smpB Gene Target Region for Specific Bacterial Detection
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Solution Overview
Problem
Current methods for detecting bacterial organisms, such as Legionella pneumophila, Haemophilus influenzae, and Mycobacterium species, are often time-consuming and lack specificity, leading to delays in diagnosis and potential false positives/negatives due to sequence homology and heterogeneity issues.
Innovation Solution
The use of the smpB gene as a nucleic acid target region, detected using specific primers and probes, allows for rapid and specific identification of these organisms through nucleic acid amplification techniques like real-time PCR, leveraging sequence variation and conservation within the bacterial kingdom.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional microbiological culture methods and biochemical methods are used to detect and identify bacterial organisms, then the identification process can be completed with basic laboratory equipment, but the methods are time-consuming (requiring several days) and have poor sensitivity
Solution Approach 1:
The patent replaces traditional mechanical microbiological culture methods with nucleic acid-based amplification methods (PCR). This substitution enables rapid detection and identification of bacterial organisms by targeting specific genetic sequences, achieving both high sensitivity and quick results within hours rather than days
Solution Approach 2:
The patent changes the detection parameter from phenotypic characteristics (used in traditional culture methods) to genotypic characteristics by targeting specific nucleic acid sequences. This parameter change allows for highly specific and sensitive detection of bacterial organisms through amplification of unique genetic markers
2Productivity
If existing nucleic acid targets (ssrA, lepA, 16sRNA genes) are used for bacterial detection, then the assays can be performed quickly with high sensitivity, but the high degree of nucleotide sequence homology across the bacterial kingdom reduces specificity and can lead to false positives
Solution Approach 1:
The patent applies local quality by selecting highly specific local regions within the 16S rRNA gene that exhibit species-specific sequence variations. Rather than using the entire gene sequence, the invention focuses on specific hypervariable regions that provide unique identifiers for different bacterial species, thereby maintaining speed while improving specificity
Solution Approach 2:
The patent segments the 16S rRNA gene into specific target regions for amplification and detection. By dividing the gene into discrete segments with species-specific characteristics, the assay can rapidly detect bacteria while distinguishing between different species through targeted analysis of unique sequence portions
3Reliability
If 16S rRNA gene is used as a diagnostic target, then the assay can detect bacterial presence, but sequence heterogeneity within single bacterial genomes (multiple heterogeneous copies) creates problems for diagnostic development and can lead to overestimation of microbial populations
Solution Approach 1:
The patent changes the detection approach from quantifying total 16S rRNA gene copies to detecting specific species-unique sequence signatures within the 16S rRNA gene. This parameter change allows reliable detection of bacterial presence while avoiding the quantification errors that arise from multiple heterogeneous copies within single genomes
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 enables rapid, specific, and sensitive detection of target bacterial species, reducing false positives and negatives, and facilitating timely and accurate diagnosis in clinical and non-clinical settings.
Implementation Method 1
determining whether a target region of the smpB gene... is present in said sample, wherein the target region can be detected using primers comprising SEQ ID NO: 10 and SEQ ID NO: 12 and a probe comprising SEQ ID NO: 14
Implementation Method 2
Nucleic acid based assays to detect and identify bacterial organisms... through nucleic acid amplification techniques like real-time PCR
Data Source
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AI summary
A method for determining the presence or absence of a member of a group of bacterial organisms in a sample, wherein the method comprises determining whether a target region of the smpB gene is present in said sample is provided. Primers, probes and kits for use in these methods also form part of the invention, as does the use of an smpB gene target region to detect the presence or absence of a member of a group of bacterial organisms in a sample, in a range of clinical and non- clinical applications.