Corporation, has developed a fully disposable cartridge system for pathogen detection in cultured blood. We propose major improvements to this platform through the development of a multiplexed, non-amplified, non-cultured, nucleic acid-based assay for the detection and identification of multidrug resistant pathogens using a novel integrated optofluidic device. Bacteria will be concentrated directly from a blood sample by cross-flow filtration, and then delivered to a lysis and DNA-shearing chamber. Target DNAs containing the genes of interest will be captured on a solid substrate by hybridization. Molecular beacons will be hybridized to specific targets on the captured nucleic acids. These complexes will be released and specific beacons detected by an advanced optofluidics system capable of detecting single molecule fluorescence. We will demonstrate identification within one hour of bacteria in blood at levels as low as 10 CFU/mL. Initially, the focus will be to detect and characterize CRE isolated directly from a blood sample. The KPC, NDM, VIM, and IMP carbapenemase genes will be identified along with the simultaneous detection of specific markers for Klebsiella pneumoniae, Escherichia coli, and Enterobacter species. This platform is readily expandable to additional pathogens and their relevant antibiotic resistance genes. This technology has the potential to significantly reduce time to diagnosis and improve clinical outcomes.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2023 ( Subtotal = -$5,854 )
2023	2019	BRIGHAM YOUNG UNIVERSITY	A-153 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	5	5/17/2023	NON-COMPETING CONTINUATION	-$5,854
														Subtotal = -$5,854

Issue Date FY: 2021 ( Subtotal = $0 )
2021	2019	BRIGHAM YOUNG UNIVERSITY	A41 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	5	2/16/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2020 ( Subtotal = $0 )
2020	2019	BRIGHAM YOUNG UNIVERSITY	A41 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	5	2/13/2020	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2019 ( Subtotal = $982,407 )
2019	2019	BRIGHAM YOUNG UNIVERSITY	A-41 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	001	5	9/12/2019	NON-COMPETING CONTINUATION	$0
2019	2019	BRIGHAM YOUNG UNIVERSITY	A-41 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	5	2/5/2019	NON-COMPETING CONTINUATION	$982,407
														Subtotal = $982,407

Issue Date FY: 2018 ( Subtotal = $988,510 )
2018	2018	BRIGHAM YOUNG UNIVERSITY	A-41 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	4	1/30/2018	NON-COMPETING CONTINUATION	$988,510
														Subtotal = $988,510

Issue Date FY: 2017 ( Subtotal = $1,002,828 )
2017	2017	BRIGHAM YOUNG UNIVERSITY	A-41 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	3	2/24/2017	NON-COMPETING CONTINUATION	$1,002,828
														Subtotal = $1,002,828

Issue Date FY: 2016 ( Subtotal = $1,069,803 )
2016	2016	BRIGHAM YOUNG UNIVERSITY	D-177 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	2	2/9/2016	NON-COMPETING CONTINUATION	$1,069,803
														Subtotal = $1,069,803

Issue Date FY: 2015 ( Subtotal = $1,383,090 )
2015	2015	BRIGHAM YOUNG UNIVERSITY	D-177 ASB	PROVO	UT	84602	UTAH	USA	Allergy and Infectious Diseases Research	000	1	2/25/2015	NEW	$1,383,090
														Subtotal = $1,383,090

Grand Total All Awards = $5,420,784

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Multiplexed, Non-Amplified, Nucleic Acid-Based Identification of Multidrug Resistant Pathogens Using an Integrated Optofluidic Platform

Award Number: R01AI116989

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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