Oligonucleotide Probe Hybridization for Rapid Microbial Identification
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Solution Overview
Problem
Conventional methods for microbial identification in clinical specimens are slow, cumbersome, and often require centralized laboratory facilities, leading to delayed treatment and potential misuse of antibiotics due to the time-consuming nature of existing techniques.
Innovation Solution
A method using oligonucleotide probes that selectively bind to rRNA molecules in clinical specimens, allowing for rapid identification of microbial species, including gram-positive and gram-negative bacteria and fungi, without the need for intervening culturing steps, using a probe panel with multiple detection regions and a detection apparatus to analyze hybridized complexes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If conventional microbial identification methods are used, then reliable identification can be achieved, but the process is slow and time-consuming
Solution Approach 1:
The patent extracts and detects specific ribosomal RNA sequences directly from clinical specimens using species-specific oligonucleotide probes. By targeting conserved rRNA regions that are present in all bacteria but have species-specific variations, the method enables rapid identification without requiring time-consuming culturing steps, thus resolving the contradiction between reliability and time consumption
Solution Approach 2:
The patent replaces traditional mechanical culturing and growth-based identification methods with molecular hybridization detection. Using oligonucleotide probe hybridization to detect rRNA sequences allows for direct identification of microbial species from clinical samples, eliminating the need for prolonged incubation periods while maintaining identification accuracy
2Productivity
If multiple species-specific probes are used to achieve rapid identification, then identification speed improves, but probe interference increases and reliability decreases
Solution Approach 1:
The patent designs probes that target specific local regions of ribosomal RNA sequences that are unique to each bacterial species. By focusing detection on species-specific rRNA regions rather than using multiple probes across the entire genome, the method achieves rapid multi-species identification while minimizing probe-probe interference and maintaining high result reliability
Solution Approach 2:
The patent optimizes probe parameters including length, melting temperature, and sequence composition to ensure specific binding to target rRNA sequences. By carefully controlling these parameters, the method enables the use of multiple species-specific probes in a single reaction mixture without significant cross-interference, thus maintaining both speed and reliability
3Ease of operation
If traditional culturing methods are used, then comprehensive microbial analysis is possible, but the process requires centralized laboratories and delays treatment
Solution Approach 1:
The patent employs a self-contained probe hybridization system that can be performed directly at the point of care or in frontline clinical settings. The method uses simple reagents (oligonucleotide probes and detection systems) that do not require complex centralized laboratory infrastructure, enabling rapid microbial identification wherever clinical specimens are collected, thus eliminating treatment delays associated with specimen transport and centralized processing
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
Enables rapid and accurate identification of microbial species in clinical specimens, facilitating timely treatment decisions and reducing the risk of antibiotic resistance by providing clinically meaningful results within minutes to hours, rather than days or weeks, and can be performed in frontline settings.
Implementation Method 1
Hybridization of target rRNA with a capture probe and detector probe
Data Source
AI summary
A method of identifying a target microbe in a specimen and including the steps of a) obtaining a specimen, b) lysing the specimen to release a plurality of rRNA molecules from one or more first target microbes in the specimen, c) contacting the specimen with a plurality of first oligonucleotide probe sets configured to selectively bind to rRNA molecules released from the target microbe thereby forming a plurality of first hybridized complexes, each first hybridized complex including one first capture probe and one first detector probe and one of the plurality of rRNA molecules, and d) analyzing the first hybridized complexes to identify a first target microbe in the specimen.