Automated Priming and Library Loading for Foodborne Pathogen Sequencing
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Solution Overview
Problem
Existing food safety monitoring systems fail to accurately and efficiently detect and distinguish foodborne pathogens, such as those from the Salmonella, Campylobacter, and Escherichia genera, leading to significant health risks and outbreaks due to contamination.
Innovation Solution
A nucleic acid sequencing apparatus and method that includes a nucleic acid library preparation compartment and sequencing chamber with automated robotic handling, capable of distinguishing live versus dead microorganisms and differentiating pathogenic from non-pathogenic strains with high sensitivity and specificity, using barcode indexing and pore sequencing reactions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If automated nucleic acid sequencing is implemented, then detection precision and sensitivity are improved, but device complexity increases
Solution Approach 1:
The automated sequencing device is divided into distinct functional modules: library preparation module, sequencing module, and data analysis module. Each module performs a specific function, allowing the system to achieve high detection precision through specialized processing while managing complexity through modular design.
Solution Approach 2:
Barcode indexing is introduced as an intermediary element that enables precise tracking and identification of nucleic acid samples throughout the sequencing process. This intermediary mechanism enhances detection precision by ensuring accurate sample-to-data correspondence without requiring complex manual tracking systems.
2Productivity
If barcode indexing and automated handling are used, then productivity increases, but device complexity increases
Solution Approach 1:
Barcode indexes are attached to nucleic acid samples during the library preparation phase, before sequencing begins. This preliminary action enables automated systems to efficiently process and track multiple samples simultaneously, increasing productivity while the modular design keeps device complexity manageable.
Solution Approach 2:
The automated robotic handling system uses barcode recognition to self-direct sample processing without human intervention. The system automatically retrieves, processes, and tracks samples based on their barcode identifiers, enabling high productivity through autonomous operation rather than complex manual coordination.
3Loss of time
If automated library preparation and sequencing are implemented, then loss of time is reduced, but device complexity increases
Solution Approach 1:
The automated system implements continuous processing where library preparation, sequencing, and data analysis occur in an integrated workflow without interruption. Samples move continuously through the system, eliminating idle time between operations and reducing total processing time while the integrated design manages complexity through unified automation.
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
Enables rapid, accurate detection and differentiation of foodborne pathogens with high sensitivity and specificity, reducing the risk of outbreaks by identifying the source and strain of contamination.
Implementation Method 1
a nanopore-based sequencing chip
Implementation Method 2
normalization of output signals from cells of a multi-cell nanopore-based sequencing chip
Data Source
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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.