Barcoded mRNA Probe Assays for Rapid Antibiotic Resistance Detection

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Solution Overview

Problem

Current methods for detecting antibiotic resistance in microbial pathogens are slow and require separate assays, leading to inefficiencies and inaccuracies in determining resistance mechanisms, which poses a significant healthcare threat due to the rise of antibiotic-resistant bacteria.

Innovation Solution

A method involving the use of nucleic acid probes to rapidly detect antibiotic resistance by hybridizing mRNA from bacterial cells with unique barcodes, enabling simultaneous detection of multiple resistance genes and identifying bacterial strains through mRNA expression signatures.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If separate PCR or sequencing assays are used to detect antibiotic resistance genes, then detection specificity is improved, but assay complexity and time consumption increase

Engineering Contradiction:

Improvedetection accuracyVSAvoidassay infrastructure

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent combines multiple resistance gene detection capabilities into a single qPCR assay using probe sets with unique barcodes. Multiple probes targeting different resistance genes are pooled together, allowing simultaneous detection of multiple resistance mechanisms in one assay rather than requiring separate PCR or sequencing assays for each gene.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The assay system is designed to detect multiple different resistance genes using a universal qPCR platform. The probe sets with unique barcodes can identify various resistance mechanisms (such as KPC, NDM, OXA-48, VIM, IMP, and SIM beta-lactamases) within a single universal assay framework, eliminating the need for multiple specialized assays.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Measurement precision

If growth-based phenotypic assays are used for antibiotic susceptibility testing, then detection accuracy is improved, but testing time is extended

Engineering Contradiction:

Improveresistance detection accuracyVSAvoidtesting duration

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent replaces the mechanical growth-based phenotypic assay system with a molecular detection system using qPCR. Instead of waiting for bacterial growth to observe phenotypic resistance, the assay directly detects resistance genes at the molecular level, providing results without requiring extended incubation periods for bacterial culture.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The assay detects resistance genes directly from clinical samples without requiring prior bacterial culture or growth. By performing resistance gene detection before or alongside susceptibility testing, the system provides preliminary resistance information that guides treatment decisions while traditional phenotypic assays are still running.

Inventive Principle:

Principle #10Preliminary action

3Adaptability or versatility

If multiple resistance genes are detected using separate assays, then comprehensive resistance profiling is achieved, but operational efficiency decreases

Engineering Contradiction:

Improveresistance gene detection coverageVSAvoidassay throughput

Core Design Contradiction:

Adaptability or versatilityVSProductivity

Solution Approach 1:

The patent merges detection of multiple resistance genes into a single qPCR reaction by pooling probes with unique barcodes. This allows simultaneous amplification and detection of multiple resistance genes (KPC, NDM, OXA-48, VIM, IMP, SIM) in one assay, dramatically increasing throughput compared to running separate assays for each gene.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The assay uses probes with unique barcodes that emit different fluorescent signals when hybridized to their target resistance genes. This allows simultaneous detection of multiple resistance genes through distinct fluorescent color changes, enabling comprehensive resistance profiling in a single assay readout.

Inventive Principle:

Principle #32Color changes

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 provides rapid and accurate phenotypic detection of antibiotic resistance, allowing for immediate identification of known and novel resistance mechanisms, and facilitates appropriate therapeutic interventions.

Implementation Method 1

hybridizing the released mRNA to at least one set of two nucleic acid probes, wherein each nucleic acid probe includes a unique barcode or tag

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS12442035B2Compositions and methods for detecting antibiotic responsive mRNA expression signatures and uses thereof

Publication Date: 2025.10.14 THE BROAD INST INC

AI summary

The present disclosure relates to compositions, methods, and kits for rapid phenotypic detection of antibiotic resistance/susceptibility.