Targeted Pathogen Sequencing for Rapid AMR Gene Detection
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Solution Overview
Problem
Current methods for pathogen and antibiotic resistance gene detection are time-consuming, laborious, and lack comprehensiveness, often requiring technical expertise, and are prone to contamination, which hinders timely and accurate diagnosis in critical cases like sepsis.
Innovation Solution
A method involving pre-sequencing with sequence-specific primers to enrich target nucleic acid regions, followed by genomic analysis and automated interpretation using metadata, enabling rapid identification of pathogens and antibiotic resistance genes in a single test.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If culture-based identification techniques are used, then comprehensive pathogen detection is achieved, but the turnaround time increases to 2-4 days or longer
Solution Approach 1:
The detection process is segmented into two distinct phases: (1) pre-sequencing enrichment using targeted PCR amplification of specific pathogen regions, and (2) rapid sequencing and analysis. This segmentation allows the method to achieve both high sensitivity through targeted enrichment and rapid results through streamlined sequencing, resolving the contradiction between comprehensive detection and fast turnaround.
Solution Approach 2:
The method performs preliminary enrichment of target pathogen regions before sequencing using sequence-specific primers and PCR amplification. This preliminary action concentrates the pathogen DNA/RNA of interest, enabling rapid and sensitive detection without requiring lengthy culture periods, thus achieving both accuracy and speed.
2Measurement precision
If sequencing technologies are used for comprehensive pathogen detection, then sensitivity is improved, but contamination from non-pathogenic nucleic acid material increases
Solution Approach 1:
The method applies local quality by using sequence-specific primers that target only specific pathogen regions (such as 16S rRNA for bacteria, ITS for fungi). This targeted approach ensures that only relevant pathogenic sequences are amplified and detected, while non-pathogenic human DNA and other background material are excluded, thus maintaining high sensitivity without contamination.
Solution Approach 2:
The method converts the potential harm of host DNA abundance into a benefit by designing primers that specifically bind to pathogen sequences. The overwhelming presence of human DNA is effectively filtered out because the targeted amplification only occurs on pathogen-specific regions, turning the challenge of complex sample matrices into an advantage for specific detection.
3Ease of operation
If PCR-based assays are used, then ease of use and cost-effectiveness are improved, but the ability to identify antibiotic resistance genes is limited
Solution Approach 1:
The method achieves universality by using a single sequencing-based platform that can simultaneously detect multiple pathogen types (bacteria, fungi, viruses), identify species-level taxonomy, and detect antibiotic resistance genes. The targeted enrichment approach with appropriate primers makes this multi-functional capability possible while maintaining ease of operation and cost-effectiveness.
4Loss of time
If molecular diagnostic methods are used for rapid detection, then turnaround time is reduced, but comprehensiveness of pathogen detection is limited
Solution Approach 1:
The method employs dynamic adaptability through the use of different primer sets that can be selected based on the suspected pathogen type. The same sequencing platform and analysis pipeline can dynamically adjust to detect bacteria, fungi, or viruses by changing only the enrichment primers, enabling rapid and comprehensive detection across multiple pathogen classes simultaneously.
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 provides a high-throughput, user-friendly method capable of identifying multiple pathogens and ARGs within 10 hours, reducing contamination and technical expertise requirements, and facilitating early informed clinical decisions.
Implementation Method 1
pre-sequencing with sequence-specific primers to enrich target nucleic acid regions
Implementation Method 2
combining sequence specific primers to obtain targeted amplicons
Data Source
AI summary
Methods and systems for detection and identification of pathogens and antibiotic resistant genes are disclosed herein. The method is a high throughput, rapid comprehensive method for identification of pathogens in a sample or subject. The method, according to embodiments herein, is also capable of identifying genes responsible for Antimicrobial Resistance (AMR) in a pathogen. The said method provides a rapid, cost-effective and scalable solution for identifying pathogens.