Microbial Pathogen Detection via Eukaryotic DNA Depletion

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Solution Overview

Problem

Current molecular diagnostics for bloodstream infections are hindered by the need for lengthy blood-culture processes and the interference of human DNA in microbial pathogen detection, limiting the sensitivity and efficiency of identifying pathogens in blood samples.

Innovation Solution

A method involving the depletion of eukaryotic DNA from samples using a selective lysis solution, followed by microbial cell lysis, genetic material isolation, amplification, and detection using DNA Invading Artificial Nucleic Acids (DIANAs) to identify specific microbial species directly from blood without culturing, enabling rapid and sensitive detection.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If blood-culture processes are used to identify pathogens, then pathogen identification can be achieved, but the process takes several days and reduces diagnostic efficiency

Engineering Contradiction:

Improvepathogen identification accuracyVSAvoiddiagnostic time

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent applies preliminary action by performing selective eukaryotic cell lysis and DNA depletion before pathogen detection. This preparatory step removes human DNA interference in advance, enabling direct molecular detection of microbial pathogens without requiring lengthy culture processes, thus reducing diagnostic time while maintaining identification accuracy

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent replaces the mechanical/biological culture system with a molecular detection system using DIANAs and next-generation sequencing. This substitution eliminates the need for time-consuming microbial cultivation while directly detecting pathogen genetic material, achieving rapid and accurate pathogen identification

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

2Measurement precision

If molecular diagnostics are performed on whole blood samples, then pathogen detection sensitivity is reduced due to human DNA interference

Engineering Contradiction:

Improvepathogen detection sensitivityVSAvoidhuman DNA interference

Core Design Contradiction:

Measurement precisionVSObject-affected harmful factors

Solution Approach 1:

The patent applies the extraction principle by selectively removing eukaryotic DNA from whole blood samples through targeted lysis and depletion steps. This extracts the harmful human DNA interference while preserving microbial genetic material, thereby enhancing pathogen detection sensitivity in molecular diagnostics

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent uses an intermediary approach by introducing selective lysis solutions and depletion reagents that differentiate between eukaryotic and microbial cells. These intermediaries enable selective removal of human DNA while leaving microbial DNA intact, resolving the interference issue without compromising pathogen detection

Inventive Principle:

Principle #24Intermediary (Mediator)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This approach allows for the rapid identification of microbial pathogens at clinically relevant levels directly from unprocessed blood, reducing the time required for diagnosis to less than 8 hours and enhancing detection sensitivity, thereby improving the management of bloodstream infections.

Implementation Method 1

depleting eukaryotic DNA from the sample includes adding an eukaryotic cell lysis solution to the sample, wherein the eukaryotic cell lysis solution selectively targets and predominantly lyses eukaryotic cells as opposed to microbial cells

Methodology Applied

Scientific EffectSelective cell lysis:

Implementation Method 2

lysing one or more microbial cells in the sample, wherein the lysing of one or more microbial cells releases a plurality of microbial genetic materials

Methodology Applied

Scientific EffectCell lysis:

Implementation Method 3

the free eukaryotic DNA is removed from the blood reaction using an anionic-exchange microparticle under conditions of a pH of about 6-9 with monovalent salt concentrations of about 0.1 M-0.85 M

Methodology Applied

Scientific EffectAnionic exchange: Ion Exchange

Implementation Method 4

amplifying the plurality of microbial genetic materials

Methodology Applied

Scientific EffectNucleic acid amplification:

Implementation Method 5

contacting the amplified microbial genetic materials with a plurality of DNA Invading Artificial Nucleic Acids (DIANAs), wherein the plurality of DIANAs comprise a sequence selected from the group consisting of SEQ ID NOS: 1-37; and detecting binding of one or more DIANAs the microbial genetic material of its respective single species or group of microbes

Methodology Applied

Scientific EffectNucleic acid hybridization:

Data Source

PatentUS20230183820A1Methods and devices for detecting and identifying microorganisms

Publication Date: 2023.06.15 HELIXBIND

AI summary

Methods and devices for isolating microbial cells from a sample, extracting eukaryotic DNA from a sample, and identifying the microbial species in the sample are disclosed herein.