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Principal Investigator: Robert K Ernst
Organization: UNIVERSITY OF MARYLAND BALTIMORE
Fiscal Year: 2024
Award: $463,500
Funding agency: National Institute of Allergy and Infectious Diseases
PROJECT SUMMARY
Infectious diseases have a substantial global health impact. Clinicians need rapid and accurate diagnoses of
infections to direct patient treatment and improve antibiotic stewardship, but current methodologies face severe
limitations in this regard. In the first funding cycle of our MPI grant “GM111066 - MS diagnostic bacterial
identification library,” we produced a novel diagnostic platform in which microbial membrane glycolipids
analyzed by mass spectrometry represent chemical “fingerprints” that were then used to differentiate Gram-
negative and –positive and fungal isolates after mono- or poly-microbial growth in standard laboratory medias
or complex biological (urine, blood bottles, and would effluent). In the second funding cycle, we aim to improve
the diagnostic as discussed below.
At the start this project, it had not been previously shown that bacterial or fungal membrane lipids could
provide a unique chemical signature or barcode that could be used for reliable pathogen identification. The fact
that these lipids (Gram-: LPS/lipid A, Gram+: Lipoteichoic acid/cardiolipin, Fungi: glycerophospholipids,
sphingolipids, and sterols) are present in high abundance (~106 copies per cell) makes them easily extractable
with a single rapid LPS-based protocol (less than 60 minutes from sample to MS identification). Importantly, for
clinical use, we successfully used our platform to solve these four major unmet needs from the protein-based
phenotyping approach: 1) removed the need for growth prior to MS analysis, 2) identification of bacterial and
fungal isolates with a single extraction protocol, 3) identification directly from complex biological fluids,
including urine, BAL fluid, wound effluent, and blood bottles, and 4) antimicrobial resistant strains could be
distinguished from the related susceptible strain. Finally, based on our thirteen peer-reviewed publications from
the first funding period and extensive preliminary data, we believe we have proven our highly innovative
original hypothesis and even advanced it past the original aims by using a design of experiment (DOE) process
to allow identification in under an hour direct from specimen.
In the second funding cycle, we propose to further innovate by i) using DOE to improve limit of detection
(LOD) from 106 to 103 which is the threshold for urinary tract infections; ii) extend the assay to direct analysis
of urine and stool samples without culture; iii) develop machine learning approaches to improve identification
of individual bacteria from polymicrobial infections; iv) expand detection of antimicrobial resistance beyond
colistin; v) develop a method for identification and structure analysis of lipids isolated from 100-1000 cells; and
vi) vastly expand our ability to identify pathogenic fungi, which are a growing healthcare issue, and Gram-
positive organisms.
Terms: <Address><Animal Model><Animal Models and Related Studies><Antibiotic Agents><Antibiotic Drugs><Antibiotics><Antimicrobial Resistance><Assay><Bacteria><Bacterial Gene Products><Bacterial Gene Proteins><Bacterial Infections><Bacterial Proteins><Bar Codes><Bioassay><Biological><Biological Assay><Blood><Blood Reticuloendothelial System><Cardiolipins><Cell Body><Cell Culture Techniques><Cell Membrane Lipids><Cells><Cessation of life><Chemicals><Clinical><Clinical Microbiology><Colimycin><Colisticin><Colistin><Communicable Diseases><Complex><Computer software><Data><Death><Detection><Development><Diagnostic><E coli><E. coli><Escherichia coli><Event><Experimental Designs><Face><Failure><Feces><Financial Hardship><Funding><Fungus Diseases><General Hospitals><Generalized Growth><Glycerophospholipids><Glycolipids><Grant><Growth><Health Facilities><Health care facility><Health system><Healthcare><Healthcare Facility><Hour><Individual><Infection><Infectious Disease Pathway><Infectious Diseases><Infectious Disorder><Intensive Care><Ions><Laboratories><Laboratory Research><Length of Stay><Libraries><Lipid A><Lipids><Liquid substance><MALDI-TOF Mass Spectrometry><Machine Learning><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Matrix-Assisted Laser Desorption Ionization Time-of-Flight MS><Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry><Membrane><Membrane Lipids><Methodology><Methods><Microbe><Minor><Miscellaneous Antibiotic><Modeling><Morbidity><Morbidity - disease rate><Mycoses><Number of Days in Hospital><Organism><Patients><Pattern><Peer Review><Phenotype><Phosphoglycerides><Polymyxin E><Predisposition><Process><Proteins><Protocol><Protocols documentation><Publications><Research Specimen><Sampling><Scientific Publication><Sepsis><Software><Solid><Specimen><Speed><Sphingolipids><Sterols><Structure><Susceptibility><Technology><Time><Tissue Growth><Urinary tract infection><Urinary tract infectious disease><Urine><Work><accurate diagnosis><anti-microbial><anti-microbial resistant><antimicrobial><bacteria infection><bacterial disease><barcode><biodefense><biologic><blood infection><bloodstream infection><care facilities><cell culture><cell cultures><chemical fingerprinting><chemotherapy><clinical relevance><clinically relevant><combat><cost><detection limit><develop software><developing computer software><developmental><diagnostic platform><diagnostic system><faces><facial><feature extraction><fecal sample><financial adversity><financial burden><financial distress><financial insecurity><financial strain><financial stress><fluid><fungal infection><fungal pathogen><fungi pathogen><fungus><fungus infection><global health><health care><hospital days><hospital length of stay><hospital stay><improved><innovate><innovation><innovative><lipo-teichoic acid><lipoteichoic acid><liquid><living system><machine based learning><membrane structure><microbial><microbial products><model of animal><mortality><new diagnostics><new drug treatments><new drugs><new pharmacological therapeutic><new technology><new therapeutics><new therapy><next generation diagnostics><next generation therapeutics><novel><novel diagnostics><novel drug treatments><novel drugs><novel pharmaco-therapeutic><novel pharmacological therapeutic><novel technologies><novel therapeutics><novel therapy><ontogeny><pathogen><pathogenic fungus><point of care><rapid diagnosis><resistance strain><resistance to anti-microbial><resistant strain><resistant to antimicrobial><simulation><software development><stool><stool sample><stool specimen><tandem mass spectrometry><tissue wound><tool><urinary infection><ward><wound><wounding><wounds>