Hybridization Probes for Antibiotic Resistance Gene Detection
Solution Overview
Problem
Current methods for detecting methicillin-resistant and vancomycin-resistant microorganisms in clinical samples are slow and lack accuracy, particularly in identifying the mecA gene and VanA/VanB genes, which are crucial for antibiotic resistance profiling.
Innovation Solution
A device and method utilizing a solid support with detectably labeled hybridization probes specifically designed to target ribosomal nucleic acids from Staphylococcus and Enterococcus species, including probes for mecA, VanA, and VanB genes, allowing for simultaneous detection and identification of these organisms using high stringency hybridization conditions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional detection methods are used for identifying antibiotic-resistant microorganisms, then the detection can be performed with standard procedures, but the detection speed is slow and accuracy is insufficient
Solution Approach 1:
The detection system is segmented into multiple specialized probe sets, each targeting specific resistance genes (mecA, VanA, VanB) or ribosomal nucleic acids of different bacterial genera (Staphylococcus, Enterococcus). This segmentation allows simultaneous detection of multiple targets in parallel, improving both accuracy through specific targeting and speed through concurrent analysis
Solution Approach 2:
The patent employs an excessive action approach by providing not just one probe per target, but multiple probes that collectively hybridize to each target sequence. For example, multiple probes are designed to collectively bind to mecA genes, VanA genes, and VanB genes, ensuring high detection sensitivity and accuracy even when target concentrations are low
2Measurement precision
If multiple probes are used to detect different resistance genes, then detection accuracy improves, but device complexity increases
Solution Approach 1:
The solid support device is designed with multi-functionality, serving as a universal platform that can detect multiple types of targets simultaneously. The same solid support structure accommodates diverse probe sets targeting different genes and bacterial genera, eliminating the need for separate detection devices for each resistance type and thereby managing complexity through consolidation
Solution Approach 2:
Different regions or loci on the solid support are assigned specific probe sets with localized functions. Each locus contains probes tailored to detect specific targets (e.g., one locus for mecA, another for VanA/VanB), allowing the system to manage complexity through spatial organization and functional specialization of different device regions
3Measurement precision
If high stringency hybridization conditions are used, then detection specificity improves, but detection sensitivity may decrease
Solution Approach 1:
Multiple probes are employed for each target sequence, providing excessive action that compensates for the stringent hybridization conditions. Even if some probes fail to hybridize under high stringency, others succeed, ensuring reliable detection while maintaining high specificity
Solution Approach 2:
The system utilizes parameter changes by employing probes with varying lengths, compositions, and hybridization characteristics. This diversity in probe parameters allows optimization of hybridization efficiency under high stringency conditions while maintaining specificity, as different probe variants respond differently to the stringent conditions
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 detection of methicillin and vancomycin resistance genes, reducing the time required for sample processing and improving the specificity and sensitivity of antibiotic resistance profiling, facilitating appropriate antibiotic choices and infection management.
Implementation Method 1
A double-stranded nucleic acid hybrid between the probe and the target sequence results if the target sequence is contacted under hybridization-promoting conditions with a probe having a sufficient number of contiguous bases complementary to the target sequence
Implementation Method 2
Probes commonly are labeled with a detectable moiety such as a radioisotope, a ligand, or a colorimetric, fluorometric or chemiluminescent moiety to facilitate the detection of hybrids
Data Source
AI summary
The invention provides a rapid sample-processing method for preparing hybridization reaction mixtures substantially depleted of RNA, and a method of identifying the methicillin-resistance status and vancomycin-resistance status of an organism.