Oligonucleotide Primer Probe Sets for ESBL Detection
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Solution Overview
Problem
Current methods for detecting extended spectrum beta-lactamases (ESBLs), particularly CTX-M genes, are time-consuming, lack specificity, and are prone to false negatives, posing risks in clinical settings due to their inability to accurately identify antibiotic-resistant bacteria in a timely manner.
Innovation Solution
The development of oligonucleotide primer and probe sets for PCR-based methods that specifically target CTX-M and other ESBL nucleic acids, enabling rapid and sensitive detection directly from patient samples without the need for additional steps like agarose gel electrophoresis, and are designed to detect newly discovered isoforms.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If manual antimicrobial susceptibility testing is performed, then antibiotic resistance can be detected, but the process takes 48 to 96 hours and lacks reproducibility
Solution Approach 1:
The patent replaces manual mechanical testing methods with automated molecular diagnostics (PCR-based detection systems). This substitution enables rapid, standardized, and reproducible detection of antibiotic resistance genes, reducing both time to result and improving reliability through automation and standardization of the detection process.
Solution Approach 2:
The patent performs preliminary identification of bacterial species and their antibiotic resistance genes through molecular typing before conducting susceptibility testing. This preliminary action allows for targeted and rapid detection of specific resistance mechanisms, significantly reducing the overall time required compared to traditional step-by-step manual testing.
2Measurement precision
If traditional detection methods are used, then ESBLs can be identified, but false negatives occur and specificity is lacking
Solution Approach 1:
The patent employs species-specific and gene-specific oligonucleotide probes that target particular sequences of bacterial 16S rRNA and antibiotic resistance genes. This localized specificity ensures accurate identification of bacterial species and their resistance profiles, eliminating false negatives by precisely matching detected sequences to known pathogen profiles rather than using broad, non-specific methods.
3Measurement precision
If comprehensive bacterial identification is performed, then accurate resistance detection is achieved, but the process becomes complex and time-consuming
Solution Approach 1:
The patent divides the complex identification process into separate, targeted PCR reactions for different bacterial species and resistance genes. Each reaction uses specific primers and probes for a particular pathogen or resistance mechanism, simplifying the overall procedure by breaking down comprehensive identification into manageable, standardized segments that can be performed in parallel.
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
These methods provide rapid, specific, and sensitive detection of ESBLs, including CTX-M genes, reducing the time to results and eliminating the need for additional steps, thereby improving clinical decision-making and reducing the risk of antibiotic resistance misdiagnosis.
Implementation Method 1
The compositions include oligonucleotide primer and probe sets for use in detecting the presence CTX-M nucleic acids, and/or other ESBL nucleic acids, in a sample
Implementation Method 2
These primers and probe sets can be used in amplification methods (such as PCR, particularly quantitative PCR)
Data Source
AI summary
Embodiments disclosed herein relate to compositions for the detection and/or identification of microbes that carry extended spectrum beta-lactamase genes. Specifically, provided herein are oligonucleotides, probes, and kits containing the same, for the detection of bacterial CTX-M sequences. Also provided are methods for the detection and/or amplification of microbes harboring extended spectrum beta-lactamase genes, including CTX-M type extended spectrum beta-lactamase genes.