Microbial RNA Isolation via Liquid Chromatography for Rapid Pathogen Detection
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Solution Overview
Problem
Current methods for detecting microbial species in clinical, environmental, or production contexts are inefficient and time-consuming due to the need for incubation and purification, which can lead to delayed detection and degradation of genetic biomarkers, and struggle to distinguish between live and dead microbes.
Innovation Solution
A computer-implemented method that preprocesses raw sequence data to filter out low-quality reads, aligns pathogen sequences with host and reference genomes, and uses k-mer annotation for rapid identification of microbial taxa, allowing for bulk filtration of microbial RNA using liquid chromatography to isolate and collect microbial RNA without significant incubation or purification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If incubation techniques are used to amplify genetic sequences, then detection sensitivity is improved, but processing time increases significantly (up to 30 hours)
Solution Approach 1:
The patent extracts and isolates microbial RNA directly from biological specimens using liquid chromatography, separating it from host RNA and other contaminants. This extraction approach eliminates the need for time-consuming incubation techniques while maintaining detection sensitivity by directly analyzing the isolated microbial genetic material.
Solution Approach 2:
The patent performs preliminary enrichment of microbial RNA through selective bulk filtration and liquid chromatography separation before sequencing. By preparing the sample in advance with targeted microbial RNA isolation, the system achieves high detection sensitivity without requiring post-isolation incubation periods.
2Measurement precision
If purification techniques are used to isolate microbial RNA, then detection accuracy is improved, but genetic biomarkers may degrade due to further processing
Solution Approach 1:
The patent replaces traditional mechanical purification techniques (filtration, centrifugation, column-based methods) with liquid chromatography separation. This substitution maintains high detection accuracy through effective microbial RNA isolation while minimizing processing steps and time, thereby preserving biomarker integrity and reducing degradation risk.
Solution Approach 2:
The patent utilizes liquid chromatography to change the separation parameters based on RNA properties, achieving high-purity microbial RNA isolation in a single continuous process. This parameter-based separation maintains biomarker integrity by avoiding repeated handling and processing steps associated with traditional purification methods.
3Measurement precision
If traditional sequencing analysis is used on raw sequence data, then comprehensive pathogen identification is achieved, but processing time increases and low-quality reads affect results
Solution Approach 1:
The patent performs preliminary quality filtering and host RNA removal from raw sequence data before pathogen identification analysis. By preprocessing the data to eliminate low-quality reads and host sequences in advance, the system achieves both high pathogen identification accuracy and improved processing speed, as the downstream analysis works with pre-cleaned, high-confidence data.
Solution Approach 2:
The patent segments the sequence analysis process into distinct stages: quality filtering, host RNA removal, and pathogen identification. This segmentation allows each stage to be optimized independently, with quality control measures ensuring accurate pathogen identification while efficient processing pipelines maintaining high productivity.
4Measurement precision
If incubation and purification techniques are used, then microbial species detection is improved, but the ability to distinguish live vs dead microbes is compromised
Solution Approach 1:
The patent extracts and analyzes microbial RNA directly from the biological specimen without incubation. Since RNA degrades rapidly after cell death, this direct extraction approach preserves viability information - live microbes with intact RNA can be distinguished from dead microbes whose RNA has degraded, while still achieving sensitive detection of viable pathogens.
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 and efficient identification of microbial species, reducing processing time and preserving genetic biomarkers, while simultaneously isolating viable microbial species from complex biological specimens.
Implementation Method 1
bulk filtration of microbial RNA using liquid chromatography to isolate and collect microbial RNA
Data Source
AI summary
A bioinformatics pipeline designed to analyze next generation sequence data as input and systematically quality filter, normalize, annotate, quantify, and identify microbial taxa of interest contained within microbial databases. In various embodiment, a bioinformatics pipeline may include a deep annotation strategy that confers an additional task that can be scaled to a limitless number of taxa of interest each time a taxa of interest is extracted for re-annotation.