Sequencing Assay for Pathogen Detection in Food Processing
Solution Overview
Problem
Current methods for detecting foodborne pathogens like Salmonella, Campylobacter, and Escherichia genus in food and environmental samples are inefficient and often fail to differentiate between pathogenic and non-pathogenic microorganisms, leading to false positives and unnecessary food recalls, which contributes to the significant annual incidence of foodborne illnesses in the United States.
Innovation Solution
A method involving nucleic acid sequencing, where a sequencing assay is deployed in food processing facilities to analyze food and environmental samples, transmitting data to a server for scanning polymorphic regions associated with microorganisms, allowing for the differentiation of live and dead microorganisms, and distinguishing between pathogenic and non-pathogenic strains, including the use of barcodes for sample identification and automated sequencing apparatuses to reduce human intervention.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Speed
If traditional pathogen detection methods are used, then detection speed is slow, but sequencing complexity and cost increase
Solution Approach 1:
The patent segments the detection process into distinct modules: sample collection, nucleic acid extraction, library preparation, sequencing, and data analysis. Each module can be independently optimized and performed by different personnel or systems, reducing overall complexity while maintaining speed.
Solution Approach 2:
The patent implements preliminary action through pre-designed probes, primers, and library preparation kits that are prepared in advance. These pre-configured reagents contain specific sequences targeting known pathogens, allowing rapid detection without requiring complex real-time analysis or custom probe design during the detection event.
2Measurement precision
If comprehensive sequencing is performed on all samples, then detection accuracy improves, but false positives increase due to inability to differentiate live and dead microorganisms
Solution Approach 1:
The patent applies local quality by targeting specific regions of the microbial genome that indicate viability, such as genes encoding for proteins only expressed in live cells or epigenetic markers present only in viable organisms. This selective targeting within the comprehensive sequencing approach allows differentiation between live and dead microorganisms, reducing false positives while maintaining overall detection accuracy.
Solution Approach 2:
The patent utilizes parameter changes by detecting epigenetic modifications (such as methylation patterns) that differ between live and dead microorganisms. These chemical parameter changes in the nucleic acid structure serve as viability indicators, allowing the system to distinguish viable pathogens from non-viable organisms even when genetic material from both is present in the sample.
3Productivity
If manual detection methods are used, then operational simplicity is maintained, but productivity and throughput are low
Solution Approach 1:
The patent implements self-service through automated library preparation systems and bioinformatics pipelines that perform multiple steps without human intervention. The system automatically extracts nucleic acids, prepares sequencing libraries, performs quality control checks, and analyzes sequencing data, reducing manual labor while increasing throughput. Only sample input and result interpretation require human involvement.
Solution Approach 2:
The patent replaces manual mechanical operations with automated systems: robotic liquid handlers perform pipetting and sample preparation, automated thermocyclers conduct PCR amplification, and computer algorithms perform data analysis. This substitution of mechanical and cognitive tasks with automated systems dramatically increases productivity while maintaining ease of operation through user-friendly interfaces.
4Reliability
If traditional detection methods are used, then cost is reduced, but food recalls occur due to false positives from non-pathogenic microorganisms
Solution Approach 1:
The patent extracts and analyzes only the specific genetic regions and epigenetic markers relevant to pathogenicity from the entire microbial genome. By focusing sequencing and analysis resources on these critical regions rather than comprehensive whole-genome sequencing of all detected organisms, the system reduces costs while improving recall accuracy through targeted detection of pathogenic characteristics.
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 timely and efficient identification of pathogens, reducing false negatives and false positives, thereby enhancing food safety by accurately distinguishing between pathogenic and non-pathogenic microorganisms, thus minimizing food recalls and improving public health outcomes.
Implementation Method 1
performing a sequencing reaction of a food sample or of an environmental sample from said one or more food processing facilities
Implementation Method 2
Said pore sequencing reaction can distinguish an epigenetic pattern on a nucleic acid from said food sample or from said environmental sample, such as a methylation pattern
Data Source
AI summary
Provided herein are methods and apparatus for the identification of pathogenic and non-pathogenic microorganisms in food and environmental samples. The disclosure solves existing challenges encountered in identifying food borne pathogens, including pathogens of the Salmonella, Campylobacter, Listeria, and Escherichia genera in a timely and efficient manner. The disclosure also provides methods for differentiating a transient versus a resident pathogen, correlating presence of non-pathogenic with pathogenic microorganisms, distinguishing live versus dead microorganisms by sequencing.